@article{goretti_methylosome_2026,
	title = {Methylosome and {SMN} complexes are dispensable for plant viability in {Arabidopsis} thaliana},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiag667},
	doi = {10.1093/plphys/kiag667},
	abstract = {The role of RNA splicing as a modulator of the molecular responses to stress is well described. In contrast, its importance in the acclimation of plants to changes in ambient temperatures has only recently started to emerge. Here, we analyzed the role of temperature in regulating the functionality of factors associated with snRNP biogenesis, a key process underlying pre-mRNA splicing. Taking advantage of mutants showing temperature-dependent phenotypes, we conducted a comprehensive study of the role that the methylosome and SMN complexes have in plant development. Genetic, phylogenetic, and confocal analyses, as well as in vivo and in vitro evidence, reveal remarkable differences in the composition and importance of these complexes between plants and vertebrate animals. The SMN complex in Arabidopsis is apparently reduced to a single protein, GEMIN2, that is not essential for plant development, and the existence of a SMN ortholog is uncertain. Similarly, components of the methylosome previously implicated in snRNP biogenesis are not essential for plant viability. Our results suggest that factors considered central to snRNP biogenesis in animals have less crucial roles in plants and highlight how an evolutionarily conserved molecular process like RNA splicing has nevertheless evolved plant specific characteristics.},
	urldate = {2026-09-11},
	journal = {Plant Physiology},
	author = {Goretti, Daniela and Collani, Silvio and Nardeli, Sarah Muniz and Ratnakaram, Hemamshu and Robert, Stéphanie and Schmid, Markus},
	month = sep,
	year = {2026},
	pages = {kiag667},
}

The role of RNA splicing as a modulator of the molecular responses to stress is well described. In contrast, its importance in the acclimation of plants to changes in ambient temperatures has only recently started to emerge. Here, we analyzed the role of temperature in regulating the functionality of factors associated with snRNP biogenesis, a key process underlying pre-mRNA splicing. Taking advantage of mutants showing temperature-dependent phenotypes, we conducted a comprehensive study of the role that the methylosome and SMN complexes have in plant development. Genetic, phylogenetic, and confocal analyses, as well as in vivo and in vitro evidence, reveal remarkable differences in the composition and importance of these complexes between plants and vertebrate animals. The SMN complex in Arabidopsis is apparently reduced to a single protein, GEMIN2, that is not essential for plant development, and the existence of a SMN ortholog is uncertain. Similarly, components of the methylosome previously implicated in snRNP biogenesis are not essential for plant viability. Our results suggest that factors considered central to snRNP biogenesis in animals have less crucial roles in plants and highlight how an evolutionarily conserved molecular process like RNA splicing has nevertheless evolved plant specific characteristics.

@article{terral_plant_2026,
	title = {Plant electrical signals: {From} scattered observations to functional understanding},
	volume = {93},
	issn = {1369-5266},
	shorttitle = {Plant electrical signals},
	url = {https://www.sciencedirect.com/science/article/pii/S136952662600097X},
	doi = {10.1016/j.pbi.2026.102954},
	abstract = {Plants generate electrical signals in response to a wide range of biotic and abiotic stresses, and these signals are increasingly recognized as important mediators of stress perception, systemic communication, and defense activation. While slow wave potentials induced by mechanical wounding and herbivory are relatively well characterized, the mechanistic understanding of many other stress-induced electrical responses remains limited. Nevertheless, electrical signals often represent some of the earliest detectable physiological responses in plants, highlighting their potential for plant phenotyping and early stress detection in agriculture. This review summarizes the different classes of plant electrical signals reported under stress conditions, their signal characteristics, physiological relevance, and proposed molecular mechanisms. We discuss their relationship with other signaling pathways, and review current electrophysiological recording approaches and emerging bioelectronic technologies for plant electrophysiology. Finally, we highlight key conceptual and technological challenges that currently limit mechanistic understanding of plant electrical signaling and discuss future opportunities for advancing the field.},
	urldate = {2026-09-11},
	journal = {Current Opinion in Plant Biology},
	author = {Terral, Océane and Melikov, Rustamzhon and Lim, Dong Un and Dar, Abdul Manan and Stavrinidou, Eleni},
	month = oct,
	year = {2026},
	pages = {102954},
}

Plants generate electrical signals in response to a wide range of biotic and abiotic stresses, and these signals are increasingly recognized as important mediators of stress perception, systemic communication, and defense activation. While slow wave potentials induced by mechanical wounding and herbivory are relatively well characterized, the mechanistic understanding of many other stress-induced electrical responses remains limited. Nevertheless, electrical signals often represent some of the earliest detectable physiological responses in plants, highlighting their potential for plant phenotyping and early stress detection in agriculture. This review summarizes the different classes of plant electrical signals reported under stress conditions, their signal characteristics, physiological relevance, and proposed molecular mechanisms. We discuss their relationship with other signaling pathways, and review current electrophysiological recording approaches and emerging bioelectronic technologies for plant electrophysiology. Finally, we highlight key conceptual and technological challenges that currently limit mechanistic understanding of plant electrical signaling and discuss future opportunities for advancing the field.

@article{kareem_plant_2026,
	title = {Plant regeneration: {From} activation to fate determination},
	volume = {94},
	issn = {1369-5266},
	shorttitle = {Plant regeneration},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526626001020},
	doi = {10.1016/j.pbi.2026.102959},
	abstract = {Plants exhibit diverse regeneration strategies to heal wounds, regrow organs, and clonally propagate. These regeneration strategies depend on inductive cues such as wounding, stress or hormones initiating cell division and cell differentiation. However, wounding activates both regeneration and defence responses, and it has become clear that plants actively decide when to regenerate and what to regenerate. By integrating cell wall, hormonal, mechanical and environmental cues, plants can initiate and shape diverse regeneration outcomes such as callus formation, root regeneration, grafting and shoot formation. Here, we discuss the latest developments in how plants activate regeneration and establish a multitude of diverse regeneration outcomes. We focus on the diversity of regeneration, the trade-off between defence and regeneration, the role of signalling in fate determination and how external cues promote regeneration plasticity. Such knowledge has implications for better understanding the adaptive relevance of regeneration and for modifying fate outcomes to enhance biotechnological applications of plant regeneration.},
	urldate = {2026-09-08},
	journal = {Current Opinion in Plant Biology},
	author = {Kareem, Abdul and Melnyk, Charles W.},
	month = dec,
	year = {2026},
	pages = {102959},
}

Plants exhibit diverse regeneration strategies to heal wounds, regrow organs, and clonally propagate. These regeneration strategies depend on inductive cues such as wounding, stress or hormones initiating cell division and cell differentiation. However, wounding activates both regeneration and defence responses, and it has become clear that plants actively decide when to regenerate and what to regenerate. By integrating cell wall, hormonal, mechanical and environmental cues, plants can initiate and shape diverse regeneration outcomes such as callus formation, root regeneration, grafting and shoot formation. Here, we discuss the latest developments in how plants activate regeneration and establish a multitude of diverse regeneration outcomes. We focus on the diversity of regeneration, the trade-off between defence and regeneration, the role of signalling in fate determination and how external cues promote regeneration plasticity. Such knowledge has implications for better understanding the adaptive relevance of regeneration and for modifying fate outcomes to enhance biotechnological applications of plant regeneration.

@article{feng_genetic_2026,
	title = {Genetic structure and diversity of four {Chinese} fir breeding populations over 60 years},
	volume = {22},
	issn = {1614-2950},
	url = {https://doi.org/10.1007/s11295-026-01750-z},
	doi = {10.1007/s11295-026-01750-z},
	abstract = {Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is the most commercially important conifer species in southern China. Since 2015, the Fujian Province has launched its fourth cycle of genetic improvement, yet the impact of intensive artificial selection for growth and wood quality traits on the genetic diversity of advanced-cycle populations remains unclear. In this study, genotyping-by-sequencing (GBS) was used to genotype 310 individuals sampled from four consecutive breeding populations (first to fourth cycle). Across cycles, diversity indices remained relatively stable, with the fourth-cycle population showing slightly higher values (Ho = 0.325, He = 0.272). The broadening of breeding objectives to include wood quality and resistance traits, together with the introduction of external elite germplasm from the second cycle onward, may have contributed to this balance. Consequently, genetic differentiation among the populations from different breeding cycles was minimal (Fst {\textless} 0.01). Comparison of the genomic and pedigree-based relationship matrices revealed discrepancies for some pairs, indicating that genomic estimates provide complementary information for characterizing relatedness. Overall, genetic diversity was maintained across the four breeding cycles. These results provide a genomic basis for managing genetic diversity and relatedness in advanced-cycle Chinese fir breeding.},
	language = {en},
	number = {5},
	urldate = {2026-09-02},
	journal = {Tree Genetics \& Genomes},
	author = {Feng, Qihang and Chen, Zhi-Qiang and Zhao, Benwen and Zhang, Long and Su, Shunde and Zhang, Xie and Chen, Yu and El-Kassaby, Yousry A. and Wu, Harry X. and Bian, Liming},
	month = aug,
	year = {2026},
	keywords = {Breeding population, Chinese fir, Genetic diversity, Genomic kinship},
	pages = {29},
}

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is the most commercially important conifer species in southern China. Since 2015, the Fujian Province has launched its fourth cycle of genetic improvement, yet the impact of intensive artificial selection for growth and wood quality traits on the genetic diversity of advanced-cycle populations remains unclear. In this study, genotyping-by-sequencing (GBS) was used to genotype 310 individuals sampled from four consecutive breeding populations (first to fourth cycle). Across cycles, diversity indices remained relatively stable, with the fourth-cycle population showing slightly higher values (Ho = 0.325, He = 0.272). The broadening of breeding objectives to include wood quality and resistance traits, together with the introduction of external elite germplasm from the second cycle onward, may have contributed to this balance. Consequently, genetic differentiation among the populations from different breeding cycles was minimal (Fst \textless 0.01). Comparison of the genomic and pedigree-based relationship matrices revealed discrepancies for some pairs, indicating that genomic estimates provide complementary information for characterizing relatedness. Overall, genetic diversity was maintained across the four breeding cycles. These results provide a genomic basis for managing genetic diversity and relatedness in advanced-cycle Chinese fir breeding.

@article{rodriguez_comparative_2026,
	title = {Comparative regulomics of wood formation across dicot and conifer trees},
	volume = {17},
	copyright = {2026 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-026-75624-2},
	doi = {10.1038/s41467-026-75624-2},
	abstract = {Understanding the regulatory program underlying wood formation is key to improving biomass production and carbon sequestration in trees. However, how wood formation evolved and how these programs have been rewired across lineages remains unclear. Here, we present the first high-spatial-resolution evo-devo resource for wood transcriptomes spanning multiple dicots and conifers, representing the two major tree-containing lineages separated by more than 300 million years of evolution. Using orthology-aware co-expression network analysis, we identified genes with conserved and lineage-specific expression patterns. By integrating chromatin accessibility data and transcription factor motif analysis, we further inferred candidate regulatory networks for xylem differentiation and secondary cell wall formation. We demonstrate how this dataset can be used to answer long standing questions in wood biology related to differences in acetylation of cell wall polymers and master regulators of xylem specification across dicot and conifer tree species. The data offer a resource for the tree biology and evo-devo communities, and are publicly available at PlantGenIE.org.},
	language = {en},
	number = {1},
	urldate = {2026-09-02},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Rodriguez, Eduardo and Birkeland, Siri and Chapple, Ellen Dimmen and Fredriksson, Samuel and Carracedo Lorenzo, Zulema and Ahlgren Kalman, Teitur and Kumar, Vikash and Mccann, Jamie and Hill, Jason and Soundiramourtty, Sivagamy and Voxeur, Aline and Røhr, Åsmund Kjendseth and Tuominen, Hannele and Mellerowicz, Ewa J. and Street, Nathaniel R. and Hvidsten, Torgeir R.},
	month = jul,
	year = {2026},
	keywords = {Comparative genomics, Gene regulatory networks, Plant evolution, Plant genetics},
	pages = {8916},
}

Understanding the regulatory program underlying wood formation is key to improving biomass production and carbon sequestration in trees. However, how wood formation evolved and how these programs have been rewired across lineages remains unclear. Here, we present the first high-spatial-resolution evo-devo resource for wood transcriptomes spanning multiple dicots and conifers, representing the two major tree-containing lineages separated by more than 300 million years of evolution. Using orthology-aware co-expression network analysis, we identified genes with conserved and lineage-specific expression patterns. By integrating chromatin accessibility data and transcription factor motif analysis, we further inferred candidate regulatory networks for xylem differentiation and secondary cell wall formation. We demonstrate how this dataset can be used to answer long standing questions in wood biology related to differences in acetylation of cell wall polymers and master regulators of xylem specification across dicot and conifer tree species. The data offer a resource for the tree biology and evo-devo communities, and are publicly available at PlantGenIE.org.

@article{liu_loss_2026,
	title = {Loss of function of the {AP2}/{ERF} transcription factor {StGAME9} abolishes activation and induction of steroidal glycoalkaloid biosynthesis in potato plants},
	volume = {237},
	issn = {0981-9428},
	url = {https://www.sciencedirect.com/science/article/pii/S0981942826005474},
	doi = {10.1016/j.plaphy.2026.111561},
	abstract = {Steroidal glycoalkaloids (SGAs) are toxic defense substances present in certain species of the Solanaceae, including major crops such as eggplant, tomato, and potato. GLYCOALKALOID METABOLISM 9 (GAME9) was first identified in tomato and potato as an APETALA 2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor regulating key genes in SGA biosynthesis. However, the spatial effects of endogenous GAME9 in potato remain largely unexplored, particularly in tubers, highlighting a knowledge gap in understanding activation and induction of SGA biosynthesis in this important staple food crop. Here, we generated StGAME9 knockout mutants in potato via DNA-free CRISPR/Cas9. Compared to the wild type, knockout mutants contained significantly reduced SGA levels in leaves, and were almost free of SGAs in tubers. Notably, SGA accumulation remained minimal in the mutant tubers even under two SGA-inducing conditions; wounding and light exposure, indicating a loss of inducible SGA biosynthesis. Integrated transcriptomic and metabolomic characterization of knockout mutants (Stgame9) revealed extensive reprogramming of gene expression and metabolism, affecting not only SGA and sterol pathways but also a broader range of metabolic processes, with stress-related metabolic responses being attenuated in Stgame9 tubers. Despite these changes, Stgame9 plants displayed a normal growth phenotype under both greenhouse and field conditions. Our findings substantiate a pivotal role of GAME9 in potato for the regulation of basal and induced SGA biosynthesis. The results further indicate that StGAME9 is involved in the regulation of a broader, complex, and interconnected network along biosynthetic pathways, where potato metabolism exhibits substantial robustness and compensatory capacity to buffer the loss of StGAME9.},
	urldate = {2026-09-02},
	journal = {Plant Physiology and Biochemistry},
	author = {Liu, Ying and Merino, Irene and Potgieter, Lizel and Flöhr, Adam and Johansson, Annika I. and Andersson, Mariette and Sitbon, Folke and Hofvander, Per},
	month = aug,
	year = {2026},
	keywords = {AP2/ERF transcription factor, Abiotic stress, Glycoalkaloids, Metabolomics, Potato (), Transcriptomics},
	pages = {111561},
}

Steroidal glycoalkaloids (SGAs) are toxic defense substances present in certain species of the Solanaceae, including major crops such as eggplant, tomato, and potato. GLYCOALKALOID METABOLISM 9 (GAME9) was first identified in tomato and potato as an APETALA 2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor regulating key genes in SGA biosynthesis. However, the spatial effects of endogenous GAME9 in potato remain largely unexplored, particularly in tubers, highlighting a knowledge gap in understanding activation and induction of SGA biosynthesis in this important staple food crop. Here, we generated StGAME9 knockout mutants in potato via DNA-free CRISPR/Cas9. Compared to the wild type, knockout mutants contained significantly reduced SGA levels in leaves, and were almost free of SGAs in tubers. Notably, SGA accumulation remained minimal in the mutant tubers even under two SGA-inducing conditions; wounding and light exposure, indicating a loss of inducible SGA biosynthesis. Integrated transcriptomic and metabolomic characterization of knockout mutants (Stgame9) revealed extensive reprogramming of gene expression and metabolism, affecting not only SGA and sterol pathways but also a broader range of metabolic processes, with stress-related metabolic responses being attenuated in Stgame9 tubers. Despite these changes, Stgame9 plants displayed a normal growth phenotype under both greenhouse and field conditions. Our findings substantiate a pivotal role of GAME9 in potato for the regulation of basal and induced SGA biosynthesis. The results further indicate that StGAME9 is involved in the regulation of a broader, complex, and interconnected network along biosynthetic pathways, where potato metabolism exhibits substantial robustness and compensatory capacity to buffer the loss of StGAME9.

@article{bhowmick_additional_2026,
	title = {An additional water is introduced into the manganese cluster during the formation of the {S3} state of photosystem {II}},
	volume = {17},
	copyright = {2026 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-026-76805-9},
	doi = {10.1038/s41467-026-76805-9},
	abstract = {During photosynthetic water oxidation, the Mn4Ca cluster in Photosystem II progresses through five intermediate Si (i = 0–4) states. X-ray crystallography studies have reported the insertion of one new O ligand during the formation of the S3 state, but recent studies question the presence of this additional ligand based on cryo-EM and earlier room-temperature crystallography data. There is also controversy about whether the O-O bond interaction already occurs in the S3 state or in the subsequent S3 to S0 transition. Here we report conventional high-resolution data for the S1, S2, and S3 states to a resolution of {\textasciitilde}1.9 Å, and anomalous diffraction data at two energies (9.5 keV and 7 keV), that was used to model the Mn positions, followed by determination of oxygen positions using the high-resolution maps. We show that the new oxygen atom, OX (or O6), in the S3 state is observable as a distinct peak without any restraints, confirming its ligation to Mn1 and Ca. The OX-O5 distance is {\textasciitilde}2.1 Å, supporting no strong interaction between them in the S3 state, suggesting that if this is the O-O bond formation site, it is formed during the S3 to S0 transition initiated by the final oxidation of the cluster.},
	language = {en},
	number = {1},
	urldate = {2026-09-02},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Bhowmick, Asmit and Zhang, Miao and Simon, Philipp S. and Makita, Hiroki and Nangca, Isabela I. and Szilagyi, Erzsi and Kretzschmar, Moritz and Doyle, Margaret D. and Minnetian, Natalie M. and Hussein, Rana and Hart, Olli and Chatterjee, Kuntal and Aydin, A. Orkun and Shevela, Dmitry and Cheah, Mun Hon and Croy, Nicholas and Chernev, Petko and Fransson, Thomas and Tiwari, Vandana and Sanchez, Humberto and Schleissner, Pamela and Lemons, Randy and Gate, Greg and Henstridge, Meredith and Glownia, James M. and Poitevin, Frédéric and Rosenberg, Daniel J. and Dehe, Sebastian and Gee, Leland B. and Tono, Kensuke and Owada, Shigeki and Oggenfuss, Roland and Ozerov, Dmitry and Sander, Mathias and Mankowsky, Roman and Lemke, Henrik T. and Young, Iris D. and Holton, James M. and Mittan-Moreau, David W. and Paley, Daniel W. and Afonine, Pavel V. and Moriarty, Nigel W. and Adams, Paul D. and Mamedov, Fikret and Dobbek, Holger and Zouni, Athina and Alonso-Mori, Roberto and Bergmann, Uwe and Brewster, Aaron S. and Sauter, Nicholas K. and Messinger, Johannes and Kern, Jan F. and Yachandra, Vittal K. and Yano, Junko},
	month = aug,
	year = {2026},
	keywords = {Bioenergetics, Physical chemistry, Structural biology},
	pages = {8818},
}

During photosynthetic water oxidation, the Mn4Ca cluster in Photosystem II progresses through five intermediate Si (i = 0–4) states. X-ray crystallography studies have reported the insertion of one new O ligand during the formation of the S3 state, but recent studies question the presence of this additional ligand based on cryo-EM and earlier room-temperature crystallography data. There is also controversy about whether the O-O bond interaction already occurs in the S3 state or in the subsequent S3 to S0 transition. Here we report conventional high-resolution data for the S1, S2, and S3 states to a resolution of ~1.9 Å, and anomalous diffraction data at two energies (9.5 keV and 7 keV), that was used to model the Mn positions, followed by determination of oxygen positions using the high-resolution maps. We show that the new oxygen atom, OX (or O6), in the S3 state is observable as a distinct peak without any restraints, confirming its ligation to Mn1 and Ca. The OX-O5 distance is ~2.1 Å, supporting no strong interaction between them in the S3 state, suggesting that if this is the O-O bond formation site, it is formed during the S3 to S0 transition initiated by the final oxidation of the cluster.

@article{wu_integrating_2026,
	title = {Integrating {GWAS}-guided markers preselection with genomic selection enhances prediction of pulpwood-related traits in slash pine ({Pinus} elliottii {Englem}.)},
	volume = {26},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-026-09114-4},
	doi = {10.1186/s12870-026-09114-4},
	abstract = {This study aimed to enhance the efficiency of genomic prediction for pulpwood-related traits in slash pine (Pinus elliottii Engelm. var. elliottii) by integrating genome-wide association study (GWAS) information with genomic selection (GS). We evaluated 12 traits related to growth, fiber, and wood chemical composition in a population of 340 individuals genotyped with 319,286 high-quality SNPs, comparing the performance of six GS models, including GBLUP and Bayesian methods, under varying training population sizes and marker densities. The results showed that while both GBLUP and Bayesian Lasso performed well, Bayesian Lasso slightly outperformed GBLUP for fiber traits. Predictive ability (PA) plateaued at approximately 100 K SNPs for fiber traits, 60 K for DBH, and 10 K for wood chemical composition traits in all models. Using 100 K random SNPs, PA ranged from 0.05 to 0.23, which expanded to 0.09–0.35 with GWAS-guided SNP preselection (maximum improvement of 16.26\%) and further broadened to 0.01–0.38 by incorporating large-effect QTLs (greatest improvement of 23.54\%). Overall, integrating GWAS information into GS frameworks significantly improved prediction accuracy as assessed by t-test, offering a cost-effective strategy to accelerate genetic improvement. These findings provide practical guidance for enhancing breeding efficiency in slash pine and other conifer breeding programs.},
	language = {en},
	number = {1},
	urldate = {2026-08-17},
	journal = {BMC Plant Biology},
	author = {Wu, Yadi and Ding, Xianyin and Diao, Shu and Huang, Qinyun and Shang, Guiqi and Tan, Zifeng and Wu, Shaoze and Hua, Xiahui and He, Chengbo and Luan, Qifu and Chen, Zhi-Qiang and Wu, Harry X.},
	month = may,
	year = {2026},
	keywords = {Bayesian Lasso, Genomic selection, Pulpwood properties, SNP preselection, Slash pine},
	pages = {1271},
}

This study aimed to enhance the efficiency of genomic prediction for pulpwood-related traits in slash pine (Pinus elliottii Engelm. var. elliottii) by integrating genome-wide association study (GWAS) information with genomic selection (GS). We evaluated 12 traits related to growth, fiber, and wood chemical composition in a population of 340 individuals genotyped with 319,286 high-quality SNPs, comparing the performance of six GS models, including GBLUP and Bayesian methods, under varying training population sizes and marker densities. The results showed that while both GBLUP and Bayesian Lasso performed well, Bayesian Lasso slightly outperformed GBLUP for fiber traits. Predictive ability (PA) plateaued at approximately 100 K SNPs for fiber traits, 60 K for DBH, and 10 K for wood chemical composition traits in all models. Using 100 K random SNPs, PA ranged from 0.05 to 0.23, which expanded to 0.09–0.35 with GWAS-guided SNP preselection (maximum improvement of 16.26%) and further broadened to 0.01–0.38 by incorporating large-effect QTLs (greatest improvement of 23.54%). Overall, integrating GWAS information into GS frameworks significantly improved prediction accuracy as assessed by t-test, offering a cost-effective strategy to accelerate genetic improvement. These findings provide practical guidance for enhancing breeding efficiency in slash pine and other conifer breeding programs.

@article{bao_chromosome-level_2026,
	title = {A chromosome-level genome assembly of \textit{{Platycladus} orientalis} and comparative genomics reveal pivotal roles of transposable elements in gene duplication and pseudogenization across gymnosperm giga-genomes},
	volume = {7},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S2590346226001227},
	doi = {10.1016/j.xplc.2026.101814},
	abstract = {Gymnosperms, particularly conifers, exhibit a high abundance of transposable elements (TEs) in their giga-scale genomes. TEs interact both antagonistically and cooperatively with the host genome, promoting structural and genetic innovations across evolutionary lineages. However, how TEs shape the coding space of gymnosperm genomes remains a key unresolved question. Here, we present a high-quality genome assembly for the keystone conifer Platycladus orientalis, with a contig N50 of 57.54 Mb—the highest continuity reported to date—to investigate the role of TEs. Comparative genomics confirms the absence of recent whole-genome duplication and the presence of genome expansion in gymnosperms, revealing complex interactions among recurrent TE proliferation, low DNA removal rates, and DNA methylation-mediated silencing. Computational evidence indicates that TE-mediated gene duplication and pseudogenization provide a genetic basis for adaptive evolution and functional innovation, significantly shaping gene family dynamics and the emergence of species-specific genes. Additionally, TEs capture and duplicate an average of ∼400,000 coding gene fragments per gymnosperm genome, facilitating exon shuffling and triggering epigenetic conflicts between source genes and captured exon fragments. Genes from which fragments are captured (donor genes) show significantly higher levels of exon methylation than genes not captured by TEs (free genes), whereas syntenic donor genes exhibit lower levels of silencing responses than non-syntenic donor genes. This study provides valuable genomic resources and offers insights into the evolutionary patterns and principles underlying the large genome size and complexity of gymnosperms.},
	number = {8},
	urldate = {2026-08-17},
	journal = {Plant Communications},
	author = {Bao, Yu-Tao and Zhang, Ren-Gang and Liu, Hui and Li, Zhi-Chao and Jiao, Si-Qian and Jia, Kai-Hua and Zhou, Shan-Shan and Nie, Shuai and Yan, Xue-Mei and Shi, Tian-Le and Tian, Xue-Chan and Zhao, Shi-Wei and Kong, Lei and Chen, Zhao-Yang and Ma, Hai-Yao and Yang, Xiao-Lei and Chen, Charles and El-Kassaby, Yousry Aly and Porth, Ilga and Wang, Xiao-Ru and Mao, Jian-Feng and Zhao, Wei},
	month = aug,
	year = {2026},
	keywords = {gene duplication, gene fragment capture, genome expansion, gymnosperms, pseudogenization, transposable elements},
	pages = {101814},
}

Gymnosperms, particularly conifers, exhibit a high abundance of transposable elements (TEs) in their giga-scale genomes. TEs interact both antagonistically and cooperatively with the host genome, promoting structural and genetic innovations across evolutionary lineages. However, how TEs shape the coding space of gymnosperm genomes remains a key unresolved question. Here, we present a high-quality genome assembly for the keystone conifer Platycladus orientalis, with a contig N50 of 57.54 Mb—the highest continuity reported to date—to investigate the role of TEs. Comparative genomics confirms the absence of recent whole-genome duplication and the presence of genome expansion in gymnosperms, revealing complex interactions among recurrent TE proliferation, low DNA removal rates, and DNA methylation-mediated silencing. Computational evidence indicates that TE-mediated gene duplication and pseudogenization provide a genetic basis for adaptive evolution and functional innovation, significantly shaping gene family dynamics and the emergence of species-specific genes. Additionally, TEs capture and duplicate an average of ∼400,000 coding gene fragments per gymnosperm genome, facilitating exon shuffling and triggering epigenetic conflicts between source genes and captured exon fragments. Genes from which fragments are captured (donor genes) show significantly higher levels of exon methylation than genes not captured by TEs (free genes), whereas syntenic donor genes exhibit lower levels of silencing responses than non-syntenic donor genes. This study provides valuable genomic resources and offers insights into the evolutionary patterns and principles underlying the large genome size and complexity of gymnosperms.

@article{liu_drought_2026,
	title = {A drought stress-induced {MYB} transcription factor regulates pavement cell shape in leaves of {European} aspen ({Populus} tremula)},
	volume = {251},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.71399},
	doi = {10.1111/nph.71399},
	abstract = {MYB305a promoter expression increases in pavement cells as they grow and acquire their complex shape.},
	language = {en},
	number = {5},
	urldate = {2026-08-17},
	journal = {New Phytologist},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Liu, Sijia and Doyle, Siamsa M. and Robinson, Kathryn M. and Rahneshan, Zahra and Street, Nathaniel R. and Robert, Stéphanie},
	month = sep,
	year = {2026},
	keywords = {Cell Shape, Droughts, European aspen (Populus tremula), GWAS, Gene Expression Regulation, Plant, Genome-Wide Association Study, Plant Leaves, Plant Proteins, Populus, Promoter Regions, Genetic, Stress, Physiological, Transcription Factors, cell shape, drought, leaf pavement cells},
	pages = {2688--2705},
}

MYB305a promoter expression increases in pavement cells as they grow and acquire their complex shape.

@article{hu_leaf_2026,
	title = {Leaf development regulates state transition capacity in trees},
	volume = {17},
	copyright = {2026 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-026-76469-5},
	doi = {10.1038/s41467-026-76469-5},
	abstract = {State transitions (ST) balance excitation energy between photosystem I and II. This process has been extensively studied in Arabidopsis but the regulation and physiological significance of ST in other angiosperms remain largely unknown. Here, we investigate ST in hybrid aspen and other tree species using physiological, biochemical, ultrastructural, and genetic approaches. We discover a pronounced canopy gradient in greenhouse-grown aspens, with young, upper leaves exhibiting substantially higher fluorescence-derived state-transition capacity (qT) than lower, older leaves. Seasonal monitoring of field-grown trees reveals a conserved developmental decline in qT across species. Reduced qT correlates with increased grana stacking and lower LHCII/PSII ratios, but not with LHCII phosphorylation, suggesting developmental remodeling of thylakoid architecture may influence the functional reorganization of PSII antenna connectivity during state transitions. Using the serine/threonine protein kinase (STN7) knockout mutant characterized outside Arabidopsis, we show that aspens lacking ST exhibit altered PSI/PSII ratios, reduced PSII operating efficiency in young leaves, and slower growth under greenhouse conditions with naturally variable light conditions but not under constant-light climate room condition. These findings indicate that ST is important for performance under dynamic light conditions, particularly in young leaves, and reveal a previously unrecognized developmental control of photosynthetic regulation.},
	language = {en},
	number = {1},
	urldate = {2026-08-17},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Hu, Chen and Nanda, Sanchali and Pissolato, Maria Dolores and Cainzos, Maximiliano and Shutova, Tatyana and Jansson, Stefan},
	month = aug,
	year = {2026},
	keywords = {Developmental biology, Photosynthesis, Plant sciences},
	pages = {7926},
}

State transitions (ST) balance excitation energy between photosystem I and II. This process has been extensively studied in Arabidopsis but the regulation and physiological significance of ST in other angiosperms remain largely unknown. Here, we investigate ST in hybrid aspen and other tree species using physiological, biochemical, ultrastructural, and genetic approaches. We discover a pronounced canopy gradient in greenhouse-grown aspens, with young, upper leaves exhibiting substantially higher fluorescence-derived state-transition capacity (qT) than lower, older leaves. Seasonal monitoring of field-grown trees reveals a conserved developmental decline in qT across species. Reduced qT correlates with increased grana stacking and lower LHCII/PSII ratios, but not with LHCII phosphorylation, suggesting developmental remodeling of thylakoid architecture may influence the functional reorganization of PSII antenna connectivity during state transitions. Using the serine/threonine protein kinase (STN7) knockout mutant characterized outside Arabidopsis, we show that aspens lacking ST exhibit altered PSI/PSII ratios, reduced PSII operating efficiency in young leaves, and slower growth under greenhouse conditions with naturally variable light conditions but not under constant-light climate room condition. These findings indicate that ST is important for performance under dynamic light conditions, particularly in young leaves, and reveal a previously unrecognized developmental control of photosynthetic regulation.

@article{yang_construction_2026,
	title = {Construction and optimization of a genomic selection model for total sugar content in tobacco},
	volume = {17},
	issn = {1664-8021},
	url = {https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2026.1886099/full},
	doi = {10.3389/fgene.2026.1886099},
	abstract = {Total sugar is one of the chemical indicators related to tobacco quality. However, due to its composition of various oligosaccharides, disaccharides, and polysaccharides, total sugar lacks a clear genetic target, making conventional breeding approaches for its improvement particularly challenging. Therefore, conducting genomic selection (GS) studies on total sugar content holds significant importance for the development of high-sugar tobacco varieties. In this study, 2,604 tobacco germplasm accessions with broad genetic diversity, sourced from the National tobacco Germplasm Repository, were used as experimental materials. High-throughput sequencing technologies were employed to perform comprehensive genetic evaluation and construct genomic selection models for total sugar content. Sixteen mainstream genomic prediction models were assessed through five-fold cross-validation to develop a high-accuracy prediction framework. Among these models, the Gradient Boosting Machine (GBM) achieved the highest prediction accuracy for total sugar content (0.85), followed by the rrBLUP model (0.81). Comparative analysis of computational speed and resource consumption revealed that GBM maintained rapid computation and low resource usage even in large sample sizes, demonstrating strong stability and superior performance. Considering all factors, GBM was preliminarily identified as the optimal model for predicting total sugar content in tobacco. The application of high-accuracy genomic prediction is expected to overcome the challenges of phenotypic evaluation in breeding programs and significantly enhance the efficiency of selecting high-sugar tobacco varieties.},
	language = {English},
	urldate = {2026-08-17},
	journal = {Frontiers in Genetics},
	publisher = {Frontiers},
	author = {Yang, Yue and Xu, Qiang and Fu, Jincun and Guo, Linjie and Huang, Zexiang and Si, Huan and Wang, Hao and Shen, Guanwang and Zan, Yanjun and Hu, Zongyu},
	month = jul,
	year = {2026},
	keywords = {genome-wide association analysis, genomic selection, machine learning, tobacco, total sugar},
}

Total sugar is one of the chemical indicators related to tobacco quality. However, due to its composition of various oligosaccharides, disaccharides, and polysaccharides, total sugar lacks a clear genetic target, making conventional breeding approaches for its improvement particularly challenging. Therefore, conducting genomic selection (GS) studies on total sugar content holds significant importance for the development of high-sugar tobacco varieties. In this study, 2,604 tobacco germplasm accessions with broad genetic diversity, sourced from the National tobacco Germplasm Repository, were used as experimental materials. High-throughput sequencing technologies were employed to perform comprehensive genetic evaluation and construct genomic selection models for total sugar content. Sixteen mainstream genomic prediction models were assessed through five-fold cross-validation to develop a high-accuracy prediction framework. Among these models, the Gradient Boosting Machine (GBM) achieved the highest prediction accuracy for total sugar content (0.85), followed by the rrBLUP model (0.81). Comparative analysis of computational speed and resource consumption revealed that GBM maintained rapid computation and low resource usage even in large sample sizes, demonstrating strong stability and superior performance. Considering all factors, GBM was preliminarily identified as the optimal model for predicting total sugar content in tobacco. The application of high-accuracy genomic prediction is expected to overcome the challenges of phenotypic evaluation in breeding programs and significantly enhance the efficiency of selecting high-sugar tobacco varieties.

@article{anjam_single-cell_2026,
	title = {Single-cell laser ablation uncovers the blueprint of plant development},
	issn = {1360-1385},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138526001329},
	doi = {10.1016/j.tplants.2026.04.029},
	abstract = {Understanding how positional information within plant tissues shapes developmental programs in real time has long remained a challenge due to technical limitations in precisely accessing and manipulating defined cellular domains within complex tissues. Recent advances in single-cell laser ablation, particularly when combined with confocal microscopy, now allow precise spatiotemporal perturbation of selected cells. This technology has enabled researchers to dissect cellular functions, communication dynamics, and mechanical responses with unprecedented accuracy. Here, we review how laser ablation has emerged as a transformative approach in plant biology, from unraveling the signaling networks governing meristem maintenance and root patterning to modeling wound responses and immune activation.},
	urldate = {2026-05-29},
	journal = {Trends in Plant Science},
	author = {Anjam, Muhammad S. and Di Fino, Luciano Martín and Ma, Xuemin and Marhavý, Peter},
	month = may,
	year = {2026},
	keywords = {phytohormone crosstalk, single-cell ablation, tissue regeneration, wound signaling},
}

Understanding how positional information within plant tissues shapes developmental programs in real time has long remained a challenge due to technical limitations in precisely accessing and manipulating defined cellular domains within complex tissues. Recent advances in single-cell laser ablation, particularly when combined with confocal microscopy, now allow precise spatiotemporal perturbation of selected cells. This technology has enabled researchers to dissect cellular functions, communication dynamics, and mechanical responses with unprecedented accuracy. Here, we review how laser ablation has emerged as a transformative approach in plant biology, from unraveling the signaling networks governing meristem maintenance and root patterning to modeling wound responses and immune activation.

@article{carlsson_cross-generational_2026,
	title = {Cross-generational decline in genomic selection accuracy in {Norway} spruce ({Picea} abies ({L}.) {H}. {Karst}) and strategies to mitigate it},
	volume = {37},
	issn = {1993-0607},
	url = {https://doi.org/10.1007/s11676-026-02108-w},
	doi = {10.1007/s11676-026-02108-w},
	abstract = {Genomic selection (GS) could be used to reduce the long cycle time for tree breeding. This assumes that marker-based predictions are sufficiently accurate without phenotypes. We evaluated GS across two linked generations of Norway spruce (Picea abies (L.) H. Karst), the first consisting of 954 plus-trees (G0) and the second of 956 progeny trees representing 34 full-sib families (G1), using 16 clonal field trials across mid- and southern Sweden. Both generations were measured for height and genotyped using a 50 K SNP chip array. Cross-validations within and across generations were compared. GS efficiency was evaluated using global prediction accuracy and within-family predictive ability, using GBLUP with phenotypes for independent validation. We used computer simulations to emulate the experimental data and repeat the same analysis under different assumptions of effective population size. Additional simulations were performed to investigate the cross-generation GS accuracy in future generations. Simulations assuming a historical effective population size of 1000 or 5000, together with experimental results, indicate that prediction accuracy decreased by 49–76\% for global prediction and by 15–65\% for within-family prediction when G1 was predicted from G0, compared with cross-validation within the G1 generation. Increasing the relatedness at the expense of training set size increased global accuracy but decreased within-family accuracy. Simulations of advanced generations showed that training on multiple generations increases GS accuracy, both for global and within-family prediction. Access to multiple generations for training and/or a higher density of markers may be recommended to increase accuracy for cross-generation and within-family GS in conifers.},
	language = {en},
	number = {1},
	urldate = {2026-08-10},
	journal = {Journal of Forestry Research},
	author = {Carlsson, Edward A. and Hallingbäck, Henrik R. and Ahlinder, Jon and Suontama, Mari and Wu, Harry X.},
	month = aug,
	year = {2026},
	keywords = {AlphaSimR, Cross-generation, Genomic selection (GS), Norway spruce, Within-family prediction},
	pages = {172},
}

Genomic selection (GS) could be used to reduce the long cycle time for tree breeding. This assumes that marker-based predictions are sufficiently accurate without phenotypes. We evaluated GS across two linked generations of Norway spruce (Picea abies (L.) H. Karst), the first consisting of 954 plus-trees (G0) and the second of 956 progeny trees representing 34 full-sib families (G1), using 16 clonal field trials across mid- and southern Sweden. Both generations were measured for height and genotyped using a 50 K SNP chip array. Cross-validations within and across generations were compared. GS efficiency was evaluated using global prediction accuracy and within-family predictive ability, using GBLUP with phenotypes for independent validation. We used computer simulations to emulate the experimental data and repeat the same analysis under different assumptions of effective population size. Additional simulations were performed to investigate the cross-generation GS accuracy in future generations. Simulations assuming a historical effective population size of 1000 or 5000, together with experimental results, indicate that prediction accuracy decreased by 49–76% for global prediction and by 15–65% for within-family prediction when G1 was predicted from G0, compared with cross-validation within the G1 generation. Increasing the relatedness at the expense of training set size increased global accuracy but decreased within-family accuracy. Simulations of advanced generations showed that training on multiple generations increases GS accuracy, both for global and within-family prediction. Access to multiple generations for training and/or a higher density of markers may be recommended to increase accuracy for cross-generation and within-family GS in conifers.

@article{rao_myb17-dfrldox_2026,
	title = {{MYB17}-{DFR}/{LDOX} {Module} {Positively} {Regulates} {Cyanidin} {Deposition} in {Cinnamomum} {Camphora}},
	copyright = {© 2026 The Author(s). Plant, Cell \& Environment published by John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.70664},
	doi = {10.1111/pce.70664},
	abstract = {Cinnamomum camphora is a cornerstone ornamental tree species in southern China, valued for its evergreen foliage and distinctive scent. However, the uniformly green foliage and brown bark limit its landscaping values. In this study, we characterised a coloured camphor variety, ‘Gantong 1’, and revealed cyanidin content as the critical factor responsible for its stem coloration. Correlation analysis indicated that the transcription factor CcMYB17 plays a crucial role in cyanidin accumulation. We functionally validated CcMYB17 through yeast one-hybrid assays, luciferase reporter assays and multi-omics analysis in a poplar model system. Our results demonstrate that CcMYB17 regulates the synergistic accumulation of cyanidin and delphinidin by activating key anthocyanin biosynthesis genes, specifically CcDFR and CcLDOX. This systematic elucidation of the colour mechanism ‘Gantong 1’ and the functional role of CcMYB17 deepens our understanding of ornamental trait improvement in C. camphora. It provides a foundation for molecular-assisted breeding of coloured woody trees.},
	language = {en},
	urldate = {2026-06-26},
	journal = {Plant, Cell \& Environment},
	author = {Rao, Shupei and Gong, Xue and Shen, Le and Li, Huihu and Zhang, Bo and Zhong, Yongda},
	month = jun,
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.70664},
	keywords = {Cinnamomum camphora, MYB, anthocyanin, metabolome, molecular mechanism},
}

Cinnamomum camphora is a cornerstone ornamental tree species in southern China, valued for its evergreen foliage and distinctive scent. However, the uniformly green foliage and brown bark limit its landscaping values. In this study, we characterised a coloured camphor variety, ‘Gantong 1’, and revealed cyanidin content as the critical factor responsible for its stem coloration. Correlation analysis indicated that the transcription factor CcMYB17 plays a crucial role in cyanidin accumulation. We functionally validated CcMYB17 through yeast one-hybrid assays, luciferase reporter assays and multi-omics analysis in a poplar model system. Our results demonstrate that CcMYB17 regulates the synergistic accumulation of cyanidin and delphinidin by activating key anthocyanin biosynthesis genes, specifically CcDFR and CcLDOX. This systematic elucidation of the colour mechanism ‘Gantong 1’ and the functional role of CcMYB17 deepens our understanding of ornamental trait improvement in C. camphora. It provides a foundation for molecular-assisted breeding of coloured woody trees.

@article{melis_conformable_2026,
	title = {Conformable {Ferrimagnetic} {Tattoo} {Electrodes} for {Plant} {Electrophysiology}},
	copyright = {© 2026 The Author(s). Advanced Materials Technologies published by Wiley-VCH GmbH},
	issn = {2365-709X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/admt.71156},
	doi = {10.1002/admt.71156},
	abstract = {Increasing global food demand and environmental stress call for technologies enabling continuous plant monitoring in precision agriculture. Electrical signals generated by plants during stress responses provide valuable information. However, their recording remains challenging, as conventional silver/silver chloride (Ag/AgCl) electrodes require gel electrolytes to interface with plant tissues, limiting mechanical stability. Here, we report conformable ferrimagnetic tattoo electrodes for minimally invasive recording of plant electrophysiology. The electrodes are based on a PEDOT:PSS ink spray-coated onto tattoo carrier paper to form free-standing electrodes. They adhere to plant leaves via van der Waals forces and remain attached for several days. Their performance was evaluated in Arabidopsis thaliana and Solanum lycopersicum (tomato). In both, the recordings of wound-activated surface potentials were comparable to those of conventional Ag/AgCl electrodes. The incorporation of ferrimagnetic particles enables magnetic coupling to the acquisition system, reducing mechanical stress and allowing repeatable electrical connections. This approach enables seamless monitoring of signal propagation and supports on-demand recordings. Importantly, electrophysiological measurements were successfully performed outside a Faraday cage, demonstrating robustness under realistic conditions. These conformable ferrimagnetic tattoo electrodes provide a scalable and adaptable interface for plant electrophysiology and open new opportunities for studying plant stress signaling and developing sensing technologies for precision agriculture.},
	language = {en},
	urldate = {2026-07-24},
	journal = {Advanced Materials Technologies},
	author = {Melis, Arianna and Spanu, Andrea and Viola, Fabrizio Antonio and Dar, Abdul Manan and Sandéhn, Alexandra and Routier, Cyril and Bonfiglio, Annalisa and Stavrinidou, Eleni},
	month = jul,
	year = {2026},
	note = {\_eprint: https://advanced.onlinelibrary.wiley.com/doi/pdf/10.1002/admt.71156},
	keywords = {conformable electronics, magnetic, plant electrophysiology, precision agriculture, slow wave potential, tattoo electrode},
	pages = {e71156},
}

Increasing global food demand and environmental stress call for technologies enabling continuous plant monitoring in precision agriculture. Electrical signals generated by plants during stress responses provide valuable information. However, their recording remains challenging, as conventional silver/silver chloride (Ag/AgCl) electrodes require gel electrolytes to interface with plant tissues, limiting mechanical stability. Here, we report conformable ferrimagnetic tattoo electrodes for minimally invasive recording of plant electrophysiology. The electrodes are based on a PEDOT:PSS ink spray-coated onto tattoo carrier paper to form free-standing electrodes. They adhere to plant leaves via van der Waals forces and remain attached for several days. Their performance was evaluated in Arabidopsis thaliana and Solanum lycopersicum (tomato). In both, the recordings of wound-activated surface potentials were comparable to those of conventional Ag/AgCl electrodes. The incorporation of ferrimagnetic particles enables magnetic coupling to the acquisition system, reducing mechanical stress and allowing repeatable electrical connections. This approach enables seamless monitoring of signal propagation and supports on-demand recordings. Importantly, electrophysiological measurements were successfully performed outside a Faraday cage, demonstrating robustness under realistic conditions. These conformable ferrimagnetic tattoo electrodes provide a scalable and adaptable interface for plant electrophysiology and open new opportunities for studying plant stress signaling and developing sensing technologies for precision agriculture.

@article{zhou_early_2026,
	title = {{EARLY} {ABORTION} 1 is an evolutionarily conserved gene required for plant reproduction},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erag142},
	doi = {10.1093/jxb/erag142},
	abstract = {The functions of approximately one-third of the proteins in the model plant Arabidopsis remain unknown. It is likely that some of the genes encoding these proteins are essential, and thus indispensable for the survival of the plant; furthermore, these genes would be included in the minimum viable set required for plant life. Evolutionarily conserved single copy genes in flowering plants are enriched in essential housekeeping functions. Building on this observation, we designed a reverse genetic screen that focuses on evolutionarily conserved single copy Arabidopsis genes of unknown function with predominant expression in meristematic cells. This approach identified a previously uncharacterized essential Arabidopsis gene, named as EARLY ABORTION 1 (EBO1). Mutation of the EBO1 locus disrupts gametophyte and/or early embryo development, resulting in defective ovule or seed development. A functional fluorescent EBO1 fusion protein was found to localize to the nucleus, and co-immunoprecipitation experiments detected an interaction between EBO1 and Nucleolar Protein 58 (NOP58) and proteins involved in RNA metabolism, chromatin modification, and transcription. The presented results open a new line of investigation into an evolutionarily conserved mechanism involved in the development of both male and female gametophytes as well as seeds.},
	urldate = {2026-04-24},
	journal = {Journal of Experimental Botany},
	author = {Zhou, Jingjing and Wang, Wei and Zhang, Li and Bruce, Ylva and Zhu, Shaochun and Mateus, André and Niittylä, Totte},
	month = mar,
	year = {2026},
	pages = {erag142},
}

The functions of approximately one-third of the proteins in the model plant Arabidopsis remain unknown. It is likely that some of the genes encoding these proteins are essential, and thus indispensable for the survival of the plant; furthermore, these genes would be included in the minimum viable set required for plant life. Evolutionarily conserved single copy genes in flowering plants are enriched in essential housekeeping functions. Building on this observation, we designed a reverse genetic screen that focuses on evolutionarily conserved single copy Arabidopsis genes of unknown function with predominant expression in meristematic cells. This approach identified a previously uncharacterized essential Arabidopsis gene, named as EARLY ABORTION 1 (EBO1). Mutation of the EBO1 locus disrupts gametophyte and/or early embryo development, resulting in defective ovule or seed development. A functional fluorescent EBO1 fusion protein was found to localize to the nucleus, and co-immunoprecipitation experiments detected an interaction between EBO1 and Nucleolar Protein 58 (NOP58) and proteins involved in RNA metabolism, chromatin modification, and transcription. The presented results open a new line of investigation into an evolutionarily conserved mechanism involved in the development of both male and female gametophytes as well as seeds.

@article{gobel_systemic_2026,
	title = {Systemic and {Local} {Regulation} of {Root} {Growth} by {Vascular} {Trehalose} 6-{Phosphate} is {Correlated} {With} {Re}-allocation of {Primary} {Metabolites} {Between} {Shoots} and {Roots}},
	volume = {49},
	copyright = {© 2026 The Author(s). Plant, Cell \& Environment published by John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.70599},
	doi = {10.1111/pce.70599},
	abstract = {Trehalose 6-phoshpate (Tre6P) is a key signalling molecule that reflects carbon status and integrates it with developmental decision making. Tre6P has been demonstrated to regulate various developmental processes, including vegetative growth, shoot branching, flowering, and root branching. Here, we investigate how vasculature-derived Tre6P influences root system architecture by expressing heterologous Tre6P synthase or Tre6P phosphatase (TPP) specifically in the plant vasculature. Plants with elevated vascular-derived Tre6P levels had smaller root systems, reduced sucrose levels, and lower root metabolite levels, whereas vascular TPP overexpression had the opposite effect. Using reciprocal grafting experiments, we identified shoot-derived vascular Tre6P to be the main driver of these systemic responses. In lines with increased Tre6P in the shoot vasculature, the shoot-to-root metabolite ratios were consistently increased, indicating that Tre6P modulates metabolite allocation and utilisation to balance carbon partitioning between shoot and root growth. Our data further suggest that vascular Tre6P contributed to optimising the carbon-to-nitrogen ratio to support growth and fitness. Besides this systemic function, this study shows that root-derived Tre6P also plays a critical local role in modulating root development. Collectively, our results demonstrate that Tre6P in the vasculature functions both systemically and locally to coordinate metabolic status with root growth and architecture.},
	language = {en},
	number = {9},
	urldate = {2026-08-07},
	journal = {Plant, Cell \& Environment},
	author = {Göbel, Moritz and Foster, Jacqueline and Westhoff, Philipp and Skorzinski, Noemi and Lepper, Hannah L. and Njo, Maria F. and Schmid, Markus and Beeckman, Tom and Tanurdžić, Miloš and Amtmann, Anna and Fichtner, Franziska},
	year = {2026},
	keywords = {resource allocation, root development, sugar partitioning, sugar signalling, trehalose 6-phosphate},
	pages = {6361--6379},
}

Trehalose 6-phoshpate (Tre6P) is a key signalling molecule that reflects carbon status and integrates it with developmental decision making. Tre6P has been demonstrated to regulate various developmental processes, including vegetative growth, shoot branching, flowering, and root branching. Here, we investigate how vasculature-derived Tre6P influences root system architecture by expressing heterologous Tre6P synthase or Tre6P phosphatase (TPP) specifically in the plant vasculature. Plants with elevated vascular-derived Tre6P levels had smaller root systems, reduced sucrose levels, and lower root metabolite levels, whereas vascular TPP overexpression had the opposite effect. Using reciprocal grafting experiments, we identified shoot-derived vascular Tre6P to be the main driver of these systemic responses. In lines with increased Tre6P in the shoot vasculature, the shoot-to-root metabolite ratios were consistently increased, indicating that Tre6P modulates metabolite allocation and utilisation to balance carbon partitioning between shoot and root growth. Our data further suggest that vascular Tre6P contributed to optimising the carbon-to-nitrogen ratio to support growth and fitness. Besides this systemic function, this study shows that root-derived Tre6P also plays a critical local role in modulating root development. Collectively, our results demonstrate that Tre6P in the vasculature functions both systemically and locally to coordinate metabolic status with root growth and architecture.

@article{lu_epigenetic_2026,
	title = {Epigenetic regulation of fruit shape determination by the {JAGGED} gene in {Capsella} rubella},
	volume = {17},
	copyright = {2026 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-026-73180-3},
	doi = {10.1038/s41467-026-73180-3},
	abstract = {Fruits are a key feature defining angiosperms, yet how local growth is coordinated during development to generate diverse fruits remains unclear. Here, we demonstrate that the Capsella rubella C2H2-zinc finger transcription factor JAGGED (CrJAG) controls fruit shape determination by promoting both cell division and anisotropic growth. At the molecular level, CrJAG physically interacts with members of the Capsella rubella MULTICOPY SUPPRESSOR OF IRA1 (CrMSI)  histone chaperone family, increasing the chromatin accessibility and thereby sustaining the expression of genes involved in fruit morphogenesis. The resulting closed chromatin state in Crjag fruits is characterized by a reduction of the active histone marker (H3K18ac) and an increase of the repressive marker (H3K27me3). Further expression and pharmacological treatment analyses indicate that the developmental defects in Crjag fruits are largely attributable to down-regulation of the key cell-cycle regulator CrAUR2. Collectively, our findings therefore suggest that fine-tuning the cell cycle via epigenetic modification represents an additional, essential layer of regulation critical to organ development and diversification.},
	language = {en},
	number = {1},
	urldate = {2026-08-07},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Lü, Tian-Feng and Chen, Xiao-Yu and Trozzi, Nicola and He, Wen and Yuan, Quan and Han, Yu and Lu, Li-Min and Li, Chao-Bin and Cheng, Jie and Sicard, Adrien and Zhang, Yao and Su, Ya-Nan and Zan, Yan-Jun and Lenhard, Michael and Kong, Hong-Zhi and Majda, Mateusz and Østergaard, Lars and Dong, Yang},
	month = jun,
	year = {2026},
	keywords = {Cell division, Fruiting, Plant development},
	pages = {7666},
}

Fruits are a key feature defining angiosperms, yet how local growth is coordinated during development to generate diverse fruits remains unclear. Here, we demonstrate that the Capsella rubella C2H2-zinc finger transcription factor JAGGED (CrJAG) controls fruit shape determination by promoting both cell division and anisotropic growth. At the molecular level, CrJAG physically interacts with members of the Capsella rubella MULTICOPY SUPPRESSOR OF IRA1 (CrMSI)  histone chaperone family, increasing the chromatin accessibility and thereby sustaining the expression of genes involved in fruit morphogenesis. The resulting closed chromatin state in Crjag fruits is characterized by a reduction of the active histone marker (H3K18ac) and an increase of the repressive marker (H3K27me3). Further expression and pharmacological treatment analyses indicate that the developmental defects in Crjag fruits are largely attributable to down-regulation of the key cell-cycle regulator CrAUR2. Collectively, our findings therefore suggest that fine-tuning the cell cycle via epigenetic modification represents an additional, essential layer of regulation critical to organ development and diversification.

@article{larsson_litter_2026,
	title = {Litter properties influence decomposition more than local soil environment in a boreal tree species common garden experiment},
	volume = {619},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S037811272600592X},
	doi = {10.1016/j.foreco.2026.124094},
	abstract = {Boreal forests store significant quantities of carbon (C), particularly in their soils. Thus, selecting tree species that promote slow decomposition, due to either their inherent litter properties or soil microbial communities, may be a suitable tool to enhance C uptake in boreal forests. In this study we used two common garden experiments and employed a reciprocal litter transplant decomposition experiment using four common Swedish tree species (Betula pendula, Larix sp., Picea abies and Pinus sylvestris), with varying plant economics strategies. We aimed to partition the relative effects of litter quality and soil environment on litter and humus decomposition rates. Our results showed that litter mass loss was much more dependent on tree species than soil environment, a result further reinforced by the lack of tree species differences in the soil microbial community. The rates of decomposition did however appear to converge over time, as humus mass loss was not responsive to either tree species or soil environment. Our result therefore suggests that tree species selection, as a forest management tool, should be based on each species site-specific growth potential, instead of initial differences in decomposition rate, which could serve to maximize the ecosystem C stock and in turn increase the climate benefits of boreal forest.},
	urldate = {2026-07-31},
	journal = {Forest Ecology and Management},
	author = {Larsson, Marcus and Gundale, Michael J. and Bizjak-Johansson, Tinkara and Spitzer, Clydecia M. and Nordin, Annika},
	month = nov,
	year = {2026},
	keywords = {Boreal forest, Decomposition, Leaf litter, Litter quality, Soil carbon, Soil microbial community, Tree species},
	pages = {124094},
}

Boreal forests store significant quantities of carbon (C), particularly in their soils. Thus, selecting tree species that promote slow decomposition, due to either their inherent litter properties or soil microbial communities, may be a suitable tool to enhance C uptake in boreal forests. In this study we used two common garden experiments and employed a reciprocal litter transplant decomposition experiment using four common Swedish tree species (Betula pendula, Larix sp., Picea abies and Pinus sylvestris), with varying plant economics strategies. We aimed to partition the relative effects of litter quality and soil environment on litter and humus decomposition rates. Our results showed that litter mass loss was much more dependent on tree species than soil environment, a result further reinforced by the lack of tree species differences in the soil microbial community. The rates of decomposition did however appear to converge over time, as humus mass loss was not responsive to either tree species or soil environment. Our result therefore suggests that tree species selection, as a forest management tool, should be based on each species site-specific growth potential, instead of initial differences in decomposition rate, which could serve to maximize the ecosystem C stock and in turn increase the climate benefits of boreal forest.

@article{vallebueno-estrada_unified_2026,
	title = {Unified {Multi}-{Caller} {Ensemble} ({UME}) {Generates} an {Unbiased} {Maize} {Haplotype} {Map} for {Variable} {Coverage} {Whole} {Genome} {Data}},
	volume = {26},
	copyright = {© 2026 The Author(s). Molecular Ecology Resources published by John Wiley \& Sons Ltd.},
	issn = {1755-0998},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.70150},
	doi = {10.1111/1755-0998.70150},
	abstract = {We present a novel diversity-focused haplotype map (HapMap) that characterizes over 64.5 million maize (Zea mays ssp. mays) single nucleotide polymorphisms (SNPs) genotyped across 818 individuals from diverse backgrounds. This HapMap aims to balance the variation obtained from domesticated landraces and inbred lines, outgroup Zea spp. and more distant Tripsacum spp. in order to minimize ascertainment bias for diversity studies. Included individuals derive from public data from various experimental setups and coverages, which is challenging for standard SNP callers to accommodate. We provide evidence of coverage biases associated with standard callers that influence resulting variation and introduce a novel approach called Unified Multi-Caller Ensemble (UME), which enhances variant calling accuracy in low-coverage and mixed-coverage genomic datasets. UME corrects for coverage bias resulting from inter-sample coverage heterogeneity by leveraging evidence from variant callers with orthogonal strategies, re-calibrating the error probabilities across callers to minimize the impact of error biases inherent to a given caller. It outperforms individual strategies and excels in de novo variant calling, taking advantage of instances of higher depth reads, even in low coverage individuals, while preserving biologically informative variant relationships across coverage levels. An important feature of UME is the independence from population allele frequencies in the discovery panel, thus avoiding ascertainment bias resulting from unbalanced input genetic diversity. Discovered variants are less affected by ascertainment bias because no population filtering is used, and the full diversity of SNPs is retained in the final variant call set to maximize the utility of the dataset for production calling newly sequenced samples. We present a strategy for filtering the recalibrated error profiles that relies on maximizing demographic signals to retain genetic relationships within the population while reducing sequencing error. After the variant discovery phase, we employ the UME production stage, which enriches genotype calling across all coverage levels, benefiting low-coverage samples. Error introduced in this process is removed through subsequent filtering. Using this approach, we generated a coverage bias-controlled maize HapMap database, providing a comprehensive representation of maize accessions and emphasizing landrace diversity. This diverse panel of domesticated maize and outgroups from across the Americas enables accurate genotyping in low-coverage samples while offering crucial context for interpreting diversity, particularly for natural diversity and paleogenomic analyses.},
	language = {en},
	number = {5},
	urldate = {2026-07-31},
	journal = {Molecular Ecology Resources},
	author = {Vallebueno-Estrada, Miguel and Swarts, Kelly},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.70150},
	keywords = {HapMap, coverage bias, ensemble approaches, maize, variant calling},
	pages = {e70150},
}

We present a novel diversity-focused haplotype map (HapMap) that characterizes over 64.5 million maize (Zea mays ssp. mays) single nucleotide polymorphisms (SNPs) genotyped across 818 individuals from diverse backgrounds. This HapMap aims to balance the variation obtained from domesticated landraces and inbred lines, outgroup Zea spp. and more distant Tripsacum spp. in order to minimize ascertainment bias for diversity studies. Included individuals derive from public data from various experimental setups and coverages, which is challenging for standard SNP callers to accommodate. We provide evidence of coverage biases associated with standard callers that influence resulting variation and introduce a novel approach called Unified Multi-Caller Ensemble (UME), which enhances variant calling accuracy in low-coverage and mixed-coverage genomic datasets. UME corrects for coverage bias resulting from inter-sample coverage heterogeneity by leveraging evidence from variant callers with orthogonal strategies, re-calibrating the error probabilities across callers to minimize the impact of error biases inherent to a given caller. It outperforms individual strategies and excels in de novo variant calling, taking advantage of instances of higher depth reads, even in low coverage individuals, while preserving biologically informative variant relationships across coverage levels. An important feature of UME is the independence from population allele frequencies in the discovery panel, thus avoiding ascertainment bias resulting from unbalanced input genetic diversity. Discovered variants are less affected by ascertainment bias because no population filtering is used, and the full diversity of SNPs is retained in the final variant call set to maximize the utility of the dataset for production calling newly sequenced samples. We present a strategy for filtering the recalibrated error profiles that relies on maximizing demographic signals to retain genetic relationships within the population while reducing sequencing error. After the variant discovery phase, we employ the UME production stage, which enriches genotype calling across all coverage levels, benefiting low-coverage samples. Error introduced in this process is removed through subsequent filtering. Using this approach, we generated a coverage bias-controlled maize HapMap database, providing a comprehensive representation of maize accessions and emphasizing landrace diversity. This diverse panel of domesticated maize and outgroups from across the Americas enables accurate genotyping in low-coverage samples while offering crucial context for interpreting diversity, particularly for natural diversity and paleogenomic analyses.

@article{hussain_progression_2026,
	title = {The progression of leaf senescence is gated by the cytosolic arginine pool},
	volume = {12},
	copyright = {2026 The Author(s)},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-026-02328-2},
	doi = {10.1038/s41477-026-02328-2},
	abstract = {Leaf senescence aims to degrade cellular components to recover valuable nutrients and reallocate them to other organs1. Once this remobilization is complete, cells undergo a vacuolar-type of programmed cell death2, ultimately leading to the death of the entire organ. But how do cells from a senescing leaf ‘know’ when to die? If the cell death process per se is initiated too early, remobilization may not be completed, rendering it futile. This suggests the presence of a ‘sensing’ mechanism that coordinates the remobilization phase with the onset of cell death during leaf senescence. Here, using Arabidopsis thaliana functional stay-green mutants, we show that senescing cells are wired to metabolically dissipate the cytosolic arginine pool, which otherwise represses the progression of leaf senescence. We propose a model in which a senescing cell uses this pool as a proxy for the completion of nitrogen remobilization and to accurately time the subsequent induction of cell death.},
	language = {en},
	number = {7},
	urldate = {2026-07-24},
	journal = {Nature Plants},
	publisher = {Nature Publishing Group},
	author = {Hussain, Shah and Boussardon, Clément and Keech, Olivier},
	month = jul,
	year = {2026},
	keywords = {Abiotic, Cell fate},
	pages = {1325--1333},
}

Leaf senescence aims to degrade cellular components to recover valuable nutrients and reallocate them to other organs1. Once this remobilization is complete, cells undergo a vacuolar-type of programmed cell death2, ultimately leading to the death of the entire organ. But how do cells from a senescing leaf ‘know’ when to die? If the cell death process per se is initiated too early, remobilization may not be completed, rendering it futile. This suggests the presence of a ‘sensing’ mechanism that coordinates the remobilization phase with the onset of cell death during leaf senescence. Here, using Arabidopsis thaliana functional stay-green mutants, we show that senescing cells are wired to metabolically dissipate the cytosolic arginine pool, which otherwise represses the progression of leaf senescence. We propose a model in which a senescing cell uses this pool as a proxy for the completion of nitrogen remobilization and to accurately time the subsequent induction of cell death.

@article{collani_soppis_2026,
	title = {{SoPPIs}: a highly parallelized protein–protein-interaction screening method in prokaryotic and eukaryotic hosts},
	volume = {54},
	issn = {1362-4962},
	shorttitle = {{SoPPIs}},
	url = {https://doi.org/10.1093/nar/gkag716},
	doi = {10.1093/nar/gkag716},
	abstract = {Protein–protein interactions (PPIs) are at the heart of most cellular processes but despite recent progress, their genome-wide analysis remains challenging. With this in mind, we have developed SoPPIs (sequencing of PPIs), a powerful method that facilitates parallelized PPI analyses using an innovative combination of the split-Cre/loxP system and high-throughput DNA sequencing. Sequential recombination of plasmids encodes information about pairs of interacting proteins in recombined DNA, facilitating their easy and cost-efficient identification by next-generation sequencing. Importantly, SoPPIs works with most soluble proteins, can be implemented in any cell type that can be transformed with episomal plasmids, and is in principle capable of interrogating all possible PPIs in an organism in a single experiment. To demonstrate the power of SoPPIs, we analyzed the composition of the Arabidopsis thaliana LSm/Sm ring, an evolutionarily highly conserved core component of the spliceosome and performed parallelized library screens to identify LSm/Sm-interacting proteins. Given its versatility and usability, we expect SoPPIs to quickly gain popularity and help provide insights into the PPI networks underlying complex biological systems.},
	number = {14},
	urldate = {2026-07-24},
	journal = {Nucleic Acids Research},
	author = {Collani, Silvio and Nardeli, Sarah Muniz and Chowdary, K V S K Arjun and Goretti, Daniela and Schmid, Markus},
	month = aug,
	year = {2026},
	pages = {gkag716},
}

Protein–protein interactions (PPIs) are at the heart of most cellular processes but despite recent progress, their genome-wide analysis remains challenging. With this in mind, we have developed SoPPIs (sequencing of PPIs), a powerful method that facilitates parallelized PPI analyses using an innovative combination of the split-Cre/loxP system and high-throughput DNA sequencing. Sequential recombination of plasmids encodes information about pairs of interacting proteins in recombined DNA, facilitating their easy and cost-efficient identification by next-generation sequencing. Importantly, SoPPIs works with most soluble proteins, can be implemented in any cell type that can be transformed with episomal plasmids, and is in principle capable of interrogating all possible PPIs in an organism in a single experiment. To demonstrate the power of SoPPIs, we analyzed the composition of the Arabidopsis thaliana LSm/Sm ring, an evolutionarily highly conserved core component of the spliceosome and performed parallelized library screens to identify LSm/Sm-interacting proteins. Given its versatility and usability, we expect SoPPIs to quickly gain popularity and help provide insights into the PPI networks underlying complex biological systems.

@article{frew_soil_2026,
	title = {Soil sampling strategy determines detection of arbuscular mycorrhizal fungi and reveals phylogenetically structured bias},
	volume = {221},
	issn = {0038-0717},
	url = {https://www.sciencedirect.com/science/article/pii/S0038071726001690},
	doi = {10.1016/j.soilbio.2026.110250},
	abstract = {Arbuscular mycorrhizal (AM) fungal communities are highly patchy at microscales, meaning sampling decisions can strongly shape the communities detected. We used a long-term fertilisation experiment to compare three sampling strategies and two sample preservation methods to assess their influence on AM fungal diversity and taxon-specific detection. We found that sequencing individual subsamples detected substantially more taxa than compositing, which missed rare fungi and introduced phylogenetically structured biases that underrepresented certain fungal lineages. Short-term drying and freezing produced comparable community profiles. Together, these results show that AM fungal detection depends strongly on sampling strategy, highlighting the need to align sampling scales with the microscale processes structuring these symbioses.},
	urldate = {2026-07-24},
	journal = {Soil Biology and Biochemistry},
	author = {Frew, Adam and Dhull, Manjeet and Power, Sally and Aguilar-Trigueros, Carlos A.},
	month = oct,
	year = {2026},
	keywords = {Arbuscular mycorrhizal fungi, Community composition, Grassland, Phosphorus fertilisation, Sampling strategy, Soil microbial diversity, Spatial heterogeneity},
	pages = {110250},
}

Arbuscular mycorrhizal (AM) fungal communities are highly patchy at microscales, meaning sampling decisions can strongly shape the communities detected. We used a long-term fertilisation experiment to compare three sampling strategies and two sample preservation methods to assess their influence on AM fungal diversity and taxon-specific detection. We found that sequencing individual subsamples detected substantially more taxa than compositing, which missed rare fungi and introduced phylogenetically structured biases that underrepresented certain fungal lineages. Short-term drying and freezing produced comparable community profiles. Together, these results show that AM fungal detection depends strongly on sampling strategy, highlighting the need to align sampling scales with the microscale processes structuring these symbioses.

@article{liu_rethinking_2026,
	title = {Rethinking {Wound} {Signaling} in {Plant} {Development}: {The} {Epigenetic} and {Metabolic} {Nexus} of {JA}-{Mediated} {Bud} {Activation}},
	issn = {0022-0957},
	shorttitle = {Rethinking {Wound} {Signaling} in {Plant} {Development}},
	url = {https://doi.org/10.1093/jxb/erag346},
	doi = {10.1093/jxb/erag346},
	urldate = {2026-07-24},
	journal = {Journal of Experimental Botany},
	author = {Liu, Puyuan and Bhalerao, Rishikesh P and Yang, Qinsong and Li, Guolei},
	month = jul,
	year = {2026},
	pages = {erag346},
}

@article{hodek_rapid_2026,
	title = {Rapid and targeted {HILIC}-{MS}/{MS} quantification of urinary metabolites reveals metabolic alterations in {COVID}-19 patients},
	volume = {18},
	issn = {1759-9660},
	url = {https://dx.doi.org/10.1039/d6ay00400h},
	doi = {10.1039/d6ay00400h},
	abstract = {Urinary metabolites and their concentrations serve as biomarkers for identification of metabolic pathways that relate to specific diseases; therefore, fast},
	language = {en},
	number = {25},
	urldate = {2026-07-24},
	journal = {Analytical Methods},
	publisher = {The Royal Society of Chemistry},
	author = {Hodek, Ondrej and Edman, Anna and Granvik, Christoffer and Lind, Alicia and Överby, Anna K. and Gutensohn, Mareike and Johansson, Annika I.},
	month = jul,
	year = {2026},
	pages = {5317--5323},
}

Urinary metabolites and their concentrations serve as biomarkers for identification of metabolic pathways that relate to specific diseases; therefore, fast

@article{mishra_plant_2026,
	title = {Plant growth-promoting {Pseudomonas} strains modulate potato tuberization signalling and development},
	volume = {77},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erag237},
	doi = {10.1093/jxb/erag237},
	abstract = {Plant growth-promoting rhizobacteria (PGPR) can influence plant development through hormone signalling, nutrient mobilization, and activation of defence pathways. While individual bacterial strains can enhance plant performance, microbial consortia may generate complementary or synergistic effects that remain poorly understood, particularly with respect to crop developmental signalling. Potato (Solanum tuberosum), the most important dicot food crop globally, represents a suitable model for investigating how beneficial microbes influence tuber development. In this study, we investigated the effects of two well-characterized PGPR strains, Pseudomonas protegens CHA0 and P. simiae WCS417, applied individually or in combination, on two potato cultivars (‘Mandel’ and ‘Désirée’) under long-day conditions. Confocal microscopy confirmed rapid root colonization by both strains within 24 h of inoculation. Metabolomic profiling of bacterial exudates revealed distinct metabolic signatures for the two strains and non-additive metabolite patterns when cultured together, suggesting metabolic interactions within the bacterial consortium. Plant responses were cultivar dependent, with bacterial treatments influencing vegetative growth and selected tuber quality traits, including starch and ascorbic acid levels. Gene expression analyses revealed strong induction of the tuberization regulator StSP6A in roots, with up to 5-fold increased expression following P. protegens and combined inoculation, accompanied by activation of jasmonic acid-related signalling pathways. Together, these results indicate that interactions between beneficial Pseudomonas strains can influence potato development through coordinated effects on root architecture and signalling pathways associated with tuberization and defence.},
	number = {13},
	urldate = {2026-07-24},
	journal = {Journal of Experimental Botany},
	author = {Mishra, Arti and Mahawar, Lovely and Tsitouri, Angeliki and Basheer, Jasim and Albrectsen, Benedicte Riber},
	month = jul,
	year = {2026},
	pages = {4177--4194},
}

Plant growth-promoting rhizobacteria (PGPR) can influence plant development through hormone signalling, nutrient mobilization, and activation of defence pathways. While individual bacterial strains can enhance plant performance, microbial consortia may generate complementary or synergistic effects that remain poorly understood, particularly with respect to crop developmental signalling. Potato (Solanum tuberosum), the most important dicot food crop globally, represents a suitable model for investigating how beneficial microbes influence tuber development. In this study, we investigated the effects of two well-characterized PGPR strains, Pseudomonas protegens CHA0 and P. simiae WCS417, applied individually or in combination, on two potato cultivars (‘Mandel’ and ‘Désirée’) under long-day conditions. Confocal microscopy confirmed rapid root colonization by both strains within 24 h of inoculation. Metabolomic profiling of bacterial exudates revealed distinct metabolic signatures for the two strains and non-additive metabolite patterns when cultured together, suggesting metabolic interactions within the bacterial consortium. Plant responses were cultivar dependent, with bacterial treatments influencing vegetative growth and selected tuber quality traits, including starch and ascorbic acid levels. Gene expression analyses revealed strong induction of the tuberization regulator StSP6A in roots, with up to 5-fold increased expression following P. protegens and combined inoculation, accompanied by activation of jasmonic acid-related signalling pathways. Together, these results indicate that interactions between beneficial Pseudomonas strains can influence potato development through coordinated effects on root architecture and signalling pathways associated with tuberization and defence.

@article{feng_development_2026,
	title = {Development of a 50 {K} liquid-phased array for {Chinese} fir and its application in genomic selection},
	volume = {249},
	issn = {0926-6690},
	url = {https://www.sciencedirect.com/science/article/pii/S0926669026011581},
	doi = {10.1016/j.indcrop.2026.123771},
	abstract = {Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is the most commercially important conifer species for artificial plantations in China and has been subject to genetic improvement since the 1950s. Conventional breeding programs for this species are constrained by long generation cycles, therefore low genetic improvement per year. Genomic selection (GS) offers a novel and effective strategy for the genetic improvement of Chinese fir. However, the large size and complex genomic structure of Chinese fir make whole-genome resequencing (WGRS) costly for large breeding populations. Therefore, there is an urgent need to develop a cost-effective, efficient, and stable genotyping platform to facilitate genomic improvement in this species. In this study, the CunLa50K SNP array was developed based on WGRS data from 548 Chinese fir individuals spanning the species range. The array comprises 49,861 high-quality, uniformly distributed SNPs and 715 functional SNPs that are significantly associated with growth, wood properties, and bioclimatic traits. Performance evaluation showed an average coverage rate of 98.14\%, an average sequencing depth of 93.16 × , and a technical replicate concordance rate of 99.24\%. The array accurately identified kinship relationships and mismatched samples during pedigree verification. The genomic based best linear unbiased prediction (GBLUP) model achieved 100\% and 94.5\% of the prediction accuracy demonstrated by the conventional ABLUP model for the traits of diameter at breast height (DBH) and wood density (WD), respectively. This study provides a key technological tool for high-throughput genotyping and establishes a foundation for a GS breeding system in Chinese fir, facilitating a paradigm shift in its breeding strategy from phenotypic-based selection towards DNA-based selection.},
	urldate = {2026-07-24},
	journal = {Industrial Crops and Products},
	author = {Feng, Qihang and Li, Xueyu and Wu, Jinzhang and Niu, Diewei and Su, Shunde and Wu, Harry X. and Bian, Liming and Chen, Zhi-Qiang},
	month = jul,
	year = {2026},
	keywords = {Chinese fir, Genomic selection, Liquid-phased array, SNP},
	pages = {123771},
}

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is the most commercially important conifer species for artificial plantations in China and has been subject to genetic improvement since the 1950s. Conventional breeding programs for this species are constrained by long generation cycles, therefore low genetic improvement per year. Genomic selection (GS) offers a novel and effective strategy for the genetic improvement of Chinese fir. However, the large size and complex genomic structure of Chinese fir make whole-genome resequencing (WGRS) costly for large breeding populations. Therefore, there is an urgent need to develop a cost-effective, efficient, and stable genotyping platform to facilitate genomic improvement in this species. In this study, the CunLa50K SNP array was developed based on WGRS data from 548 Chinese fir individuals spanning the species range. The array comprises 49,861 high-quality, uniformly distributed SNPs and 715 functional SNPs that are significantly associated with growth, wood properties, and bioclimatic traits. Performance evaluation showed an average coverage rate of 98.14%, an average sequencing depth of 93.16 × , and a technical replicate concordance rate of 99.24%. The array accurately identified kinship relationships and mismatched samples during pedigree verification. The genomic based best linear unbiased prediction (GBLUP) model achieved 100% and 94.5% of the prediction accuracy demonstrated by the conventional ABLUP model for the traits of diameter at breast height (DBH) and wood density (WD), respectively. This study provides a key technological tool for high-throughput genotyping and establishes a foundation for a GS breeding system in Chinese fir, facilitating a paradigm shift in its breeding strategy from phenotypic-based selection towards DNA-based selection.

@article{yadav_primary_2026,
	title = {The primary beta-galactosidase {BGAL10} modulates pavement cell shape acquisition in {Arabidopsis}},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erag320},
	doi = {10.1093/jxb/erag320},
	abstract = {Cell shape acquisition is a fundamental biological process that allows cells to establish and maintain morphologies adapted to their specialised functions while preserving tissue integrity. In plants, this process is strongly influenced by the presence of the cell wall, a dynamic extracellular network of polysaccharides and proteins that surrounds the plasma membrane and physically connects neighbouring cells. By constraining and directing cellular expansion, the cell wall plays a central role in controlling cell shape. In Arabidopsis leaves, epidermal pavement cells adopt a characteristic jigsaw-puzzle–like morphology through the formation of interdigitating lobes and necks, providing a powerful model system for dissecting the mechanisms underlying complex plant cell shape acquisition. Here, we demonstrate the involvement of the glycoside hydrolase BETA-GALACTOSIDASE 10 (BGAL10) in pavement cell morphogenesis. Using high-resolution time-series imaging, we analysed cell growth dynamics alongside the spatial expression and subcellular localisation of BGAL10, revealing a prominent role for BGAL10 in mature cells, particularly at curved regions of the cell wall along pavement cell lobes. Furthermore, Brillouin microscopy revealed altered mechanical properties in the bgal10-1 mutant, most notably at lobe–indentation interfaces and cell junctions. Together, our results indicate that BGAL10 fine-tunes lobe outgrowth, likely through modification of the hemicellulose matrix, thereby regulating cell wall extensibility and mechanical stress distribution during pavement cell shape acquisition.},
	urldate = {2026-07-07},
	journal = {Journal of Experimental Botany},
	author = {Yadav, Sandeep and Kumar, Vinod and Heymans, Adrien and Sabooni, Nasrin and Jobert, François and Lin, Mengzhuo and Grones, Peter and Bacete, Laura and Robert, Stéphanie},
	month = jul,
	year = {2026},
	pages = {erag320},
}

Cell shape acquisition is a fundamental biological process that allows cells to establish and maintain morphologies adapted to their specialised functions while preserving tissue integrity. In plants, this process is strongly influenced by the presence of the cell wall, a dynamic extracellular network of polysaccharides and proteins that surrounds the plasma membrane and physically connects neighbouring cells. By constraining and directing cellular expansion, the cell wall plays a central role in controlling cell shape. In Arabidopsis leaves, epidermal pavement cells adopt a characteristic jigsaw-puzzle–like morphology through the formation of interdigitating lobes and necks, providing a powerful model system for dissecting the mechanisms underlying complex plant cell shape acquisition. Here, we demonstrate the involvement of the glycoside hydrolase BETA-GALACTOSIDASE 10 (BGAL10) in pavement cell morphogenesis. Using high-resolution time-series imaging, we analysed cell growth dynamics alongside the spatial expression and subcellular localisation of BGAL10, revealing a prominent role for BGAL10 in mature cells, particularly at curved regions of the cell wall along pavement cell lobes. Furthermore, Brillouin microscopy revealed altered mechanical properties in the bgal10-1 mutant, most notably at lobe–indentation interfaces and cell junctions. Together, our results indicate that BGAL10 fine-tunes lobe outgrowth, likely through modification of the hemicellulose matrix, thereby regulating cell wall extensibility and mechanical stress distribution during pavement cell shape acquisition.

@article{bladh_role_2026,
	title = {The role of mucosal {IgA} in protection against influenza {A} {H1N1} virus infection in a real-world setting},
	volume = {129},
	issn = {2352-3964},
	url = {https://www.sciencedirect.com/science/article/pii/S2352396426002422},
	doi = {10.1016/j.ebiom.2026.106359},
	abstract = {Background
Parenteral vaccines against influenza virus prevent severe disease but provide limited protection against infection, likely due to limited induction of mucosal immunity. However, direct clinical evidence for mucosal antibody-mediated protection against influenza virus infection in humans has been lacking. The aim of this study was to evaluate the role of antigen-specific mucosal IgA as a correlate of protection against influenza virus infection. We investigated H1-specific nasal IgA and serum IgG and the effect on influenza virus infection, with corresponding SARS-CoV-2 data from the same cohort as an internal comparator.
Methods
Using a prospective cohort study design, we analysed paired antigen-specific serum IgG and nasal IgA responses at baseline, after influenza A (H1N1) virus and SARS-CoV-2 infections, and after intramuscular influenza and SARS-CoV-2 vaccination. We then evaluated associations between baseline antibody levels, vaccination, and the risk of subsequent influenza A (H1N1) virus infection or SARS-CoV-2 infections in a 4-month home-based qPCR screening in Stockholm, Sweden (2023–2024). A Poisson regression model with a log offset for time at risk was used to evaluate if baseline antigen-specific nasal IgA or serum IgG levels or recent vaccination was associated with protection against infection. Antibody quantification was performed using a highly sensitive electrochemiluminescence immunoassay (Meso Scale Diagnostics, USA) optimised for mucosal sampling.
Findings
A total of 926 study participants were enrolled. After influenza A (H1N1) virus infection, H1-specific nasal IgA and serum IgG increased (p = 0.007 and p {\textless} 0.001 respectively), while vaccination boosted serum IgG (p = 0.006) but not nasal IgA. Baseline nasal H1-specific IgA were lower in H1N1-infected individuals (p = 0.024), and notably, baseline nasal H1-specific IgA above median was associated with reduced H1N1 infection risk (IRR 0.23, 95\% CI 0.05–0.75, p = 0.026), while serum IgG and recent vaccination were not (IRR 2.03, 0.70–6.62, p = 0.206 and IRR 1.06, 0.38–3.03, p = 0.917, respectively). Moreover, each two-fold increase in baseline nasal H1-specific IgA levels was associated with a significantly lower infection risk (IRR 0.69, 95\% CI 0.51–0.92; p = 0.014). Similar findings were observed for SARS-CoV-2 for mucosal IgA, whereas baseline serum spike-specific IgG above the median was also associated with reduced risk of infection.
Interpretation
Leveraging fit-for-purpose sampling, a validated and highly sensitive assay, and a large real-world cohort, we directly link mucosal IgA to protection against influenza virus infection. While currently employed vaccines provide robust protection against severe disease and hospital admissions, these findings highlight the need for novel approaches generating robust mucosal protection against infection per se, and the need to incorporate mucosal endpoints into next-generation vaccine development aiming for infection-blocking immunity.
Funding
This work was funded by the European Research Council (101164772 - D-MAP), the Swedish Society for Medical Research (SSMF CG-24-0191-B-H-01), the Knut and Alice Wallenberg Foundation (KAW 2024.0108), and the SciLifeLab Pandemic Laboratory Preparedness Program.},
	urldate = {2026-07-07},
	journal = {eBioMedicine},
	author = {Bladh, Oscar and Pongrácz, Tamás and Aguilera, Katherina and Berkell, Matilda and Marking, Ulrika and Greilert Norin, Nina and Rihani, Ali and Alm, Jessica J. and Krammer, Florian and Åberg, Mikael and Thålin, Charlotte},
	month = jul,
	year = {2026},
	keywords = {Correlate of protection, Infection, Influenza A, Mucosal antibodies, SARS-CoV-2, Vaccines},
	pages = {106359},
}

Background Parenteral vaccines against influenza virus prevent severe disease but provide limited protection against infection, likely due to limited induction of mucosal immunity. However, direct clinical evidence for mucosal antibody-mediated protection against influenza virus infection in humans has been lacking. The aim of this study was to evaluate the role of antigen-specific mucosal IgA as a correlate of protection against influenza virus infection. We investigated H1-specific nasal IgA and serum IgG and the effect on influenza virus infection, with corresponding SARS-CoV-2 data from the same cohort as an internal comparator. Methods Using a prospective cohort study design, we analysed paired antigen-specific serum IgG and nasal IgA responses at baseline, after influenza A (H1N1) virus and SARS-CoV-2 infections, and after intramuscular influenza and SARS-CoV-2 vaccination. We then evaluated associations between baseline antibody levels, vaccination, and the risk of subsequent influenza A (H1N1) virus infection or SARS-CoV-2 infections in a 4-month home-based qPCR screening in Stockholm, Sweden (2023–2024). A Poisson regression model with a log offset for time at risk was used to evaluate if baseline antigen-specific nasal IgA or serum IgG levels or recent vaccination was associated with protection against infection. Antibody quantification was performed using a highly sensitive electrochemiluminescence immunoassay (Meso Scale Diagnostics, USA) optimised for mucosal sampling. Findings A total of 926 study participants were enrolled. After influenza A (H1N1) virus infection, H1-specific nasal IgA and serum IgG increased (p = 0.007 and p \textless 0.001 respectively), while vaccination boosted serum IgG (p = 0.006) but not nasal IgA. Baseline nasal H1-specific IgA were lower in H1N1-infected individuals (p = 0.024), and notably, baseline nasal H1-specific IgA above median was associated with reduced H1N1 infection risk (IRR 0.23, 95% CI 0.05–0.75, p = 0.026), while serum IgG and recent vaccination were not (IRR 2.03, 0.70–6.62, p = 0.206 and IRR 1.06, 0.38–3.03, p = 0.917, respectively). Moreover, each two-fold increase in baseline nasal H1-specific IgA levels was associated with a significantly lower infection risk (IRR 0.69, 95% CI 0.51–0.92; p = 0.014). Similar findings were observed for SARS-CoV-2 for mucosal IgA, whereas baseline serum spike-specific IgG above the median was also associated with reduced risk of infection. Interpretation Leveraging fit-for-purpose sampling, a validated and highly sensitive assay, and a large real-world cohort, we directly link mucosal IgA to protection against influenza virus infection. While currently employed vaccines provide robust protection against severe disease and hospital admissions, these findings highlight the need for novel approaches generating robust mucosal protection against infection per se, and the need to incorporate mucosal endpoints into next-generation vaccine development aiming for infection-blocking immunity. Funding This work was funded by the European Research Council (101164772 - D-MAP), the Swedish Society for Medical Research (SSMF CG-24-0191-B-H-01), the Knut and Alice Wallenberg Foundation (KAW 2024.0108), and the SciLifeLab Pandemic Laboratory Preparedness Program.

@article{laudon_increasing_2026,
	title = {Increasing temporal variations in growth of {Swedish} forests call for better mechanistic insights},
	volume = {618},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112726004949},
	doi = {10.1016/j.foreco.2026.123996},
	abstract = {In recent decades, Swedish forests have experienced increasing variability of annual growth rate both in amplitude and frequency, jeopardizing national contribution to EU targets for carbon sequestration and climate change mitigation during periods of time. We postulate a set of hypotheses that with variable strengths can help explain and evaluate five major phases of growth variability observed the last three decades. We suggest that each phase needs to be understood based on its unique combinations of long-term monotonic trends and short-term extreme events, both that directly and indirectly influence growth rate. While the mechanistic understanding underlying this variability remains elusive, our set of hypotheses suggest that we need to move beyond traditional correlative approaches and instead combine observational data with process-based studies, large scale experiments, and modelling to will help support the development of adaptive management strategies to ensure forest resilience.},
	urldate = {2026-06-26},
	journal = {Forest Ecology and Management},
	author = {Laudon, Hjalmar and Näsholm, Torgny and Fridman, Jonas and Mensah, Alex Appiah and Lim, Hyungwoo and Jämtgård, Sandra and Nilsson, Ove},
	month = oct,
	year = {2026},
	keywords = {Adaptive forest management, Climate change, Forest production, Inter-annual variability, Nordic forests, Swedish National Forest Inventory},
	pages = {123996},
}

In recent decades, Swedish forests have experienced increasing variability of annual growth rate both in amplitude and frequency, jeopardizing national contribution to EU targets for carbon sequestration and climate change mitigation during periods of time. We postulate a set of hypotheses that with variable strengths can help explain and evaluate five major phases of growth variability observed the last three decades. We suggest that each phase needs to be understood based on its unique combinations of long-term monotonic trends and short-term extreme events, both that directly and indirectly influence growth rate. While the mechanistic understanding underlying this variability remains elusive, our set of hypotheses suggest that we need to move beyond traditional correlative approaches and instead combine observational data with process-based studies, large scale experiments, and modelling to will help support the development of adaptive management strategies to ensure forest resilience.

@article{jeong_phenotyping_2026,
	title = {Phenotyping seasonal photosynthetic energy-partitioning states in temperate evergreen conifers using hyperspectral imaging},
	volume = {8},
	issn = {2643-6515},
	url = {https://www.sciencedirect.com/science/article/pii/S2643651526000786},
	doi = {10.1016/j.plaphe.2026.100241},
	abstract = {Evergreen conifers retain needles and photosynthetic capacity during winter despite prolonged exposure to freezing temperatures and high irradiance, yet it remains unclear which aspects of this seasonal photosynthetic regulation can be reliably detected using passive optical sensing. Here, we phenotype seasonal photosynthetic energy-partitioning states in two temperate evergreen conifers, Pinus densiflora and Pinus koraiensis, by integrating chlorophyll (Chl) fluorescence imaging, pigment analyses, photosynthetic oxygen evolution, and hyperspectral reflectance imaging. Across three years, Chl fluorescence parameters (e.g., Fv/Fm, YPSII, YNPQ, and YNR) indicated reduced PSII photochemical efficiency and increased energy dissipation during winter, accompanied by changes in carotenoid-to-chlorophyll (Car/Chl) ratio, xanthophyll cycle de-epoxidation (DEPS), and photosynthetic oxygen evolution. Despite reduced PSII photochemical efficiency, photosynthetic oxygen evolution and pigment pools remained comparatively stable, indicating that reductions in PSII photochemistry were not accompanied by proportional declines in whole-leaf photosynthetic capacity. These seasonal physiological states were consistently reflected in hyperspectral vegetation indices. Photochemical Reflectance Index (PRI) showed correlations with both regulated (r = 0.57) and non-regulated light energy dissipation (r = −0.67), consistent with its sensitivity to Car/Chl ratio (r = −0.87) and DEPS (r = −0.85). Indices including Fluorescence Curvature Index (FCI) and Ratio Analysis of Reflectance Spectra chlorophyll b (RARSb) showed consistent seasonal correlations with photosynthetic oxygen evolution (r = −0.68 and −0.68), while also reflecting variation in pigment composition (e.g., Chl content; r = 0.73 and 0.78). Drone-based hyperspectral imaging further indicated that these needle-level physiological patterns were detected at the canopy level under the conditions examined. Indices such as FCI exhibited clear seasonal profiles, with separation between summer and winter values. By framing seasonal photosynthetic regulation as a phenotyping problem rather than a mechanistic one, this study provides a data-supported proof-of-concept framework for non-invasive, scalable monitoring of evergreen forests using hyperspectral sensing.},
	number = {3},
	urldate = {2026-06-26},
	journal = {Plant Phenomics},
	author = {Jeong, Seok-Won and Choi, Myoung-Goo and Kim, Young-Won and Kim, Jaewook and Hurry, Vaughan and Ivanov, Alexander G. and Chow, Wah Soon and Park, Youn-Il},
	month = sep,
	year = {2026},
	keywords = {Chlorophyll fluorescence, Cold acclimation, Hyperspectral vegetation indices, PSII energy partitioning, Temperate conifers},
	pages = {100241},
}

Evergreen conifers retain needles and photosynthetic capacity during winter despite prolonged exposure to freezing temperatures and high irradiance, yet it remains unclear which aspects of this seasonal photosynthetic regulation can be reliably detected using passive optical sensing. Here, we phenotype seasonal photosynthetic energy-partitioning states in two temperate evergreen conifers, Pinus densiflora and Pinus koraiensis, by integrating chlorophyll (Chl) fluorescence imaging, pigment analyses, photosynthetic oxygen evolution, and hyperspectral reflectance imaging. Across three years, Chl fluorescence parameters (e.g., Fv/Fm, YPSII, YNPQ, and YNR) indicated reduced PSII photochemical efficiency and increased energy dissipation during winter, accompanied by changes in carotenoid-to-chlorophyll (Car/Chl) ratio, xanthophyll cycle de-epoxidation (DEPS), and photosynthetic oxygen evolution. Despite reduced PSII photochemical efficiency, photosynthetic oxygen evolution and pigment pools remained comparatively stable, indicating that reductions in PSII photochemistry were not accompanied by proportional declines in whole-leaf photosynthetic capacity. These seasonal physiological states were consistently reflected in hyperspectral vegetation indices. Photochemical Reflectance Index (PRI) showed correlations with both regulated (r = 0.57) and non-regulated light energy dissipation (r = −0.67), consistent with its sensitivity to Car/Chl ratio (r = −0.87) and DEPS (r = −0.85). Indices including Fluorescence Curvature Index (FCI) and Ratio Analysis of Reflectance Spectra chlorophyll b (RARSb) showed consistent seasonal correlations with photosynthetic oxygen evolution (r = −0.68 and −0.68), while also reflecting variation in pigment composition (e.g., Chl content; r = 0.73 and 0.78). Drone-based hyperspectral imaging further indicated that these needle-level physiological patterns were detected at the canopy level under the conditions examined. Indices such as FCI exhibited clear seasonal profiles, with separation between summer and winter values. By framing seasonal photosynthetic regulation as a phenotyping problem rather than a mechanistic one, this study provides a data-supported proof-of-concept framework for non-invasive, scalable monitoring of evergreen forests using hyperspectral sensing.

@article{sharathkumar_trehalose_2026,
	title = {Trehalose 6-phosphate: {A} master regulator of plant development},
	issn = {1360-1385},
	shorttitle = {Trehalose 6-phosphate},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138526001378},
	doi = {10.1016/j.tplants.2026.05.001},
	abstract = {Trehalose 6-phosphate (T6P), a trehalose synthesis intermediate and sugar phosphate, serves as a signaling molecule coordinating sucrose status with plant growth and development. Beyond its metabolic role, the T6P pathway integrates exogenous and other endogenous cues to regulate key developmental transitions, including embryogenesis, seed maturation and filling, shoot branching, vegetative and reproductive phase transitions, and tuber and lateral root formation. Dynamic spatiotemporal expression patterns of T6P-pathway genes correlate with developmental stages, though their specific contributions to the initiation and progression of these transitions remain under investigation. Here, we provide recent insights and future perspectives on the T6P pathway, emphasizing its role in orchestrating diverse plant developmental programs across model and crop species and highlighting emerging mechanistic insights into its functions.},
	urldate = {2026-06-26},
	journal = {Trends in Plant Science},
	author = {SharathKumar, Malleshaiah and Zacharaki, Vasiliki and Muniz Nardeli, Sarah and Seibert, Tanja and Wahl, Vanessa},
	month = jun,
	year = {2026},
	keywords = {T6P–SnRK1 axis, crop improvement, crop resilience, energy management, trehalose 6-phosphate synthase genes, trehalose6-phosphate phosphatase genes},
}

Trehalose 6-phosphate (T6P), a trehalose synthesis intermediate and sugar phosphate, serves as a signaling molecule coordinating sucrose status with plant growth and development. Beyond its metabolic role, the T6P pathway integrates exogenous and other endogenous cues to regulate key developmental transitions, including embryogenesis, seed maturation and filling, shoot branching, vegetative and reproductive phase transitions, and tuber and lateral root formation. Dynamic spatiotemporal expression patterns of T6P-pathway genes correlate with developmental stages, though their specific contributions to the initiation and progression of these transitions remain under investigation. Here, we provide recent insights and future perspectives on the T6P pathway, emphasizing its role in orchestrating diverse plant developmental programs across model and crop species and highlighting emerging mechanistic insights into its functions.

@article{turco_comparative_2026,
	title = {Comparative {Metabarcoding} of {ITS1}, {ITS2}, and {Full}-{Length} {ITS} {Reveals} {Marker}- and {Tissue}-{Specific} {Variation} in {Fungal} {Community} {Profiling} in {Potato}},
	volume = {7},
	copyright = {© 2026 The Author(s). Plant-Environment Interactions published by John Wiley \& Sons Ltd and New Phytologist Foundation.},
	issn = {2575-6265},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pei3.70168},
	doi = {10.1002/pei3.70168},
	abstract = {Accurate profiling of plant-associated fungal and oomycete communities depends critically on the choice of ITS marker. Using Illumina sequencing for ITS1/ITS2 and PacBio HiFi sequencing for full-length ITS (ITSf), we compared read recovery, taxonomic assignment depth, and diversity patterns across potato leaf and root tissues. ITS2 generally recovered more diverse and even community profiles in leaves, whereas ITSf recovered comparatively more even and taxonomically broad profiles in roots. In contrast, ITS1 showed high read recovery but produced strongly skewed compositional profiles and was frequently dominated by host-derived sequences. Beta-diversity analyses indicated that ITS marker choice was associated with substantial variation in observed community composition, while functional annotation highlighted communities composed of taxa associated with multiple ecological guilds, including endophytes and opportunistic pathogens such as Cladosporium and Ilyonectria. Overall, the results demonstrate that ITS marker choice strongly influences the observed structure and diversity of plant-associated communities. ITS2 was generally more suitable for phyllosphere-associated communities, whereas ITSf provided broader recovery of root-associated taxa. Combining complementary markers therefore offers a more comprehensive representation of potato-associated microbial eukaryotic communities than single-marker approaches alone.},
	language = {en},
	number = {3},
	urldate = {2026-06-05},
	journal = {Plant-Environment Interactions},
	author = {Turco, Silvia and Giubilei, Irene and Mahawar, Lovely and Mazzaglia, Angelo and Albrectsen, Benedicte Riber},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/pei3.70168},
	keywords = {ITS markers, Solanum tuberosum L., amplicon sequencing, metabarcoding, mycobiome},
	pages = {e70168},
}

Accurate profiling of plant-associated fungal and oomycete communities depends critically on the choice of ITS marker. Using Illumina sequencing for ITS1/ITS2 and PacBio HiFi sequencing for full-length ITS (ITSf), we compared read recovery, taxonomic assignment depth, and diversity patterns across potato leaf and root tissues. ITS2 generally recovered more diverse and even community profiles in leaves, whereas ITSf recovered comparatively more even and taxonomically broad profiles in roots. In contrast, ITS1 showed high read recovery but produced strongly skewed compositional profiles and was frequently dominated by host-derived sequences. Beta-diversity analyses indicated that ITS marker choice was associated with substantial variation in observed community composition, while functional annotation highlighted communities composed of taxa associated with multiple ecological guilds, including endophytes and opportunistic pathogens such as Cladosporium and Ilyonectria. Overall, the results demonstrate that ITS marker choice strongly influences the observed structure and diversity of plant-associated communities. ITS2 was generally more suitable for phyllosphere-associated communities, whereas ITSf provided broader recovery of root-associated taxa. Combining complementary markers therefore offers a more comprehensive representation of potato-associated microbial eukaryotic communities than single-marker approaches alone.

@article{casanova-saez_comprehensive_2026,
	title = {Comprehensive characterisation of {IAA} inactivation pathways reveals the impact of glycosylation on auxin metabolism and plant development in {Arabidopsis}},
	volume = {9},
	copyright = {2026 The Author(s)},
	issn = {2399-3642},
	url = {https://www.nature.com/articles/s42003-026-10431-5},
	doi = {10.1038/s42003-026-10431-5},
	abstract = {Alongside biosynthesis and transport, inactivation regulates indole-3-acetic acid (IAA) concentration, a compound with numerous functions in plant development. The main inactive IAA metabolites are oxidised forms and ester- or amide-linked conjugates. DIOXYGENASE FOR AUXIN OXIDATION1 (DAO1) and DAO2, 2-oxoglutarate and iron-dependent dioxygenases, contribute to IAA oxidative inactivation with group II GRETCHEN HAGEN3 (GH3) IAA-amido synthetases, while UDP-glycosyltransferases (UGTs) conjugate IAA to sugars. To study IAA inactivation routes, we generated combinatorial Arabidopsis mutants between all group II GH3s (gh3oct) and DAO1 or DAO2, and between DAOs and the main UGTs. In vivo [13C6]IAA feeding experiments traced exogenously applied IAA’s metabolic fate, supporting the main IAA inactivation pathway where DAOs act downstream of GH3s. Results from these experiments also indicated UGT-mediated IAA glycosylation is more important than previously assumed for modulating IAA levels and plant development. Our metabolic and transcriptomic data revealed that gh3oct may still retain some GH3 activity, explaining previously reported phenotypic inconsistencies. Our data additionally suggest that unidentified metabolic activities might play a role in IAA overproducing plants, and that premature downregulation of flowering time regulators like FLOWERING LOCUS C (FLC) likely underlies early flowering of gh3oct and gh3oct dao1-6 plants.},
	language = {en},
	number = {1},
	urldate = {2026-06-12},
	journal = {Communications Biology},
	publisher = {Nature Publishing Group},
	author = {Casanova-Sáez, Rubén and Pěnčík, Aleš and Brunoni, Federica and Ament, Anita and Hladík, Pavel and Žukauskaitė, Asta and Šimura, Jan and Voß, Ute and Novák, Ondřej and Bennett, Malcolm and Ljung, Karin and Mateo-Bonmatí, Eduardo},
	month = jun,
	year = {2026},
	keywords = {Auxin, Plant development},
	pages = {762},
}

Alongside biosynthesis and transport, inactivation regulates indole-3-acetic acid (IAA) concentration, a compound with numerous functions in plant development. The main inactive IAA metabolites are oxidised forms and ester- or amide-linked conjugates. DIOXYGENASE FOR AUXIN OXIDATION1 (DAO1) and DAO2, 2-oxoglutarate and iron-dependent dioxygenases, contribute to IAA oxidative inactivation with group II GRETCHEN HAGEN3 (GH3) IAA-amido synthetases, while UDP-glycosyltransferases (UGTs) conjugate IAA to sugars. To study IAA inactivation routes, we generated combinatorial Arabidopsis mutants between all group II GH3s (gh3oct) and DAO1 or DAO2, and between DAOs and the main UGTs. In vivo [13C6]IAA feeding experiments traced exogenously applied IAA’s metabolic fate, supporting the main IAA inactivation pathway where DAOs act downstream of GH3s. Results from these experiments also indicated UGT-mediated IAA glycosylation is more important than previously assumed for modulating IAA levels and plant development. Our metabolic and transcriptomic data revealed that gh3oct may still retain some GH3 activity, explaining previously reported phenotypic inconsistencies. Our data additionally suggest that unidentified metabolic activities might play a role in IAA overproducing plants, and that premature downregulation of flowering time regulators like FLOWERING LOCUS C (FLC) likely underlies early flowering of gh3oct and gh3oct dao1-6 plants.

@article{shi_alleleauto_2026,
	title = {Alleleauto: a pipeline for allele identification and analysis of allele-specific gene expression with haplotype-resolved diploid genome assemblies},
	volume = {7},
	issn = {2662-1738},
	shorttitle = {Alleleauto},
	url = {https://www.sciencedirect.com/science/article/pii/S2662173826000706},
	doi = {10.1016/j.abiote.2026.100056},
	abstract = {Advanced sequencing now enables haplotype resolution of genomes from non-model diploid plant species, facilitating allele identification and the use of allele-specific expression (ASE) analysis to uncover the relationships between genes and phenotypes in heterozygous genomes. However, identification of true allelic pairs remains challenging due to the presence of paralogous genes from ancient genome duplications, and existing methods lack systematic, reproducible filtering criteria. In this study, we developed Alleleauto, a workflow integrating the parametric 3σ rule and the non-parametric Tukey's method as two complementary outlier detection methods to precisely identify alleles and perform ASE analysis from haplotype-resolved assemblies. Alleleauto first searches for homologous genes across homologous chromosomes, then applies statistical filtering criteria based on synonymous substitution rates (Ks) and synteny to systematically remove false alleles (paralogs). This dual-method framework offers flexible filtering strategies with adjustable parameters, enabling optimization for diverse genomes. We validated the workflow on tea plant (Camellia sinensis), ginger (Zingiber officinale), and lychee (Litchi chinensis), three plant species with distinct genomic features, demonstrating that statistical filtering significantly improves accuracy over the use of sequence similarity alone. Using the alleles identified by Alleleauto, we performed ASE analysis and calculated sequence divergence parameters to investigate ASE and heterosis mechanisms. Our open-source, and easy-to-use pipeline provides significant value for reproducible, scalable investigation of ASE and heterosis with haplotype-resolved genome assemblies.},
	number = {3},
	urldate = {2026-06-12},
	journal = {aBIOTECH},
	author = {Shi, Tian-Le and Nie, Shuai and Bao, Yu-Tao and Li, Zhi-Chao and Chen, Zhao-Yang and Zhao, Shi-Wei and Yan, Xue-Mei and Ma, Hai-Yao and Tian, Xue-Chan and Jia, Kai-Hua and Guo, Jing-Fang and Zhang, Jun-Ke and Mao, Jian-Feng},
	month = sep,
	year = {2026},
	keywords = {Allele identification, Allele-specific expression, Haplotype-resolved, Non-model diploid plant genome, Sequence similarity},
	pages = {100056},
}

Advanced sequencing now enables haplotype resolution of genomes from non-model diploid plant species, facilitating allele identification and the use of allele-specific expression (ASE) analysis to uncover the relationships between genes and phenotypes in heterozygous genomes. However, identification of true allelic pairs remains challenging due to the presence of paralogous genes from ancient genome duplications, and existing methods lack systematic, reproducible filtering criteria. In this study, we developed Alleleauto, a workflow integrating the parametric 3σ rule and the non-parametric Tukey's method as two complementary outlier detection methods to precisely identify alleles and perform ASE analysis from haplotype-resolved assemblies. Alleleauto first searches for homologous genes across homologous chromosomes, then applies statistical filtering criteria based on synonymous substitution rates (Ks) and synteny to systematically remove false alleles (paralogs). This dual-method framework offers flexible filtering strategies with adjustable parameters, enabling optimization for diverse genomes. We validated the workflow on tea plant (Camellia sinensis), ginger (Zingiber officinale), and lychee (Litchi chinensis), three plant species with distinct genomic features, demonstrating that statistical filtering significantly improves accuracy over the use of sequence similarity alone. Using the alleles identified by Alleleauto, we performed ASE analysis and calculated sequence divergence parameters to investigate ASE and heterosis mechanisms. Our open-source, and easy-to-use pipeline provides significant value for reproducible, scalable investigation of ASE and heterosis with haplotype-resolved genome assemblies.

@article{tiziani_deciphering_2026,
	title = {Deciphering underexplored rhizosphere processes: root acquisition of citric acid and its metabolic journey in tomato},
	issn = {0022-0957},
	shorttitle = {Deciphering underexplored rhizosphere processes},
	url = {https://doi.org/10.1093/jxb/erag066},
	doi = {10.1093/jxb/erag066},
	abstract = {Root-exuded organic acids are crucial in mitigating iron (Fe) and phosphorus (P) deficiencies, and their biosynthesis and secretion require significant metabolic investment. Recent studies have shown that roots can also uptake exudates. We hypothesized that citric acid uptake increases under Fe and P deficiencies, declines over time, and contributes to primary metabolism. We investigated citric acid uptake, translocation, and metabolization in Fe- and P-deficient tomato plants grown hydroponically using 13C-labelling with bulk stable-isotope and compound-specific stable-isotope analysis. Physiological parameters, root morphology, and elemental composition were also assessed. Deficient plants showed reduced P and Fe contents, reduced photosynthesis, altered root morphology, and an altered citric acid uptake that could not be attributed to morphological differences. Iron deficiency reduced citric acid uptake, indicating its role in rhizospheric Fe mobilization, while P deficiency increased the uptake, enhancing resource use efficiency. Unexpectedly, citric acid uptake increased with plant development. In Fe deficiency, citric acid-derived carbon was allocated to secondary metabolites, while in P deficiency it supported the tricarboxylic acid and GS-GOGAT cycles. This study is the first to demonstrate that citric acid uptake is a multifunctional process, underscoring its critical role in plant responses to nutrient starvation, especially under P deficiency.},
	urldate = {2026-04-24},
	journal = {Journal of Experimental Botany},
	author = {Tiziani, Raphael and Trevisan, Fabio and Hodek, Ondřej and Jämtgård, Sandra and Moritz, Thomas and Bouaicha, Oussama and Chibesa, Mirriam C and Fracasso, Ilaria and Mimmo, Tanja},
	month = feb,
	year = {2026},
	pages = {erag066},
}

Root-exuded organic acids are crucial in mitigating iron (Fe) and phosphorus (P) deficiencies, and their biosynthesis and secretion require significant metabolic investment. Recent studies have shown that roots can also uptake exudates. We hypothesized that citric acid uptake increases under Fe and P deficiencies, declines over time, and contributes to primary metabolism. We investigated citric acid uptake, translocation, and metabolization in Fe- and P-deficient tomato plants grown hydroponically using 13C-labelling with bulk stable-isotope and compound-specific stable-isotope analysis. Physiological parameters, root morphology, and elemental composition were also assessed. Deficient plants showed reduced P and Fe contents, reduced photosynthesis, altered root morphology, and an altered citric acid uptake that could not be attributed to morphological differences. Iron deficiency reduced citric acid uptake, indicating its role in rhizospheric Fe mobilization, while P deficiency increased the uptake, enhancing resource use efficiency. Unexpectedly, citric acid uptake increased with plant development. In Fe deficiency, citric acid-derived carbon was allocated to secondary metabolites, while in P deficiency it supported the tricarboxylic acid and GS-GOGAT cycles. This study is the first to demonstrate that citric acid uptake is a multifunctional process, underscoring its critical role in plant responses to nutrient starvation, especially under P deficiency.

@article{soro_minimum_2026,
	title = {Minimum marker densities for accurate genomic predictions and heritability estimates in three major {North} {American} and {European} spruce species},
	volume = {135},
	copyright = {2026 His Majesty the King in Right of Canada, as represented by the Minister of Natural Resources and the Authors},
	issn = {1365-2540},
	url = {https://www.nature.com/articles/s41437-026-00836-7},
	doi = {10.1038/s41437-026-00836-7},
	abstract = {Genomic selection (GS) is being increasingly used in tree breeding with the aim to accelerate genetic gains by shortening the long breeding cycles. However, high genotyping costs remain a challenge. This study aimed to determine the optimal marker density in genome coverage to maximize GS accuracy and precision of heritability estimates for growth and wood quality traits. Thousands of SNPs representative of the exome of three major spruce species were used: 18,275 SNPs for black spruce (representing 10,894 distinct gene loci), 11,328 SNPs for white spruce (8647 gene loci), and 116,765 SNPs for Norway spruce (20,695 gene loci). For each species, a similar experimental design was used with related full-sib families replicated on two sites, and GBLUP prediction models were developed. The effect of varying the number of SNPs was examined by resampling subsets from 500 to 100,000 SNPs. Results indicated that plateaus in heritability estimates were reached as the marker density increased, stabilizing between 4000 and 8000 SNPs for a spruce genome size of around 2000 centimorgans, a trend consistent across all traits and species. Predictive ability and prediction accuracy both increased with the number of SNPs up to a similar level, beyond which further improvements were marginal. Such minimum marker densities should be financially affordable for most spruce breeding programs, striking a balance between the need for maximizing GS accuracy and that for minimizing genotyping costs. These findings should support the further deployment of GS in conifer breeding programs, with high selection precision and by reducing the financial burden of very high-density SNP coverage, even for conifers characterized by large giga-genomes.},
	language = {en},
	number = {5},
	urldate = {2026-05-29},
	journal = {Heredity},
	publisher = {Nature Publishing Group},
	author = {Soro, André and Lenz, Patrick and Beaulieu, Jean and Laverdière, Jean-Philippe and Nadeau, Simon and Gagnon, France and Ogut, Funda and Wu, Harry X. and Perron, Martin and Bousquet, Jean},
	month = may,
	year = {2026},
	keywords = {Comparative genomics, Ecological genetics, Forestry},
	pages = {342--357},
}

Genomic selection (GS) is being increasingly used in tree breeding with the aim to accelerate genetic gains by shortening the long breeding cycles. However, high genotyping costs remain a challenge. This study aimed to determine the optimal marker density in genome coverage to maximize GS accuracy and precision of heritability estimates for growth and wood quality traits. Thousands of SNPs representative of the exome of three major spruce species were used: 18,275 SNPs for black spruce (representing 10,894 distinct gene loci), 11,328 SNPs for white spruce (8647 gene loci), and 116,765 SNPs for Norway spruce (20,695 gene loci). For each species, a similar experimental design was used with related full-sib families replicated on two sites, and GBLUP prediction models were developed. The effect of varying the number of SNPs was examined by resampling subsets from 500 to 100,000 SNPs. Results indicated that plateaus in heritability estimates were reached as the marker density increased, stabilizing between 4000 and 8000 SNPs for a spruce genome size of around 2000 centimorgans, a trend consistent across all traits and species. Predictive ability and prediction accuracy both increased with the number of SNPs up to a similar level, beyond which further improvements were marginal. Such minimum marker densities should be financially affordable for most spruce breeding programs, striking a balance between the need for maximizing GS accuracy and that for minimizing genotyping costs. These findings should support the further deployment of GS in conifer breeding programs, with high selection precision and by reducing the financial burden of very high-density SNP coverage, even for conifers characterized by large giga-genomes.

@article{wang_phytocell_2026,
	title = {{PhytoCell}: {An} ensemble learning framework for identifying cell states in plant {scRNA}-seq data},
	issn = {2214-5141},
	shorttitle = {{PhytoCell}},
	url = {https://www.sciencedirect.com/science/article/pii/S2214514126000760},
	doi = {10.1016/j.cj.2026.02.021},
	abstract = {Single-cell transcriptome sequencing (scRNA-seq) can reveal the roles of diverse cells in an organism, but accurately classifying cell subpopulations and their marker genes remains a challenge. Here, we present PhytoCell, an ensemble learning framework that combines feature selection engineering with machine learning to uncover cell markers and annotate cell subpopulations. We evaluated our approach on 120,000 cells from corollas of the dicotyledonous plant species coyote tobacco (Nicotiana attenuata) and eight tissues from the monocotyledonous plant species rice (Oryza sativa). Comprehensive evaluation across species and tissues demonstrated that PhytoCell effectively eliminates redundant information, identifies key cell markers, improves clustering performance, and accurately classifies cell subpopulations. Importantly, PhytoCell did not rely on prior biological knowledge for selecting cell markers, preserving the biological landscape of the original data. For broader accessibility, we developed a user-friendly web interface that provides convenient tools for users to access cell marker resources and perform predictions for cell type. PhytoCell is freely accessible at https://cgris.net/phyto. PhytoCell is scalable to different sizes of single-cell datasets, representing a valuable resource for precise identification in cell research.},
	urldate = {2026-05-19},
	journal = {The Crop Journal},
	author = {Wang, Hao and Yan, Shen and Ma, Xiaoding and Si, Huan and Lu, Qiong and Chen, Yanqing and Liu, Lijia and Hong, Jingpeng and Xu, Xingjian and Fang, Wei and He, Qiang and Zan, Yanjun and Yang, Aiguo},
	month = mar,
	year = {2026},
	keywords = {Cell subpopulations, Ensemble learning, Machine learning, PhytoCell, scRNA-seq},
}

Single-cell transcriptome sequencing (scRNA-seq) can reveal the roles of diverse cells in an organism, but accurately classifying cell subpopulations and their marker genes remains a challenge. Here, we present PhytoCell, an ensemble learning framework that combines feature selection engineering with machine learning to uncover cell markers and annotate cell subpopulations. We evaluated our approach on 120,000 cells from corollas of the dicotyledonous plant species coyote tobacco (Nicotiana attenuata) and eight tissues from the monocotyledonous plant species rice (Oryza sativa). Comprehensive evaluation across species and tissues demonstrated that PhytoCell effectively eliminates redundant information, identifies key cell markers, improves clustering performance, and accurately classifies cell subpopulations. Importantly, PhytoCell did not rely on prior biological knowledge for selecting cell markers, preserving the biological landscape of the original data. For broader accessibility, we developed a user-friendly web interface that provides convenient tools for users to access cell marker resources and perform predictions for cell type. PhytoCell is freely accessible at https://cgris.net/phyto. PhytoCell is scalable to different sizes of single-cell datasets, representing a valuable resource for precise identification in cell research.

@article{cainzos_loss_2026,
	title = {Loss of {qE} {Does} {Not} {Necessarily} {Lead} to {Photoinhibition}: {Sustained} {Non}-{Photochemical} {Quenching} in the {Absence} of {PsbS} and {Zeaxanthin}},
	volume = {49},
	copyright = {© 2026 The Author(s). Plant, Cell \& Environment published by John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	shorttitle = {Loss of {qE} {Does} {Not} {Necessarily} {Lead} to {Photoinhibition}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.70477},
	doi = {10.1111/pce.70477},
	abstract = {Photosynthetic light-harvesting complexes mediate light absorption and energy dissipation. By modulating the photosystems' absorption cross-section, they affect both photosynthetic activity and non-photochemical quenching (NPQ). These processes are often studied by spectrally integrated chlorophyll fluorescence, masking their associated spectral information. We explore in Aspen and Arabidopsis npq mutants how qE affects the development of NPQ spectra under two contrasting conditions: in the absence and the presence of photoinhibition. We introduce a new parameter, the development of new emitting species (NESD), during time- and spectrally resolved NPQ inductions, and develop a pipeline to resolve PSII energy-partitioning heterogeneity. LHCII, PsbS, and zeaxanthin are required for NESD. Combining gas exchange, P700 oxidation, and spectrally resolved kinetics, we show that under photoinhibitory conditions, NES can develop even without PsbS or zeaxanthin, producing sustained quenching independent of photoinhibition of PSII or PSI. Furthermore, the absence of LHCII and CURVATURE THYLAKOID 1 leads to increased photoinhibition, indicating that long-term photoprotection relies on LHCII and thylakoid plasticity, whereas PsbS and zeaxanthin mainly facilitate LHCII-dependent quenching. Finally, we show the limitations of traditional parameters in discriminating between photoinhibition and photoprotective sustained quenching and propose time-resolved monitoring of CO₂ assimilation and Y(II) for their accurate assessment.},
	language = {en},
	number = {6},
	urldate = {2026-05-15},
	journal = {Plant, Cell \& Environment},
	author = {Cainzos, Maximiliano and Hu, Chen and Pissolato, Maria Dolores and Fataftah, Nazeer and Nanda, Sanchali and Jansson, Stefan},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.70477},
	keywords = {NPQ, high light, new emitting species development, photoinhibition, photosynthesis: carbon reactions, photosynthesis: electron transport, sustained quenching},
	pages = {3405--3425},
}

Photosynthetic light-harvesting complexes mediate light absorption and energy dissipation. By modulating the photosystems' absorption cross-section, they affect both photosynthetic activity and non-photochemical quenching (NPQ). These processes are often studied by spectrally integrated chlorophyll fluorescence, masking their associated spectral information. We explore in Aspen and Arabidopsis npq mutants how qE affects the development of NPQ spectra under two contrasting conditions: in the absence and the presence of photoinhibition. We introduce a new parameter, the development of new emitting species (NESD), during time- and spectrally resolved NPQ inductions, and develop a pipeline to resolve PSII energy-partitioning heterogeneity. LHCII, PsbS, and zeaxanthin are required for NESD. Combining gas exchange, P700 oxidation, and spectrally resolved kinetics, we show that under photoinhibitory conditions, NES can develop even without PsbS or zeaxanthin, producing sustained quenching independent of photoinhibition of PSII or PSI. Furthermore, the absence of LHCII and CURVATURE THYLAKOID 1 leads to increased photoinhibition, indicating that long-term photoprotection relies on LHCII and thylakoid plasticity, whereas PsbS and zeaxanthin mainly facilitate LHCII-dependent quenching. Finally, we show the limitations of traditional parameters in discriminating between photoinhibition and photoprotective sustained quenching and propose time-resolved monitoring of CO₂ assimilation and Y(II) for their accurate assessment.

@article{forsman_structure_2026,
	title = {The structure of intact and active {Photosystem} {II} from {Arabidopsis} thaliana at 2.44 Å resolution},
	volume = {250},
	copyright = {© 2026 The Author(s). New Phytologist © 2026 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.71085},
	doi = {10.1111/nph.71085},
	abstract = {Photosystem II (PS II) is a large membrane-bound protein complex that catalyses light-driven water oxidation in plants and cyanobacteria. The structure of PS II is well studied in cyanobacteria; however, there are very few PS II structures from plants. The currently available plant PS II structures are comparatively low resolution and are frequently incomplete, that is, missing subunits or cofactors. We optimized the procedure for isolating PS II from Arabidopsis thaliana and employed cryo-electron microscopy to generate a high-resolution structure of an intact and oxygen-evolving PS II from Arabidopsis thaliana at 2.44 Å resolution, which to date represents the highest resolution structure of PS II from higher plants. At this resolution, many water molecules within the PS II structure can be detected, including waters around the water-splitting manganese cluster, the nonheme iron, and within the water/proton channels connecting these active sites to the protein exterior, allowing for the first detailed description of the water networks in Arabidopsis thaliana and comparison with the highly resolved cyanobacterial PS II. Our findings further the understanding of design principles of protein–water–cofactor interactions in photosynthetic water splitting, quinone reduction/exchange, and about the role of lipids at the interface between PS II and the light-harvesting proteins.},
	language = {en},
	number = {5},
	urldate = {2026-05-15},
	journal = {New Phytologist},
	author = {Forsman, Jack and Graça, André T. and Aydin, Abuzer Orkun and Hall, Michael and Hussein, Rana and Schröder, Wolfgang P. and Messinger, Johannes},
	year = {2026},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.71085},
	keywords = {Arabidopsis thaliana, Cryo-EM, Photosystem II structure, manganese cluster, photosynthesis, protein–water–cofactor interactions, water channels},
	pages = {3014--3025},
}

Photosystem II (PS II) is a large membrane-bound protein complex that catalyses light-driven water oxidation in plants and cyanobacteria. The structure of PS II is well studied in cyanobacteria; however, there are very few PS II structures from plants. The currently available plant PS II structures are comparatively low resolution and are frequently incomplete, that is, missing subunits or cofactors. We optimized the procedure for isolating PS II from Arabidopsis thaliana and employed cryo-electron microscopy to generate a high-resolution structure of an intact and oxygen-evolving PS II from Arabidopsis thaliana at 2.44 Å resolution, which to date represents the highest resolution structure of PS II from higher plants. At this resolution, many water molecules within the PS II structure can be detected, including waters around the water-splitting manganese cluster, the nonheme iron, and within the water/proton channels connecting these active sites to the protein exterior, allowing for the first detailed description of the water networks in Arabidopsis thaliana and comparison with the highly resolved cyanobacterial PS II. Our findings further the understanding of design principles of protein–water–cofactor interactions in photosynthetic water splitting, quinone reduction/exchange, and about the role of lipids at the interface between PS II and the light-harvesting proteins.

@article{zhu_mmgs_2026,
	title = {{MMGS}: a novel genomic prediction framework to integrate genotype, environment and their interactions for multi-environment breeding trials},
	volume = {13},
	issn = {2662-6810},
	shorttitle = {{MMGS}},
	url = {https://doi.org/10.1093/hr/uhag035},
	doi = {10.1093/hr/uhag035},
	abstract = {Accurately predicting the performance of trees and crops across diverse and changing climates is essential for matching genotypes to both current and future environments. Yet modelling the complex interplay among genotype, environment, and phenotype in multi-environment trials remains a major challenge. Here, we introduce a unified framework, polygenic environmental interaction (PEI), directly models genotype-by-environment interactions through integrating genotypes and environmental covariates. We implemented an ensemble of 15 estimators spanning parametric, non-parametric, and machine-learning approaches. We then benchmarked our framework against the classical reaction norm (RN) using three genetically distinct populations and three traits with variable genetic architectures. Furthermore, we released an open-source R package, Multiple-environments genomic selection (MMGS), on GitHub. Together, our study offers a flexible and computationally efficient approach for multi-environment genomic prediction, enhancing breeding efficiency, providing deeper insights into modelling the genotype-environment-phenotype continuum.},
	number = {5},
	urldate = {2026-05-15},
	journal = {Horticulture Research},
	author = {Zhu, Mingjia and Zheng, Zeyu and Liu, Wei and Han, Yu and Mou, Wenjie and Yin, Tongming and Dai, Xiaogang and Wu, Huaitong and Yang, Yongzhi and Zan, Yanjun and Liu, Jianquan},
	month = may,
	year = {2026},
	pages = {uhag035},
}

Accurately predicting the performance of trees and crops across diverse and changing climates is essential for matching genotypes to both current and future environments. Yet modelling the complex interplay among genotype, environment, and phenotype in multi-environment trials remains a major challenge. Here, we introduce a unified framework, polygenic environmental interaction (PEI), directly models genotype-by-environment interactions through integrating genotypes and environmental covariates. We implemented an ensemble of 15 estimators spanning parametric, non-parametric, and machine-learning approaches. We then benchmarked our framework against the classical reaction norm (RN) using three genetically distinct populations and three traits with variable genetic architectures. Furthermore, we released an open-source R package, Multiple-environments genomic selection (MMGS), on GitHub. Together, our study offers a flexible and computationally efficient approach for multi-environment genomic prediction, enhancing breeding efficiency, providing deeper insights into modelling the genotype-environment-phenotype continuum.

@article{bizjak-johansson_norway_2026,
	title = {Norway {Spruce} and {Scots} {Pine} {Fungal} and {Bacterial} {Microbiomes} in a {Boreal} {Forest} {Common} {Garden} {Experiment}},
	volume = {17},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/17/4/446},
	doi = {10.3390/f17040446},
	abstract = {Soil- and plant-associated fungi and bacteria are an important part of many ecosystems as they can affect plant health, growth and stress tolerance. However, it remains poorly understood whether the microbiomes differ between conifer species growing in the same site conditions and between tree ecosystem compartments. The main aim of the study was to describe and compare the microbiomes of Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies (L.) H. Karst.), growing in a boreal forest common garden experiment on adjacent forest plots, to analyse the tree species effect on the composition of the needle and surface soil organic-mineral horizon microbiomes. The needle and surface soil organic-mineral horizon bacterial and fungal microbiomes were simultaneously analysed by full-length 16S and ITS sequencing on a long-read sequencing platform; however, the bacterial analysis was restricted to soil samples. The highly abundant bacterial phyla in both pine and spruce soil were Actinomycetota, Pseudomonadota, Planctomycetota and Acidobacteriota. The dominant fungal phyla in pine and spruce surface organic-mineral soil was Basidiomycota, while the needles were dominated by Ascomycota. The results showed an effect of tree species on the soil bacterial and fungal microbiomes and needle fungal microbiomes based on alpha diversity, which was higher for Norway spruce compared to Scots pine. The results indicated that Norway spruce might be able to support higher microbial diversity, which could potentially be due to differences in needle longevity, root exudates, litter input and its degradation, between pine and spruce. Furthermore, the results indicated distinct microbiomes between the soil and needle compartments.},
	language = {en},
	number = {4},
	urldate = {2026-05-06},
	journal = {Forests},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Bizjak-Johansson, Tinkara and Larsson, Marcus and Gundale, Michael J. and Nordin, Annika},
	month = apr,
	year = {2026},
	keywords = {Norway spruce, Scots pine, bacteria, boreal forest, fungi, microbiome},
	pages = {446},
}

Soil- and plant-associated fungi and bacteria are an important part of many ecosystems as they can affect plant health, growth and stress tolerance. However, it remains poorly understood whether the microbiomes differ between conifer species growing in the same site conditions and between tree ecosystem compartments. The main aim of the study was to describe and compare the microbiomes of Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies (L.) H. Karst.), growing in a boreal forest common garden experiment on adjacent forest plots, to analyse the tree species effect on the composition of the needle and surface soil organic-mineral horizon microbiomes. The needle and surface soil organic-mineral horizon bacterial and fungal microbiomes were simultaneously analysed by full-length 16S and ITS sequencing on a long-read sequencing platform; however, the bacterial analysis was restricted to soil samples. The highly abundant bacterial phyla in both pine and spruce soil were Actinomycetota, Pseudomonadota, Planctomycetota and Acidobacteriota. The dominant fungal phyla in pine and spruce surface organic-mineral soil was Basidiomycota, while the needles were dominated by Ascomycota. The results showed an effect of tree species on the soil bacterial and fungal microbiomes and needle fungal microbiomes based on alpha diversity, which was higher for Norway spruce compared to Scots pine. The results indicated that Norway spruce might be able to support higher microbial diversity, which could potentially be due to differences in needle longevity, root exudates, litter input and its degradation, between pine and spruce. Furthermore, the results indicated distinct microbiomes between the soil and needle compartments.

@article{wang_recurrent_2026,
	title = {Recurrent sex chromosome turnover mediated by distinct {ARR17} and {PISTILLATA} duplications in willows},
	volume = {27},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-026-04026-w},
	doi = {10.1186/s13059-026-04026-w},
	abstract = {Sex chromosome turnovers evolve via translocation or duplication of established sex-determining genes, or their replacement by newly evolved ones. Few cases of replacements by new factors have been documented in dioecious plants, but are suspected in Salix, in which both XY and ZW systems occur, with sex-linked regions (SLRs) of different species on various chromosomes. The male-determining genes in XY species’ SLRs are partial duplicates of autosomal ARR17-like genes and regulate the expression of downstream genes involved in stamen development by producing small RNAs that suppress the expression of intact copies.},
	language = {en},
	number = {1},
	urldate = {2026-04-24},
	journal = {Genome Biology},
	author = {Wang, Yuàn and Xue, Zhi-Qing and Zhang, Ren-Gang and Zhu, Zhi-Ying and Hörandl, Elvira and Wang, Xiao-Ru and Mao, Yan-Fei and Charlesworth, Deborah and He, Li},
	month = mar,
	year = {2026},
	keywords = {Pericentromeric regions, Recombination landscape, Salix, Sex chromosome turnovers, Sex determination, Translocation},
	pages = {137},
}

Sex chromosome turnovers evolve via translocation or duplication of established sex-determining genes, or their replacement by newly evolved ones. Few cases of replacements by new factors have been documented in dioecious plants, but are suspected in Salix, in which both XY and ZW systems occur, with sex-linked regions (SLRs) of different species on various chromosomes. The male-determining genes in XY species’ SLRs are partial duplicates of autosomal ARR17-like genes and regulate the expression of downstream genes involved in stamen development by producing small RNAs that suppress the expression of intact copies.

@article{corthals_conserved_2026,
	title = {Conserved molecular signatures of hygrosensory neurons in two dipteran species},
	volume = {21},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0347993},
	doi = {10.1371/journal.pone.0347993},
	abstract = {Small poikilothermic animals like insects rely on environmental sensing for survival. The ability to detect humidity through specialized sensory neurons is particularly critical, allowing them to maintain water balance across diverse environments. While recent studies have identified key receptors associated with humidity sensing, our understanding of the underlying molecular architecture of these sensory systems remains incomplete. Here, we conducted a comparative analysis of single-nucleus transcriptomes of humidity receptor neurons (HRNs) between the vinegar fly Drosophila melanogaster and the yellow fever mosquito Aedes aegypti. We identified 21 shared genes that contribute to the molecular identity of HRNs in both species. These genes encode proteins involved in transcriptional regulation, cellular signalling, enzymatic pathways and cellular organization. Through behavioural analyses, we demonstrate that two of these genes, the serotonin receptor 5-HT7 and the kinesin motor protein Kif19A, are both necessary for humidity-guided behaviours in adult flies. The conservation of these genes between species separated by over 150 million years of evolution suggests shared functional requirements for humidity sensing in dipterans. Our findings provide insights into fundamental principles of sensory neuron organization and offer a framework for understanding how specialized sensory systems evolve and maintain their function.},
	language = {en},
	number = {4},
	urldate = {2026-04-30},
	journal = {PLOS ONE},
	publisher = {Public Library of Science},
	author = {Corthals, Kristina and Giri, Ganesh and Reimegård, Johan and Churcher, Allison and Enjin, Anders},
	month = apr,
	year = {2026},
	keywords = {Behavior, Drosophila melanogaster, Gene expression, Humidity, Marker genes, Neurons, Sensory perception, Serotonin},
	pages = {e0347993},
}

Small poikilothermic animals like insects rely on environmental sensing for survival. The ability to detect humidity through specialized sensory neurons is particularly critical, allowing them to maintain water balance across diverse environments. While recent studies have identified key receptors associated with humidity sensing, our understanding of the underlying molecular architecture of these sensory systems remains incomplete. Here, we conducted a comparative analysis of single-nucleus transcriptomes of humidity receptor neurons (HRNs) between the vinegar fly Drosophila melanogaster and the yellow fever mosquito Aedes aegypti. We identified 21 shared genes that contribute to the molecular identity of HRNs in both species. These genes encode proteins involved in transcriptional regulation, cellular signalling, enzymatic pathways and cellular organization. Through behavioural analyses, we demonstrate that two of these genes, the serotonin receptor 5-HT7 and the kinesin motor protein Kif19A, are both necessary for humidity-guided behaviours in adult flies. The conservation of these genes between species separated by over 150 million years of evolution suggests shared functional requirements for humidity sensing in dipterans. Our findings provide insights into fundamental principles of sensory neuron organization and offer a framework for understanding how specialized sensory systems evolve and maintain their function.

@article{chaudhary_breeding_2026,
	title = {Breeding for climate adaptation: genetic variation and genomic selection for drought response in {Scots} pine},
	volume = {27},
	issn = {1471-2164},
	shorttitle = {Breeding for climate adaptation},
	url = {https://doi.org/10.1186/s12864-026-12849-x},
	doi = {10.1186/s12864-026-12849-x},
	abstract = {Drought intensity and frequency are increasing under global warming in the boreal forests, and breeding for drought resistance will facilitate adaptation of new planting material to changing climate conditions. We used a tree-ring dataset of 559 individuals to study Scots pine genetic variation and the efficiency of genomic selection of drought-response traits (drought resistance, recovery and resilience), for the first time. From genotyping-by-sequencing (GBS), 31,101 SNPs were generated and used for the study.},
	language = {en},
	number = {1},
	urldate = {2026-04-30},
	journal = {BMC Genomics},
	author = {Chaudhary, Rajiv and Estravis Barcala, Maximiliano and Fundova, Irena and Funda, Tomas and Chen, Zhi-qiang and Wu, Harry X.},
	month = apr,
	year = {2026},
	keywords = {Climate adaptation, Dendroecology, Drought, GBS, Genomic selection, Scots pine},
	pages = {416},
}

Drought intensity and frequency are increasing under global warming in the boreal forests, and breeding for drought resistance will facilitate adaptation of new planting material to changing climate conditions. We used a tree-ring dataset of 559 individuals to study Scots pine genetic variation and the efficiency of genomic selection of drought-response traits (drought resistance, recovery and resilience), for the first time. From genotyping-by-sequencing (GBS), 31,101 SNPs were generated and used for the study.

@article{giubilei_clearing_2026,
	title = {Clearing the {Noise}: {Seasonal} {Dynamics} of {Endophytic} {Bacteria} in {Fagus} sylvatica {Leaves} {Revealed} by {Application} of {PNA} {Clamps}},
	volume = {178},
	issn = {1399-3054},
	shorttitle = {Clearing the {Noise}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70897},
	doi = {10.1111/ppl.70897},
	abstract = {The characterization of the seasonal dynamics of endophytic bacteria in beech leaves can be hindered by co-amplification of chloroplast and mitochondrial plant DNA. This study applies established peptide nucleic acid (PNA) clamps to suppress host-derived amplification while resolving bacterial succession across the vegetative season. Chloroplast- and mitochondrion-specific PNAs inverted the proportion of host to bacterial reads, enabled the recovery of bacterial sequence variants, and increased alpha diversity accordingly. Beta-diversity analyses showed that, once host contamination was removed, samples displayed a clear seasonal trajectory. Early-season leaves contained high abundances of Pseudomonas together with taxa likely introduced through plant–insect–microbe interactions. As leaves matured, the microbiome shifted toward a more stable composition dominated by well-established genera. The transition from early transient taxa to the later enrichment of phyllosphere-adapted and nutrient-cycling genera demonstrates that beech leaves host a temporally structured microbiome shaped by leaf development and seasonal environmental stress.},
	language = {en},
	number = {3},
	urldate = {2026-04-27},
	journal = {Physiologia Plantarum},
	author = {Giubilei, Irene and Turco, Silvia and Cardacino, Antonella and Mahawar, Lovely and Albrectsen, Benedicte Riber and Mazzaglia, Angelo},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70897},
	keywords = {Fagus sylvatica, PNA clamps, endophytes, metabarcoding, microbiome},
	pages = {e70897},
}

The characterization of the seasonal dynamics of endophytic bacteria in beech leaves can be hindered by co-amplification of chloroplast and mitochondrial plant DNA. This study applies established peptide nucleic acid (PNA) clamps to suppress host-derived amplification while resolving bacterial succession across the vegetative season. Chloroplast- and mitochondrion-specific PNAs inverted the proportion of host to bacterial reads, enabled the recovery of bacterial sequence variants, and increased alpha diversity accordingly. Beta-diversity analyses showed that, once host contamination was removed, samples displayed a clear seasonal trajectory. Early-season leaves contained high abundances of Pseudomonas together with taxa likely introduced through plant–insect–microbe interactions. As leaves matured, the microbiome shifted toward a more stable composition dominated by well-established genera. The transition from early transient taxa to the later enrichment of phyllosphere-adapted and nutrient-cycling genera demonstrates that beech leaves host a temporally structured microbiome shaped by leaf development and seasonal environmental stress.

@article{yang_natural_2026,
	title = {Natural selection and recombination interact to structure genome-wide variation in pines},
	volume = {126},
	copyright = {© 2026 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.70866},
	doi = {10.1111/tpj.70866},
	abstract = {Genetic differentiation among populations often varies significantly across the genome due to factors such as selection and recombination, resulting in a heterogeneous genomic landscape. However, variation in low-differentiation regions—genomic valleys—remains poorly understood. Moreover, most insights into plant genomic landscapes come from flowering plants, while comparable genome-wide studies in other taxa, such as conifers, remain limited. We analyzed whole-genome sequencing data from 100 individuals of three pine species—Pinus banksiana, Pinus contorta, and Pinus nigra. We found substantial genome-wide variation in recombination rates, with intergenic regions exhibiting higher recombination than genic regions, and rates decreasing with increasing distance from genes. Recombination rate was negatively correlated with gene length, driven primarily by intron length, suggesting that long introns in conifers may promote the retention of exceptionally long genes by maintaining low recombination in these regions. Genomic scans further revealed that genomic valleys are maintained through either balancing, background, or parallel selection. Additionally, multiple forms of selection were strongly associated with local recombination rate variation, highlighting the significant role of recombination in shaping patterns of genomic differentiation. Our findings provide new insight into the evolution and maintenance of extremely long genes in conifers. Moreover, the results indicate that allopatric selection in regions of low recombination is a major force structuring genomic variation in these species.},
	language = {en},
	number = {1},
	urldate = {2026-04-24},
	journal = {The Plant Journal},
	author = {Yang, Chen-Jui and Funda, Tomas and Chaudhary, Rajiv and Chen, Zhi-Qiang and Barcala, Maximiliano Estravis and Wu, Harry},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.70866},
	keywords = {Pinus, comparative genomics, conifer genome, genomic landscapes, long gene, natural selection, recombination},
	pages = {e70866},
}

Genetic differentiation among populations often varies significantly across the genome due to factors such as selection and recombination, resulting in a heterogeneous genomic landscape. However, variation in low-differentiation regions—genomic valleys—remains poorly understood. Moreover, most insights into plant genomic landscapes come from flowering plants, while comparable genome-wide studies in other taxa, such as conifers, remain limited. We analyzed whole-genome sequencing data from 100 individuals of three pine species—Pinus banksiana, Pinus contorta, and Pinus nigra. We found substantial genome-wide variation in recombination rates, with intergenic regions exhibiting higher recombination than genic regions, and rates decreasing with increasing distance from genes. Recombination rate was negatively correlated with gene length, driven primarily by intron length, suggesting that long introns in conifers may promote the retention of exceptionally long genes by maintaining low recombination in these regions. Genomic scans further revealed that genomic valleys are maintained through either balancing, background, or parallel selection. Additionally, multiple forms of selection were strongly associated with local recombination rate variation, highlighting the significant role of recombination in shaping patterns of genomic differentiation. Our findings provide new insight into the evolution and maintenance of extremely long genes in conifers. Moreover, the results indicate that allopatric selection in regions of low recombination is a major force structuring genomic variation in these species.

@article{pravdova_rapid_2026,
	title = {Rapid {Analysis} of {NAD} and {Other} {Phosphorylated} {Metabolites} in {Complex} {Biological} {Samples} by {Hydrophilic} {Interaction} {Liquid} {Chromatography} {Coupled} with {Tandem} {Mass} {Spectrometry}},
	volume = {98},
	issn = {0003-2700},
	url = {https://doi.org/10.1021/acs.analchem.6c00721},
	doi = {10.1021/acs.analchem.6c00721},
	abstract = {Nucleotides and coenzymes play critical roles in energy metabolism and cellular signaling and as building blocks of nucleic acids. This work addresses the challenges in the measurement of the phosphorylated metabolites using hydrophilic interaction liquid chromatography coupled with mass spectrometry, which facilitates the separation and detection of polar metabolites. Here, we present optimized HILIC-MS/MS methods for rapid analysis of polar metabolites including nucleotides and their derivatives in complex biological matrices, such as murine adipose, skeletal, and liver tissues, human plasma, and bacteria. The developed methodologies enable separation of key nucleotides and other phosphorylated metabolites within 6 min and cofactors such as NAD+, NADH, NADP+, and NADPH within 4 min. Validation of these methods demonstrated high accuracy, precision, and sensitivity and stresses the substantial impact of matrix effects. The applicability of the methods was also tested on 13C-labeling experiments with mouse pluripotent stem cells. Additionally, sample pretreatment techniques, such as liquid–liquid extraction and solid-phase extraction, were evaluated as a tool to decrease the negative impact of matrix effects in complex samples. This work enhances the analytical capabilities for nucleotide quantification in metabolomics, facilitating the study of metabolic pathways and disease markers.},
	number = {15},
	urldate = {2026-04-24},
	journal = {Analytical Chemistry},
	publisher = {American Chemical Society},
	author = {Pravdova, Adela and Kleinert, Maximilian and Henderson, John and Kafkia, Eleni and Pladevall-Morera, David and Yonamine, Caio Y. and Treebak, Jonas T. and Brodiazhenko, Tetiana and Terenin, Ilya and Zylicz, Jan Jakub and Moritz, Thomas and Hodek, Ondrej},
	month = apr,
	year = {2026},
	pages = {11428--11437},
}

Nucleotides and coenzymes play critical roles in energy metabolism and cellular signaling and as building blocks of nucleic acids. This work addresses the challenges in the measurement of the phosphorylated metabolites using hydrophilic interaction liquid chromatography coupled with mass spectrometry, which facilitates the separation and detection of polar metabolites. Here, we present optimized HILIC-MS/MS methods for rapid analysis of polar metabolites including nucleotides and their derivatives in complex biological matrices, such as murine adipose, skeletal, and liver tissues, human plasma, and bacteria. The developed methodologies enable separation of key nucleotides and other phosphorylated metabolites within 6 min and cofactors such as NAD+, NADH, NADP+, and NADPH within 4 min. Validation of these methods demonstrated high accuracy, precision, and sensitivity and stresses the substantial impact of matrix effects. The applicability of the methods was also tested on 13C-labeling experiments with mouse pluripotent stem cells. Additionally, sample pretreatment techniques, such as liquid–liquid extraction and solid-phase extraction, were evaluated as a tool to decrease the negative impact of matrix effects in complex samples. This work enhances the analytical capabilities for nucleotide quantification in metabolomics, facilitating the study of metabolic pathways and disease markers.

@article{nagahage_arabidopsis_2026,
	title = {The {Arabidopsis} thaliana {METACASPASE} {IIf} {Regulates} {Sugar} {Metabolism} and {Delays} {Dark}-{Induced} {Leaf} {Senescence}},
	volume = {178},
	copyright = {© 2026 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70888},
	doi = {10.1111/ppl.70888},
	abstract = {The Arabidopsis thaliana METACASPASE IIf (AtMCA-IIf) is expressed during both developmental cell death and leaf senescence in Arabidopsis thaliana. It has been shown to contribute to developmental cell death but its role in regulating leaf senescence has remained unclear. To investigate this, we conducted dark-induced senescence assays using atmca-IIf mutant lines, which exhibited an accelerated senescence phenotype accompanied by increased levels of glycolytic sugars in light and slow degradation of starch in dark-incubated leaves. Our findings therefore support AtMCA-IIf function in leaf senescence through modulation of sugar metabolism. We propose, on the basis of both in vitro and in vivo data, that one of the proteolytic targets of AtMCA-IIf in this process is PFPβ1, a subunit of the pyrophosphate-dependent fructose-6-phosphate phosphotransferase β1 (PFPβ1), a key enzyme in the glycolytic pathway. Accordingly, pfpβ1 mutants displayed accelerated senescence of dark-incubated leaves. Together, our results suggest that AtMCA-IIf mitigates leaf senescence through targeted modulation of sugar metabolism, thereby delaying the progression of senescence under dark conditions.},
	language = {en},
	number = {2},
	urldate = {2026-04-24},
	journal = {Physiologia Plantarum},
	author = {Nagahage, Isura Sumeda Priyadarshana and Carrio-Segui, Angela and Pandey, Shashank K. and Tuominen, Hannele},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70888},
	keywords = {Arabidopsis thaliana, leaf senescence, metacaspase, metacaspase-dependent proteolysis, sugar metabolism},
	pages = {e70888},
}

The Arabidopsis thaliana METACASPASE IIf (AtMCA-IIf) is expressed during both developmental cell death and leaf senescence in Arabidopsis thaliana. It has been shown to contribute to developmental cell death but its role in regulating leaf senescence has remained unclear. To investigate this, we conducted dark-induced senescence assays using atmca-IIf mutant lines, which exhibited an accelerated senescence phenotype accompanied by increased levels of glycolytic sugars in light and slow degradation of starch in dark-incubated leaves. Our findings therefore support AtMCA-IIf function in leaf senescence through modulation of sugar metabolism. We propose, on the basis of both in vitro and in vivo data, that one of the proteolytic targets of AtMCA-IIf in this process is PFPβ1, a subunit of the pyrophosphate-dependent fructose-6-phosphate phosphotransferase β1 (PFPβ1), a key enzyme in the glycolytic pathway. Accordingly, pfpβ1 mutants displayed accelerated senescence of dark-incubated leaves. Together, our results suggest that AtMCA-IIf mitigates leaf senescence through targeted modulation of sugar metabolism, thereby delaying the progression of senescence under dark conditions.

@article{tunnermann_applying_2026,
	title = {Applying nephelometry for analyzing liquid yeast cultures},
	volume = {46},
	issn = {2405-5808},
	url = {https://www.sciencedirect.com/science/article/pii/S2405580826001329},
	doi = {10.1016/j.bbrep.2026.102572},
	abstract = {Saccharomyces cerevisiae is a widely used model organism for the molecular analysis of genes and proteins. Several methods have been developed to study protein function and activity through heterologous gene expression, including yeast two-hybrid and yeast complementation. Traditionally, these yeast-based assays were performed on solid agar plates. While this approach provides an easy visual readout, it is difficult to quantify the results accurately. To overcome this limitation, liquid-based methods were introduced. Most of these methods rely on the use of spectrophotometry to measure reduction in light transmission as a result of light scattering and monitor culture growth. In this study, we propose nephelometry as an additional method for performing and analyzing liquid-culture yeast complementation assays. More specifically, we compare the suitability of using nephelometry for the functional analysis of two homologous proteins using yeast complementation: The amino acid transporter homologues Arabidopsis thaliana LYSINE HISTIDINE TRANSPORTER 1 (AtLHT1) and Populus tremula L. x tremuloides Michx LYSINE HISTIDINE TRANSPORTER 1.2 (PtrLHT1.2). In previous reports, no differences in microbial growth were detected, irrespective of which homolog was used to rescue an amino acid-deficient yeast mutant strain. By using nephelometry to record yeast growth, we demonstrated that it is a robust and reproducible method. When comparing to spectrophotometric measurements of yeast cultures, it proved to be a suitable alternative. The novel approach even revealed previously undetected differences in culture growth of both homologues, highlighting nephelometry's potential to improve sensitivity in yeast-based functional assays. We present the use of nephelometry as an equal method to yeast complementation traditionally executed on solid agar medium or in liquid culture with spectrophotometric analysis.},
	urldate = {2026-04-17},
	journal = {Biochemistry and Biophysics Reports},
	author = {Tünnermann, Laura and Colou, Justine and Näsholm, Torgny and Löfstedt, Tommy and Gratz, Regina},
	month = jun,
	year = {2026},
	keywords = {Lag time, Lysine histidine transporter 1 (LHT1), Maximum slope time, Nephelometry, Spectrophotometry},
	pages = {102572},
}

Saccharomyces cerevisiae is a widely used model organism for the molecular analysis of genes and proteins. Several methods have been developed to study protein function and activity through heterologous gene expression, including yeast two-hybrid and yeast complementation. Traditionally, these yeast-based assays were performed on solid agar plates. While this approach provides an easy visual readout, it is difficult to quantify the results accurately. To overcome this limitation, liquid-based methods were introduced. Most of these methods rely on the use of spectrophotometry to measure reduction in light transmission as a result of light scattering and monitor culture growth. In this study, we propose nephelometry as an additional method for performing and analyzing liquid-culture yeast complementation assays. More specifically, we compare the suitability of using nephelometry for the functional analysis of two homologous proteins using yeast complementation: The amino acid transporter homologues Arabidopsis thaliana LYSINE HISTIDINE TRANSPORTER 1 (AtLHT1) and Populus tremula L. x tremuloides Michx LYSINE HISTIDINE TRANSPORTER 1.2 (PtrLHT1.2). In previous reports, no differences in microbial growth were detected, irrespective of which homolog was used to rescue an amino acid-deficient yeast mutant strain. By using nephelometry to record yeast growth, we demonstrated that it is a robust and reproducible method. When comparing to spectrophotometric measurements of yeast cultures, it proved to be a suitable alternative. The novel approach even revealed previously undetected differences in culture growth of both homologues, highlighting nephelometry's potential to improve sensitivity in yeast-based functional assays. We present the use of nephelometry as an equal method to yeast complementation traditionally executed on solid agar medium or in liquid culture with spectrophotometric analysis.

@article{han_development_2026,
	title = {Development and application of a genotyping by target sequencing single-nucleotide polymorphism array panel in {Salix} suchowensis},
	volume = {27},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/s12864-026-12690-2},
	doi = {10.1186/s12864-026-12690-2},
	abstract = {Salix suchowensis is an important species of Salix, known for its rapid growth property and wide application in environmental construction, ecological restoration, wicker production, and biomass energy production. Due to its significance as a sustainable biological resource, S. suchowensis has been the centre of intensive breeding. However, rapid improvement of growth and biomass has been hindered by a lack of genomic resources. To address this limitation, we designed a liquid-phase probe array by genotyping by target sequencing technology. Using whole-genome resequencing data, a total of 39,076 SNPs were selected for the array panel, consisting of trait-associated SNPs, intragenic SNPs, and intergenic SNPs. This panel was validated by genotyping 550 new samples, demonstrating high call rates and effective capture of the population structure. Genome-wide association analysis identified 72 SNPs associated with plant height and ground diameter. Additionally, the array panel shows a high potential for genomic selection, with high prediction accuracy for various traits. These results highlight the efficiency of this panel in capturing genomic variations that are highly valuable for future genetic research and breeding applications.},
	language = {en},
	number = {1},
	urldate = {2026-04-17},
	journal = {BMC Genomics},
	author = {Han, Yu and Gu, Shaobo and Zhu, Mingjia and Liu, Wei and Feng, Landi and Yin, Tongming and Gao, Xuemeng and Zan, Yanjun and Huang, Rui and Ji, Yan and Liu, Jianquan},
	month = mar,
	year = {2026},
	keywords = {Genome-wide association study, Genomic selection, Ground diameter, Liquid-phase probe array, Plant height},
	pages = {355},
}

Salix suchowensis is an important species of Salix, known for its rapid growth property and wide application in environmental construction, ecological restoration, wicker production, and biomass energy production. Due to its significance as a sustainable biological resource, S. suchowensis has been the centre of intensive breeding. However, rapid improvement of growth and biomass has been hindered by a lack of genomic resources. To address this limitation, we designed a liquid-phase probe array by genotyping by target sequencing technology. Using whole-genome resequencing data, a total of 39,076 SNPs were selected for the array panel, consisting of trait-associated SNPs, intragenic SNPs, and intergenic SNPs. This panel was validated by genotyping 550 new samples, demonstrating high call rates and effective capture of the population structure. Genome-wide association analysis identified 72 SNPs associated with plant height and ground diameter. Additionally, the array panel shows a high potential for genomic selection, with high prediction accuracy for various traits. These results highlight the efficiency of this panel in capturing genomic variations that are highly valuable for future genetic research and breeding applications.

@article{liu_photosynthesis-related_2026,
	title = {Photosynthesis-related genetic and transcriptomic variations contribute to adaptive trait diversity in global {Arabidopsis} thaliana populations},
	volume = {26},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-026-08279-2},
	doi = {10.1186/s12870-026-08279-2},
	abstract = {Photosynthesis is the foundational process for carbon fixation in terrestrial ecosystems. Although allelic variations in photosynthesis-related genes have the potential to enhance carbon assimilation efficiency, their functional roles in local adaptation are still not well understood. In this study, we systematically examined the genetic and transcriptomic diversity among globally distributed natural accessions of Arabidopsis thaliana, focusing on 1,103 genes associated with photosynthetic pathways. By assembling chloroplast genomes from 28 representative accessions and integrating whole-genome and transcriptome sequencing data from over 1,000 accessions, we identified extensive allelic variation. Notably, 34.0\% of these genes exhibited regulatory variations through expression quantitative trait locus mapping, including key components such as Rubisco and Rubisco activase. Functional validation demonstrated that overexpression of these genes increased cotyledon size and root length. Additionally, genome-wide and transcriptome-wide association studies revealed that natural selection acting on these allelic variations significantly contributes to local environmental adaptation. Our findings elucidate the connection between genetic variation in photosynthetic pathways and their ecological significance, providing valuable insights for optimizing carbon fixation in dynamic environments.},
	language = {en},
	number = {1},
	urldate = {2026-04-10},
	journal = {BMC Plant Biology},
	author = {Liu, Wei and Hao, Ruili and Liu, Li and Hou, Jing and Lei, Mengyu and Han, Yu and Zhu, Mingjia and Liang, Lei and Yu, Le and Si, Huan and Liu, Jianquan and Zan, Yanjun and Ji, Yan},
	month = feb,
	year = {2026},
	keywords = {Arabidopsis thaliana, Local adaptation, Natural variation, Photosynthesis pathways},
	pages = {468},
}

Photosynthesis is the foundational process for carbon fixation in terrestrial ecosystems. Although allelic variations in photosynthesis-related genes have the potential to enhance carbon assimilation efficiency, their functional roles in local adaptation are still not well understood. In this study, we systematically examined the genetic and transcriptomic diversity among globally distributed natural accessions of Arabidopsis thaliana, focusing on 1,103 genes associated with photosynthetic pathways. By assembling chloroplast genomes from 28 representative accessions and integrating whole-genome and transcriptome sequencing data from over 1,000 accessions, we identified extensive allelic variation. Notably, 34.0% of these genes exhibited regulatory variations through expression quantitative trait locus mapping, including key components such as Rubisco and Rubisco activase. Functional validation demonstrated that overexpression of these genes increased cotyledon size and root length. Additionally, genome-wide and transcriptome-wide association studies revealed that natural selection acting on these allelic variations significantly contributes to local environmental adaptation. Our findings elucidate the connection between genetic variation in photosynthetic pathways and their ecological significance, providing valuable insights for optimizing carbon fixation in dynamic environments.

@article{moreno-sanguino_phloem_2026,
	title = {Phloem {Proteomics} to {Identify} {Small} {Open} {Reading} {Frame} ({sORF})-encoded {Peptides} {With} a {Putative} {Role} in the {Control} of {Flowering} {Time} in {Arabidopsis}},
	volume = {178},
	copyright = {© 2026 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70860},
	doi = {10.1111/ppl.70860},
	abstract = {Phloem sap proteomic studies have previously revealed that phloem sap composition varies during development and upon floral induction. Specific proteins, lipids, messenger RNAs (mRNAs), and peptides have been shown to accumulate at different developmental stages. Peptides are of special interest since they have the potential to act as regulatory molecules controlling plant responses to environmental changes, such as salinity and water stress, plant–microbe interactions, and developmental changes. In this context, we have characterized Arabidopsis thaliana phloem exudates to identify proteins and peptides with the potential to control flowering time, acting as signals fine-tuning plant development. In this work, we present the proteomic profiles of the phloem sap samples during floral transition along with the identification of proteins and peptides that showed changes in abundance during floral transition, suggesting that they could potentially have a role in the control of flowering. Among those, we have described the abundance pattern of the sORF1511 peptide in the phloem sap, which varies upon floral induction. We show that sORF1511 overexpression affects bolting time and alters the expression of several genes involved in the control of flowering time.},
	language = {en},
	number = {2},
	urldate = {2026-04-10},
	journal = {Physiologia Plantarum},
	author = {Moreno-Sanguino, Irene and Collás, Lucía Argente and Samuelsson, Göran and Wingsle, Gunnar and Benlloch, Reyes},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70860},
	keywords = {flowering time, peptides, phloem proteomics, small open reading frames},
	pages = {e70860},
}

Phloem sap proteomic studies have previously revealed that phloem sap composition varies during development and upon floral induction. Specific proteins, lipids, messenger RNAs (mRNAs), and peptides have been shown to accumulate at different developmental stages. Peptides are of special interest since they have the potential to act as regulatory molecules controlling plant responses to environmental changes, such as salinity and water stress, plant–microbe interactions, and developmental changes. In this context, we have characterized Arabidopsis thaliana phloem exudates to identify proteins and peptides with the potential to control flowering time, acting as signals fine-tuning plant development. In this work, we present the proteomic profiles of the phloem sap samples during floral transition along with the identification of proteins and peptides that showed changes in abundance during floral transition, suggesting that they could potentially have a role in the control of flowering. Among those, we have described the abundance pattern of the sORF1511 peptide in the phloem sap, which varies upon floral induction. We show that sORF1511 overexpression affects bolting time and alters the expression of several genes involved in the control of flowering time.

@article{guo_genomic_2026,
	title = {Genomic selection for tar content in {Nicotiana} tabacum: genetic architecture analysis and model evaluation},
	volume = {17},
	issn = {1664-462X},
	shorttitle = {Genomic selection for tar content in {Nicotiana} tabacum},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2026.1721129/full},
	doi = {10.3389/fpls.2026.1721129},
	abstract = {IntroductionDespite its economic importance, reducing tobacco tar content remains challenging due to its complex genetic basis.MethodsHere, we evaluated 436 diverse tobacco accessions to characterize the genetic architecture of tar content and develop an optimized genomic selection strategy. Based on these findings, sixteen genomic prediction models were assessed using five-fold cross-validation.ResultsGenome-wide association analysis detected no major-effect loci, and regional heritability mapping revealed localized enrichment of small-effect variants, particularly on chromosome 17, indicating a predominantly polygenic architecture. rrBLUP achieved the highest prediction accuracy (0.84) with superior computational efficiency, followed closely by GBM (0.83). The robustness of rrBLUP was further confirmed in an independent panel of 36 accessions (Pearson r = 0.888).DiscussionTogether, our results demonstrate that tobacco tar content is governed by dispersed small-effect loci with regional aggregation and establish rrBLUP as a robust and practical model for genome-wide prediction, providing methodological guidance for low-tar tobacco breeding.},
	language = {English},
	urldate = {2026-04-10},
	journal = {Frontiers in Plant Science},
	publisher = {Frontiers},
	author = {Guo, Linjie and Kong, Bo and Chen, Hui and Ren, Min and Cheng, Lirui and Yang, Aiguo and Liang, Lei and Zan, Yanjun and Si, Huan and Cai, Changchun},
	month = mar,
	year = {2026},
	keywords = {genome-wide association analysis, genomic selection, model evaluation, tar content, tobacco},
}

IntroductionDespite its economic importance, reducing tobacco tar content remains challenging due to its complex genetic basis.MethodsHere, we evaluated 436 diverse tobacco accessions to characterize the genetic architecture of tar content and develop an optimized genomic selection strategy. Based on these findings, sixteen genomic prediction models were assessed using five-fold cross-validation.ResultsGenome-wide association analysis detected no major-effect loci, and regional heritability mapping revealed localized enrichment of small-effect variants, particularly on chromosome 17, indicating a predominantly polygenic architecture. rrBLUP achieved the highest prediction accuracy (0.84) with superior computational efficiency, followed closely by GBM (0.83). The robustness of rrBLUP was further confirmed in an independent panel of 36 accessions (Pearson r = 0.888).DiscussionTogether, our results demonstrate that tobacco tar content is governed by dispersed small-effect loci with regional aggregation and establish rrBLUP as a robust and practical model for genome-wide prediction, providing methodological guidance for low-tar tobacco breeding.

@article{yu_construction_2026,
	title = {Construction of genomic prediction models for leaf protein content in \textit{{Nicotiana} tabacum}},
	volume = {243},
	issn = {0926-6690},
	url = {https://www.sciencedirect.com/science/article/pii/S0926669026004772},
	doi = {10.1016/j.indcrop.2026.123090},
	abstract = {With its high soluble protein content, large biomass yield, and ease of cultivation, tobacco leaves show strong potential as a novel protein source for livestock. However, the genetic basis underlying leaf protein content remains poorly understood, necessitating the use of genomic prediction models to screen germplasm resources and accelerate the improvement of this trait in future breeding programs. To address this, we analyzed 2517 tobacco germplasm accessions from the Chinese National Tobacco Germplasm Resource Bank, which represent broad genetic diversity, to investigate the genetic architecture of leaf protein content and construct genomic prediction models. Tobacco leaf protein content exhibited a moderate heritability of 0.16, and association analysis identified a significant peak that explained approximately 1\% of the phenotypic variance. We further evaluated the performance of 16 mainstream genomic prediction models using five-fold cross-validation. Among these models, best linear unbiased prediction (rrBLUP) model achieved the highest prediction accuracy (0.87). In addition, rrBLUP required less computational time and resources compared with other models, highlighting its stability and efficiency. Field validation (Longshan County, Hunan Province, 111°37′45″E, 27°30′52″N) confirmed the robustness and accuracy of our genomic selection model. Overall, our results demonstrate that genomic prediction can enable rapid screening of tobacco germplasm resources and substantially enhance the efficiency of developing high-protein varieties.},
	urldate = {2026-04-10},
	journal = {Industrial Crops and Products},
	author = {Yu, Le and Guo, Linjie and Liu, Li and Ren, Min and Cheng, Lirui and Liang, Lei and Yang, Aiguo and Si, Huan and Cai, Changchun and Zan, Yanjun},
	month = apr,
	year = {2026},
	keywords = {Genome-wide association study, Genomic selection, Germplasm, Leaf protein content, Nicotiana tabacum},
	pages = {123090},
}

With its high soluble protein content, large biomass yield, and ease of cultivation, tobacco leaves show strong potential as a novel protein source for livestock. However, the genetic basis underlying leaf protein content remains poorly understood, necessitating the use of genomic prediction models to screen germplasm resources and accelerate the improvement of this trait in future breeding programs. To address this, we analyzed 2517 tobacco germplasm accessions from the Chinese National Tobacco Germplasm Resource Bank, which represent broad genetic diversity, to investigate the genetic architecture of leaf protein content and construct genomic prediction models. Tobacco leaf protein content exhibited a moderate heritability of 0.16, and association analysis identified a significant peak that explained approximately 1% of the phenotypic variance. We further evaluated the performance of 16 mainstream genomic prediction models using five-fold cross-validation. Among these models, best linear unbiased prediction (rrBLUP) model achieved the highest prediction accuracy (0.87). In addition, rrBLUP required less computational time and resources compared with other models, highlighting its stability and efficiency. Field validation (Longshan County, Hunan Province, 111°37′45″E, 27°30′52″N) confirmed the robustness and accuracy of our genomic selection model. Overall, our results demonstrate that genomic prediction can enable rapid screening of tobacco germplasm resources and substantially enhance the efficiency of developing high-protein varieties.

@article{devi_art_2026,
	title = {The art of interdigitation: {Current} views on pavement cell shape acquisition},
	volume = {91},
	issn = {1369-5266},
	shorttitle = {The art of interdigitation},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526626000233},
	doi = {10.1016/j.pbi.2026.102880},
	abstract = {Cell shape acquisition is a central feature of morphogenesis, governing tissue organization, organ development, and organismal architecture. In vascular plants, leaf epidermal cells often adopt wavy, interlocking geometries, creating intricate jigsaw puzzle-like patterns. These complex shapes, which develop from simple polyhedral progenitors, provide an excellent model for investigating the mechanisms driving cell shape acquisition. Lobed, interdigitated pavement cells contribute to planar leaf expansion and mechanical stability. Recent advances reveal that the coordination of cell wall remodeling, cytoskeletal organization, and mechanical forces underlies the emergence of lobes (outgrowths) and necks (indentations) that stabilize the tissue and support organ growth. Biomechanical models further demonstrate how spatial modulation of wall stiffness and cytoskeletal dynamics drive interdigitated growth, while phytohormone signaling and communication among neighboring cells fine-tune patterning across the epidermal layer. Here, we bring together current insights into the mechanical, molecular and signaling frameworks that shape pavement cell morphogenesis and highlight key knowledge gaps and future research directions.},
	urldate = {2026-03-27},
	journal = {Current Opinion in Plant Biology},
	author = {Devi, Loitongbam Lorinda and Kumar, Vinod and Ratnakaram, Hemamshu and Lin, Mengzhuo and Robert, Stéphanie},
	month = jun,
	year = {2026},
	pages = {102880},
}

Cell shape acquisition is a central feature of morphogenesis, governing tissue organization, organ development, and organismal architecture. In vascular plants, leaf epidermal cells often adopt wavy, interlocking geometries, creating intricate jigsaw puzzle-like patterns. These complex shapes, which develop from simple polyhedral progenitors, provide an excellent model for investigating the mechanisms driving cell shape acquisition. Lobed, interdigitated pavement cells contribute to planar leaf expansion and mechanical stability. Recent advances reveal that the coordination of cell wall remodeling, cytoskeletal organization, and mechanical forces underlies the emergence of lobes (outgrowths) and necks (indentations) that stabilize the tissue and support organ growth. Biomechanical models further demonstrate how spatial modulation of wall stiffness and cytoskeletal dynamics drive interdigitated growth, while phytohormone signaling and communication among neighboring cells fine-tune patterning across the epidermal layer. Here, we bring together current insights into the mechanical, molecular and signaling frameworks that shape pavement cell morphogenesis and highlight key knowledge gaps and future research directions.

@article{moazzami_farida_dopamine_2026,
	title = {Dopamine modulates antioxidant and phenolic responses to alleviate nickel stress in {Salvia} officinalis},
	volume = {26},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-026-08365-5},
	doi = {10.1186/s12870-026-08365-5},
	abstract = {Nickel (Ni) contamination is a significant constraint to agricultural sustainability and medicinal plant productivity, leading to oxidative stress, nutrient imbalance, and disruption of secondary metabolism. Dopamine (DA) has been reported as a stress-mitigating agent in plants. Still, its role in shaping antioxidants and phenolic responses to Ni toxicity in medicinal species, such as Salvia officinalis, remains poorly understood.},
	language = {en},
	number = {1},
	urldate = {2026-03-27},
	journal = {BMC Plant Biology},
	author = {Moazzami Farida, Seyed Hamed and Rahmani, Nosrat and Taghizadeh, Marzieh and Albrectsen, Benedicte Riber},
	month = feb,
	year = {2026},
	keywords = {Antioxidant defense, Dopamine, Heavy metal, Nickel stress, Phenolic metabolism, Salvia officinalis l},
	pages = {491},
}

Nickel (Ni) contamination is a significant constraint to agricultural sustainability and medicinal plant productivity, leading to oxidative stress, nutrient imbalance, and disruption of secondary metabolism. Dopamine (DA) has been reported as a stress-mitigating agent in plants. Still, its role in shaping antioxidants and phenolic responses to Ni toxicity in medicinal species, such as Salvia officinalis, remains poorly understood.

@article{eklof_contrasting_2026,
	title = {Contrasting {Patterns} of {Local} {Adaptation} and {Adaptive} {Potential} {Under} {Climate} {Change} for {Old}-{Growth} and {Planted} {Stands} of {Norway} {Spruce} ({Picea} abies)},
	volume = {19},
	copyright = {© 2026 The Author(s). Evolutionary Applications published by John Wiley \& Sons Ltd.},
	issn = {1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.70217},
	doi = {10.1111/eva.70217},
	abstract = {Genetic diversity is a key prerequisite for adaptation to changing environments. Maintaining genetic diversity in forest trees is crucial amid climate change, given their long generation times. Forest management practices can affect the genetic diversity of forest ecosystems through selective felling or reforestation strategies following harvests. To assess how managed forests respond to climate-driven changes, we investigated patterns of genetic diversity and local adaptation by contrasting old-growth and recently planted stands of Norway spruce (Picea abies). We assess both neutral and adaptive genetic variation by sequencing pooled samples collected from 45 first stands across northern Sweden. Our results reveal no significant differences in overall genetic diversity between natural and planted populations, indicating that current forest management practices have not substantially reduced genetic variation. Analyses of adaptive variation demonstrate strong signatures of local adaptation in old-growth populations, with clear correlations between genetic and environmental distances. In contrast, planted stands show weaker adaptive signals and are also at greater risk of non-adaptiveness under future climate scenarios. While current forest management practices preserve much of the neutral genetic diversity necessary for long-term forest health, our findings highlight the importance of conserving and promoting adaptive genetic variation available in old-growth stands to ensure resilience against ongoing climate change.},
	language = {en},
	number = {3},
	urldate = {2026-03-20},
	journal = {Evolutionary Applications},
	author = {Eklöf, Helena and Bernhardsson, Carolina and Ingvarsson, Pär K.},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.70217},
	keywords = {Norway spruce, forest regeneration, forestry, genetic differentiation, genetic diversity},
	pages = {e70217},
}

Genetic diversity is a key prerequisite for adaptation to changing environments. Maintaining genetic diversity in forest trees is crucial amid climate change, given their long generation times. Forest management practices can affect the genetic diversity of forest ecosystems through selective felling or reforestation strategies following harvests. To assess how managed forests respond to climate-driven changes, we investigated patterns of genetic diversity and local adaptation by contrasting old-growth and recently planted stands of Norway spruce (Picea abies). We assess both neutral and adaptive genetic variation by sequencing pooled samples collected from 45 first stands across northern Sweden. Our results reveal no significant differences in overall genetic diversity between natural and planted populations, indicating that current forest management practices have not substantially reduced genetic variation. Analyses of adaptive variation demonstrate strong signatures of local adaptation in old-growth populations, with clear correlations between genetic and environmental distances. In contrast, planted stands show weaker adaptive signals and are also at greater risk of non-adaptiveness under future climate scenarios. While current forest management practices preserve much of the neutral genetic diversity necessary for long-term forest health, our findings highlight the importance of conserving and promoting adaptive genetic variation available in old-growth stands to ensure resilience against ongoing climate change.

@article{alonso-serra_growth_2026,
	title = {On growth and flow: hydraulic aspects of aboveground meristems},
	volume = {249},
	copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.},
	issn = {1469-8137},
	shorttitle = {On growth and flow},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.70713},
	doi = {10.1111/nph.70713},
	abstract = {Water is essential for plant growth under both normal and stress conditions. Aboveground, two key meristems control plant development: the shoot apical meristem and the vascular cambium. Here, stem cell maintenance and cell differentiation are affected by hydraulic fluctuations across seasons, days, or even hours. Water fluxes, turgor pressure, osmotic gradients, and tissue mechanics are integrated by molecular signals to provide a robust control of meristematic activity. Despite this fundamental connection, our understanding of how meristems sense and respond to hydraulic changes is only beginning to emerge. Thus, integrating insights from research on plant stress and development opens exciting avenues to study meristem plasticity.},
	language = {en},
	number = {2},
	urldate = {2026-03-18},
	journal = {New Phytologist},
	author = {Alonso-Serra, Juan},
	year = {2026},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.70713},
	keywords = {biomechanics, cambium, hydraulics, meristem, shoot apical meristem, water},
	pages = {722--728},
}

Water is essential for plant growth under both normal and stress conditions. Aboveground, two key meristems control plant development: the shoot apical meristem and the vascular cambium. Here, stem cell maintenance and cell differentiation are affected by hydraulic fluctuations across seasons, days, or even hours. Water fluxes, turgor pressure, osmotic gradients, and tissue mechanics are integrated by molecular signals to provide a robust control of meristematic activity. Despite this fundamental connection, our understanding of how meristems sense and respond to hydraulic changes is only beginning to emerge. Thus, integrating insights from research on plant stress and development opens exciting avenues to study meristem plasticity.

@article{kasige_interactions_2026,
	title = {Interactions between beneficial fungi and plant silicon: {A} review},
	volume = {114},
	copyright = {© 2025 The Author(s). Journal of Ecology © 2025 British Ecological Society.},
	issn = {1365-2745},
	shorttitle = {Interactions between beneficial fungi and plant silicon},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2745.70207},
	doi = {10.1111/1365-2745.70207},
	abstract = {Silicon (Si) accumulation in plants often plays an important functional role by alleviating the adverse impacts of the plant antagonists (e.g. invertebrate herbivores). Mutualistic associations with beneficial fungi, such as below-ground arbuscular mycorrhizal (AM) fungi and above-ground Epichloë endophytes, play similar roles for plant protection. Evidence suggests that beneficial fungi significantly influence Si uptake, often increasing Si in plant tissues while Si supplementation may in turn enhance fungal colonisation. However, this two-way association remains poorly understood due to the fragmented nature of existing literature. We assess the current state of knowledge on interactions between Si and beneficial fungi by extracting and comparing effect sizes (Cohen's d) from peer-reviewed literature for various reported relationships. We aim to understand the (i) interactions between Si and beneficial fungi, (ii) potential mechanisms underlying their interactions and (iii) role of Si-fungal interactions in enhancing plant resilience to environmental stresses. The Glomeraceae AM family was the most frequently investigated and was generally associated with increased Si accumulation in plants (overall effect size, d = 0.7). Additionally, Si supplementation was commonly reported to have a positive effect, with a modest overall increase in AM fungal colonisation (overall effect size, d = 0.3). These observations are often associated with changes in plant growth, morphology, physiology and chemistry by either Si or fungi. The literature covering Epichloë endophytes was limited and showed highly variable, strain-specific trends. Interactions between Si supply and beneficial fungi have mostly been studied in the context of abiotic stresses with limited focus on biotic antagonists (only nine studies). However, the extent to which Si and beneficial fungi increased plant resistance to stresses suggests that their interactions could play a significant role in plant community dynamics, potentially disadvantaging plant species that lack these traits. Synthesis. This review aims to help predict how beneficial fungi may interact with Si supply to enhance resistance to environmental stresses. Overall, Si supply and beneficial fungi seem to work ‘synergistically’ especially when Si availability is low, or when the plant species is a low Si accumulator. Finally, we identified potential avenues for future research based on existing knowledge and key knowledge gaps.},
	language = {en},
	number = {1},
	urldate = {2026-03-17},
	journal = {Journal of Ecology},
	author = {Kasige, Ramalka Heshani and Cibils-Stewart, Ximena and Frew, Adam and Johnson, Scott Nicholas},
	year = {2026},
	note = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2745.70207},
	keywords = {Epichloë endophytes, arbuscular mycorrhizal fungi, silica, silicon accumulation, silicon uptake},
	pages = {e70207},
}

Silicon (Si) accumulation in plants often plays an important functional role by alleviating the adverse impacts of the plant antagonists (e.g. invertebrate herbivores). Mutualistic associations with beneficial fungi, such as below-ground arbuscular mycorrhizal (AM) fungi and above-ground Epichloë endophytes, play similar roles for plant protection. Evidence suggests that beneficial fungi significantly influence Si uptake, often increasing Si in plant tissues while Si supplementation may in turn enhance fungal colonisation. However, this two-way association remains poorly understood due to the fragmented nature of existing literature. We assess the current state of knowledge on interactions between Si and beneficial fungi by extracting and comparing effect sizes (Cohen's d) from peer-reviewed literature for various reported relationships. We aim to understand the (i) interactions between Si and beneficial fungi, (ii) potential mechanisms underlying their interactions and (iii) role of Si-fungal interactions in enhancing plant resilience to environmental stresses. The Glomeraceae AM family was the most frequently investigated and was generally associated with increased Si accumulation in plants (overall effect size, d = 0.7). Additionally, Si supplementation was commonly reported to have a positive effect, with a modest overall increase in AM fungal colonisation (overall effect size, d = 0.3). These observations are often associated with changes in plant growth, morphology, physiology and chemistry by either Si or fungi. The literature covering Epichloë endophytes was limited and showed highly variable, strain-specific trends. Interactions between Si supply and beneficial fungi have mostly been studied in the context of abiotic stresses with limited focus on biotic antagonists (only nine studies). However, the extent to which Si and beneficial fungi increased plant resistance to stresses suggests that their interactions could play a significant role in plant community dynamics, potentially disadvantaging plant species that lack these traits. Synthesis. This review aims to help predict how beneficial fungi may interact with Si supply to enhance resistance to environmental stresses. Overall, Si supply and beneficial fungi seem to work ‘synergistically’ especially when Si availability is low, or when the plant species is a low Si accumulator. Finally, we identified potential avenues for future research based on existing knowledge and key knowledge gaps.

@article{huang_contrasting_2026,
	title = {Contrasting strategies of two \textit{{Camellia} oleifera} cultivars in shaping arbuscular mycorrhizal fungi communities under different phosphorus forms},
	volume = {128},
	issn = {1164-5563},
	url = {https://www.sciencedirect.com/science/article/pii/S1164556326000129},
	doi = {10.1016/j.ejsobi.2026.103814},
	abstract = {Phosphorus (P) availability regulates the arbuscular mycorrhizal fungi (AMF) symbiosis, but the distinct effects of different P forms (soluble, insoluble, organic) and host plant genotypes on AMF communities remain underexplored. Using Camellia oleifera cultivars with contrasting P-use efficiencies (low-P-sensitive CL3 and low-P-tolerant CL40), we examined how P forms and cultivar identity shape AMF communities and their functional linkages to plant growth and soil nutrients. The results showed that soluble inorganic P (SP) maximized plant height and biomass but suppressed AMF diversity and simplified co-occurrence networks. In contrast, insoluble inorganic P (IP) enhanced AMF colonization rates and stabilized microbial interactions. The low-P-sensitive CL3 hosted a higher Chao1 index under P limitation, suggesting compensatory recruitment for P acquisition, while CL40 exhibited stronger soil P activation and maintained complex AMF networks. Glomus and Paraglomus were identified as core taxa in the rhizosphere AMF networks of C. oleifera. RDA and Mantel analyses showed that variation in plant growth and root traits was aligned with AMF characteristics, particularly colonization and core taxa (Glomus, Paraglomus), and strongly associated with soil nutrients, with SP treatment reducing mycorrhizal dependence and shifting associations toward Paraglomus. These insights inform targeted cultivar selection and phosphorus management to optimize C. oleifera production and maintain soil health.},
	urldate = {2026-03-17},
	journal = {European Journal of Soil Biology},
	author = {Huang, Yuxuan and You, Xin and Frew, Adam and Wu, Fei and Zhang, Linping and Liu, Xinping and Xing, Jiaoping},
	month = mar,
	year = {2026},
	keywords = {Arbuscular mycorrhizal fungi diversity, Cultivar, Phosphorus forms, Rhizosphere},
	pages = {103814},
}

Phosphorus (P) availability regulates the arbuscular mycorrhizal fungi (AMF) symbiosis, but the distinct effects of different P forms (soluble, insoluble, organic) and host plant genotypes on AMF communities remain underexplored. Using Camellia oleifera cultivars with contrasting P-use efficiencies (low-P-sensitive CL3 and low-P-tolerant CL40), we examined how P forms and cultivar identity shape AMF communities and their functional linkages to plant growth and soil nutrients. The results showed that soluble inorganic P (SP) maximized plant height and biomass but suppressed AMF diversity and simplified co-occurrence networks. In contrast, insoluble inorganic P (IP) enhanced AMF colonization rates and stabilized microbial interactions. The low-P-sensitive CL3 hosted a higher Chao1 index under P limitation, suggesting compensatory recruitment for P acquisition, while CL40 exhibited stronger soil P activation and maintained complex AMF networks. Glomus and Paraglomus were identified as core taxa in the rhizosphere AMF networks of C. oleifera. RDA and Mantel analyses showed that variation in plant growth and root traits was aligned with AMF characteristics, particularly colonization and core taxa (Glomus, Paraglomus), and strongly associated with soil nutrients, with SP treatment reducing mycorrhizal dependence and shifting associations toward Paraglomus. These insights inform targeted cultivar selection and phosphorus management to optimize C. oleifera production and maintain soil health.

@article{kyaschenko_consistent_2026,
	title = {Consistent {Species} {Richness} {Patterns} but {Not} {Richness} {Estimates} {Based} on {Both} {ASV} and {OTU} {Inference} {Methods} on {ITS2}-{Based} {Soil} {Fungal} {Communities}},
	volume = {8},
	issn = {2637-4943},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/edn3.70246},
	doi = {10.1002/edn3.70246},
	abstract = {Fungi play essential roles in key ecosystem functions and processes, yet they often occur in inconspicuous, species-rich, and complex communities that remain difficult to study. Studies of fungal communities based on DNA extracted from environmental samples commonly rely on clustering sequence reads into units of diversity, followed by taxonomic identification and, in some cases, linkage to ecological traits. In this study, we evaluated how two clustering approaches—amplicon sequence variants (ASVs) and operational taxonomic units (OTUs)—affect the characterization of fungal communities. Despite minor differences, both approaches recovered consistent taxonomic patterns and community structure. Although both methods produced a similar total number of sequence clusters, they differed in representation of fungal community composition. All ASV representative sequences matched OTU representative sequences with at least 92.2\% similarity, whereas several rare OTUs showed low similarity to ASV reads, suggesting differences in the detection of low-abundance taxa. However, only a small fraction of OTU reads ({\textless} 0.1\%) lacked a corresponding ASV, indicating that ASVs captured nearly all OTU-defined taxa. In contrast, 14\% of ASV reads assigned to species hypotheses (SHs) did not match any OTU reads assigned to SHs, whereas only 1.3\% of OTU SH-assigned reads lacked a corresponding ASV match. ASVs generally provided higher resolution than OTUs, as abundant SHs were often represented by multiple ASVs, suggesting that ASVs capture intraspecific diversity. Consequently, ASVs should not be used as direct species proxies but instead require post hoc grouping to reflect species-level diversity. OTUs-based community composition aligned more clearly with soil properties, particularly the N:C ratio. Overall, both approaches provided a similar overview of broad-scale species richness. The choice between two clustering methods depends on the research question and the desired level of taxonomic resolution, and our results provide little support for the claim that ASVs should categorically replace taxonomic units in marker-gene data analysis.},
	language = {en},
	number = {1},
	urldate = {2026-03-16},
	journal = {Environmental DNA},
	author = {Kyaschenko, Julia and Tångrot, Jeanette and Dahlberg, Anders and Lindahl, Björn D. and Rosling, Anna},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/edn3.70246},
	keywords = {DNA barcoding, community dynamics, ecosystem, fungi, high-throughput nucleotide sequencing, molecular taxonomy, soil biodiversity, species specificity, taxonomy},
	pages = {e70246},
}

Fungi play essential roles in key ecosystem functions and processes, yet they often occur in inconspicuous, species-rich, and complex communities that remain difficult to study. Studies of fungal communities based on DNA extracted from environmental samples commonly rely on clustering sequence reads into units of diversity, followed by taxonomic identification and, in some cases, linkage to ecological traits. In this study, we evaluated how two clustering approaches—amplicon sequence variants (ASVs) and operational taxonomic units (OTUs)—affect the characterization of fungal communities. Despite minor differences, both approaches recovered consistent taxonomic patterns and community structure. Although both methods produced a similar total number of sequence clusters, they differed in representation of fungal community composition. All ASV representative sequences matched OTU representative sequences with at least 92.2% similarity, whereas several rare OTUs showed low similarity to ASV reads, suggesting differences in the detection of low-abundance taxa. However, only a small fraction of OTU reads (\textless 0.1%) lacked a corresponding ASV, indicating that ASVs captured nearly all OTU-defined taxa. In contrast, 14% of ASV reads assigned to species hypotheses (SHs) did not match any OTU reads assigned to SHs, whereas only 1.3% of OTU SH-assigned reads lacked a corresponding ASV match. ASVs generally provided higher resolution than OTUs, as abundant SHs were often represented by multiple ASVs, suggesting that ASVs capture intraspecific diversity. Consequently, ASVs should not be used as direct species proxies but instead require post hoc grouping to reflect species-level diversity. OTUs-based community composition aligned more clearly with soil properties, particularly the N:C ratio. Overall, both approaches provided a similar overview of broad-scale species richness. The choice between two clustering methods depends on the research question and the desired level of taxonomic resolution, and our results provide little support for the claim that ASVs should categorically replace taxonomic units in marker-gene data analysis.

@article{muraro_early_2026,
	title = {Early establishment of fast-growing tree species on forest land and forested arable land in southern {Sweden}: {Implications} for forest diversification},
	volume = {609},
	issn = {0378-1127},
	shorttitle = {Early establishment of fast-growing tree species on forest land and forested arable land in southern {Sweden}},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112726001404},
	doi = {10.1016/j.foreco.2026.123642},
	abstract = {Climate change and pest outbreaks are increasingly threatening conifer-dominated forests in Northern Europe, highlighting the need for greater species diversity to improve resilience. This study assessed early establishment success of six tree species: European aspen (Populus tremula), hybrid aspen (P. tremula × P. tremuloides), silver birch (Betula pendula), Norway spruce (Picea abies), Scots pine (Pinus sylvestris), and hybrid poplar (P. trichocarpa × P. maximowiczii), across seven sites in southern Sweden. Sites were categorized as either forest land (continuous forest cover {\textgreater}100 years) or forested arable land (former arable land afforested with Norway spruce for 40–70 years). Over three years, we monitored survival, height, and diameter growth. All experimental sites were fenced to exclude browsing. Wood ash was applied to a subset of hybrid poplars to assess its effect on establishment in acidic soils. Our results showed that hybrid aspen, birch, and European aspen had high survival and growth on forest land. On forested arable land, untreated Norway spruce, Scots pine, and hybrid poplar showed low survival, likely due to competition from dense vegetation. However, ash-treated poplar improved survival to approximately 80\% and showed strong growth on forested arable sites. Principal Component Analysis indicated overall higher establishment success on forest land for most species, whereas hybrid poplar performed similarly on forest and forested arable land when wood ash was applied. These findings underscore the importance of matching species to site conditions during early establishment and provide empirical evidence to inform species selection for forest regeneration under similar site conditions in southern Sweden.},
	urldate = {2026-03-13},
	journal = {Forest Ecology and Management},
	author = {Muraro, Luca and Robinson, Kathryn and Liziniewicz, Mateusz and Böhlenius, Henrik},
	month = jun,
	year = {2026},
	keywords = {Broadleaved trees, Forest land, Forest regeneration, Forested arable land, Populus, Species diversification, Tree establishment},
	pages = {123642},
}

Climate change and pest outbreaks are increasingly threatening conifer-dominated forests in Northern Europe, highlighting the need for greater species diversity to improve resilience. This study assessed early establishment success of six tree species: European aspen (Populus tremula), hybrid aspen (P. tremula × P. tremuloides), silver birch (Betula pendula), Norway spruce (Picea abies), Scots pine (Pinus sylvestris), and hybrid poplar (P. trichocarpa × P. maximowiczii), across seven sites in southern Sweden. Sites were categorized as either forest land (continuous forest cover \textgreater100 years) or forested arable land (former arable land afforested with Norway spruce for 40–70 years). Over three years, we monitored survival, height, and diameter growth. All experimental sites were fenced to exclude browsing. Wood ash was applied to a subset of hybrid poplars to assess its effect on establishment in acidic soils. Our results showed that hybrid aspen, birch, and European aspen had high survival and growth on forest land. On forested arable land, untreated Norway spruce, Scots pine, and hybrid poplar showed low survival, likely due to competition from dense vegetation. However, ash-treated poplar improved survival to approximately 80% and showed strong growth on forested arable sites. Principal Component Analysis indicated overall higher establishment success on forest land for most species, whereas hybrid poplar performed similarly on forest and forested arable land when wood ash was applied. These findings underscore the importance of matching species to site conditions during early establishment and provide empirical evidence to inform species selection for forest regeneration under similar site conditions in southern Sweden.

@article{wahl_plant_2026,
	title = {The plant energy management machinery: an essential hub for stress resilience and developmental dynamics with great potential for crop improvement},
	volume = {77},
	issn = {0022-0957},
	shorttitle = {The plant energy management machinery},
	url = {https://doi.org/10.1093/jxb/erag032},
	doi = {10.1093/jxb/erag032},
	abstract = {Plants coordinate resource uptake, developmental pace, and morphological efficiency. This ensures that energy use is balanced across time and tissues, enabling resilience and stable growth under fluctuating environmental conditions. The plant energy management machinery encompasses the interconnected signalling and metabolic networks that coordinate energy acquisition, storage, mobilization, and utilization to support growth, development, and environmental adaptation. In contrast to animals, where dedicated organs such as fat bodies in Drosophila and the liver in mammals, play crucial roles in energy metabolism and sensing (Chatterjee and Perrimon, 2021), plants exhibit a more integrative concept of nutrient and energy regulation. Here, the term ‘nutrients’ extends beyond simple energy carriers to include a broad spectrum of organic and inorganic compounds, such as sugars, amino acids, nitrate, phosphate, and lipids, that function both as metabolic substrates and as signalling molecules, influencing gene expression, enzyme activity, developmental transitions, and growth.},
	number = {5},
	urldate = {2026-03-10},
	journal = {Journal of Experimental Botany},
	author = {Wahl, Vanessa and Hanson, Johannes and Menand, Benoît},
	month = mar,
	year = {2026},
	pages = {1357--1361},
}

Plants coordinate resource uptake, developmental pace, and morphological efficiency. This ensures that energy use is balanced across time and tissues, enabling resilience and stable growth under fluctuating environmental conditions. The plant energy management machinery encompasses the interconnected signalling and metabolic networks that coordinate energy acquisition, storage, mobilization, and utilization to support growth, development, and environmental adaptation. In contrast to animals, where dedicated organs such as fat bodies in Drosophila and the liver in mammals, play crucial roles in energy metabolism and sensing (Chatterjee and Perrimon, 2021), plants exhibit a more integrative concept of nutrient and energy regulation. Here, the term ‘nutrients’ extends beyond simple energy carriers to include a broad spectrum of organic and inorganic compounds, such as sugars, amino acids, nitrate, phosphate, and lipids, that function both as metabolic substrates and as signalling molecules, influencing gene expression, enzyme activity, developmental transitions, and growth.

@article{mahawar_straw_2026,
	title = {Straw {Mulching} {Differentially} {Shapes} the {Structure} and {Function} of {Below}-{Ground} {Bacterial} {Communities} in {Potato} {Depending} on {eDNA} {Source} and {Cultivar}},
	volume = {7},
	copyright = {© 2026 The Author(s). Plant-Environment Interactions published by New Phytologist Foundation and John Wiley \& Sons Ltd.},
	issn = {2575-6265},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pei3.70131},
	doi = {10.1002/pei3.70131},
	abstract = {Potato is the world's third most important food crop, yet its production relies heavily on pesticides, creating a need for sustainable alternatives. We assessed how straw mulching, a practice known to improve soil fertility, enrich microbial activity, and suppress diseases, affects below-ground bacterial community structure and functional potential across different potato-associated sample types. A field experiment was conducted in northern Sweden using two potato cultivars under mulched and control soil conditions. Samples from the rhizosphere, root, soil, and tuber peel were analyzed using 16S ribosomal RNA (rRNA) gene sequencing (Illumina platform) to assess bacterial diversity and community composition. Straw mulching significantly increased bacterial richness and altered community structure across sample types and cultivars. Copiotrophic genera, which thrive in nutrient-rich environments, included Rhodanobacter, Mucilaginibacter, Flavobacterium, and Pseudomonas, and were enriched in rhizosphere, root, and tuber peel. Oligotrophs such as Bryobacter and Candidatus Solibacter dominated the soil and are known to contribute to organic matter turnover and plant growth. Notably, in the peel of one cultivar (King Edward), the abundance of Pseudomonas increased 5–7-fold, correlating with elevated starch and ascorbic acid contents of the tubers. In conclusion, the effect of straw mulching on soil bacterial communities and tuber quality appears to be diverse and cultivar dependent. Long-term and large-scale studies are needed to evaluate cumulative impacts on soil health, yield, and resilience.},
	language = {en},
	number = {1},
	urldate = {2026-02-20},
	journal = {Plant-Environment Interactions},
	author = {Mahawar, Lovely and Mishra, Arti and Tsitouri, Angeliki and Albrectsen, Benedicte Riber},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/pei3.70131},
	keywords = {bacterial communities, cv King Edward, cv Mandel, illumina amplicon sequencing, metabarcoding},
	pages = {e70131},
}

Potato is the world's third most important food crop, yet its production relies heavily on pesticides, creating a need for sustainable alternatives. We assessed how straw mulching, a practice known to improve soil fertility, enrich microbial activity, and suppress diseases, affects below-ground bacterial community structure and functional potential across different potato-associated sample types. A field experiment was conducted in northern Sweden using two potato cultivars under mulched and control soil conditions. Samples from the rhizosphere, root, soil, and tuber peel were analyzed using 16S ribosomal RNA (rRNA) gene sequencing (Illumina platform) to assess bacterial diversity and community composition. Straw mulching significantly increased bacterial richness and altered community structure across sample types and cultivars. Copiotrophic genera, which thrive in nutrient-rich environments, included Rhodanobacter, Mucilaginibacter, Flavobacterium, and Pseudomonas, and were enriched in rhizosphere, root, and tuber peel. Oligotrophs such as Bryobacter and Candidatus Solibacter dominated the soil and are known to contribute to organic matter turnover and plant growth. Notably, in the peel of one cultivar (King Edward), the abundance of Pseudomonas increased 5–7-fold, correlating with elevated starch and ascorbic acid contents of the tubers. In conclusion, the effect of straw mulching on soil bacterial communities and tuber quality appears to be diverse and cultivar dependent. Long-term and large-scale studies are needed to evaluate cumulative impacts on soil health, yield, and resilience.

@article{brun_chip-ms_2026,
	title = {{ChIP}-{MS} in {Plant} {Systems}: {Mapping} the {H3K27ac} {Proteome} {During} the {Greening} {Process}},
	volume = {178},
	copyright = {© 2026 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	shorttitle = {{ChIP}-{MS} in {Plant} {Systems}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70797},
	doi = {10.1111/ppl.70797},
	abstract = {We have established a method for chromatin immunoprecipitation coupled to mass spectrometry (ChIP-MS) in Arabidopsis thaliana. We demonstrate its utility by investigating proteins associated with histone H3 lysine 27 acetylation (H3K27ac), a key epigenetic mark regulating photosynthesis-associated nuclear genes (PhANGs) during chloroplast development and establishment of photosynthesis. Purification of chromatin-associated proteins from light-grown Arabidopsis cell cultures identified 66 proteins associated with H3K27ac that met the selection criteria in the two replicate experiments: (i) 2-fold change in relation to IgG, (ii) at least two unique peptides, and (iii) relevant biological annotations. The identified proteins included chromatin remodelers, chromatin regulators and transcription factors with potential roles in H3K27ac deposition. To evaluate the physiological role of the candidates associated with the H3K27ac mark, we developed a rapid and reproducible phenotyping method based on controlled light scanning to determine chlorophyll accumulation in mutant seedlings. We complemented with pigment quantification and analysis of photosynthesis-associated nuclear genes (PhANGs) expression. Several mutants displayed altered greening, pigment accumulation, or affected photosynthetic gene expression consistent with a role during chloroplast development. Notably, chr11, chr17, and atpds5a mutants showed impaired pigment accumulation and reduced expression of PhANGs, whereas hmgb4 and mbd10 mutants exhibited increased greening and induction of PhANGs. Together, these findings establish ChIP-MS as a robust approach to identify histone mark-associated proteins in plants and provide a first set of candidate regulators of H3K27ac during chloroplast biogenesis. This technical advance opens new possibilities to discover chromatin-based regulation of plant development and environmental responses.},
	language = {en},
	number = {1},
	urldate = {2026-02-20},
	journal = {Physiologia Plantarum},
	author = {Brun, Alexis and Quevedo, Marti and Sterling, Luis A. and Dekkers, Dick H. W. and Demmers, Jeroen and Hudson, Elton Paul and Strand, Åsa},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70797},
	keywords = {MS, chromatin, histone modifications, photosynthesis},
	pages = {e70797},
}

We have established a method for chromatin immunoprecipitation coupled to mass spectrometry (ChIP-MS) in Arabidopsis thaliana. We demonstrate its utility by investigating proteins associated with histone H3 lysine 27 acetylation (H3K27ac), a key epigenetic mark regulating photosynthesis-associated nuclear genes (PhANGs) during chloroplast development and establishment of photosynthesis. Purification of chromatin-associated proteins from light-grown Arabidopsis cell cultures identified 66 proteins associated with H3K27ac that met the selection criteria in the two replicate experiments: (i) 2-fold change in relation to IgG, (ii) at least two unique peptides, and (iii) relevant biological annotations. The identified proteins included chromatin remodelers, chromatin regulators and transcription factors with potential roles in H3K27ac deposition. To evaluate the physiological role of the candidates associated with the H3K27ac mark, we developed a rapid and reproducible phenotyping method based on controlled light scanning to determine chlorophyll accumulation in mutant seedlings. We complemented with pigment quantification and analysis of photosynthesis-associated nuclear genes (PhANGs) expression. Several mutants displayed altered greening, pigment accumulation, or affected photosynthetic gene expression consistent with a role during chloroplast development. Notably, chr11, chr17, and atpds5a mutants showed impaired pigment accumulation and reduced expression of PhANGs, whereas hmgb4 and mbd10 mutants exhibited increased greening and induction of PhANGs. Together, these findings establish ChIP-MS as a robust approach to identify histone mark-associated proteins in plants and provide a first set of candidate regulators of H3K27ac during chloroplast biogenesis. This technical advance opens new possibilities to discover chromatin-based regulation of plant development and environmental responses.

@article{pinosio_forgenius_2026,
	title = {The {FORGENIUS} {Genomic} {Resources}: {New} {Genotyping} {Tools} and {Genomic} {Data} for 23 {Forest} {Tree} {Species} and {Their} {Genetic} {Conservation} {Units}},
	volume = {26},
	issn = {1755-0998},
	shorttitle = {The {FORGENIUS} {Genomic} {Resources}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.70115},
	doi = {10.1111/1755-0998.70115},
	abstract = {Genetic diversity is a critical but often overlooked component of biological diversity. The European H2020 FORGENIUS project is aimed at increasing the quality and quantity of genetic data to start monitoring the European network of forest Genetic Conservation Units (GCUs). A first step in this direction was developing standardised genomic resources for 23 forest tree species, spanning from rare and scattered (e.g., Abies nebrodensis and Torminalis glaberrima) to widespread and stand-forming, economically relevant ones (e.g., Fagus sylvatica, Picea abies and Pinus sylvestris). Here, we describe the development and application of targeted genotyping tools, primarily based on Single Primer Enrichment Technology (SPET), along with existing SNP arrays for the selected species. The SPET panels developed in FORGENIUS were designed to capture ⁓10,000 loci per species, balancing species-specific and randomly distributed regions to ensure broad genome coverage and minimise ascertainment bias. Across 7220 genotyped trees, we identified over 1.8 million single nucleotide polymorphisms (SNPs) covering approximately 50 Mb of DNA sequence. SPET panels demonstrated high genotyping efficiency and cross-species transferability, especially within genera such as Quercus and Abies. They represent a cost-effective, flexible, and scalable solution for population-level genetic assessments across diverse taxa, enabling standardised, genome-wide characterisation of the GCU network. These resources not only promote the establishment of genetic monitoring, support genetically informed conservation strategies and improve our understanding of adaptive responses in European forests, but also enhance species delimitation and hybrid detection, and enable the characterisation of phylogenetically related but previously underexplored species.},
	language = {en},
	number = {3},
	urldate = {2026-03-09},
	journal = {Molecular Ecology Resources},
	author = {Pinosio, Sara and Bagnoli, Francesca and Avanzi, Camilla and Castellani, Maria B. and Frascella, Arcangela and McEvoy, Susan L. and Olsson, Sanna and Spanu, Ilaria and Vajana, Elia and Consortium, the FORGENIUS and González-Martínez, Santiago C. and Pyhäjärvi, Tanja and Scotti, Ivan and Vendramin, Giovanni G. and Piotti, Andrea},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.70115},
	keywords = {forest tree species, genetic conservation units, genetic diversity, genetic monitoring, single primer enrichment technology, targeted genotyping},
	pages = {e70115},
}

Genetic diversity is a critical but often overlooked component of biological diversity. The European H2020 FORGENIUS project is aimed at increasing the quality and quantity of genetic data to start monitoring the European network of forest Genetic Conservation Units (GCUs). A first step in this direction was developing standardised genomic resources for 23 forest tree species, spanning from rare and scattered (e.g., Abies nebrodensis and Torminalis glaberrima) to widespread and stand-forming, economically relevant ones (e.g., Fagus sylvatica, Picea abies and Pinus sylvestris). Here, we describe the development and application of targeted genotyping tools, primarily based on Single Primer Enrichment Technology (SPET), along with existing SNP arrays for the selected species. The SPET panels developed in FORGENIUS were designed to capture ⁓10,000 loci per species, balancing species-specific and randomly distributed regions to ensure broad genome coverage and minimise ascertainment bias. Across 7220 genotyped trees, we identified over 1.8 million single nucleotide polymorphisms (SNPs) covering approximately 50 Mb of DNA sequence. SPET panels demonstrated high genotyping efficiency and cross-species transferability, especially within genera such as Quercus and Abies. They represent a cost-effective, flexible, and scalable solution for population-level genetic assessments across diverse taxa, enabling standardised, genome-wide characterisation of the GCU network. These resources not only promote the establishment of genetic monitoring, support genetically informed conservation strategies and improve our understanding of adaptive responses in European forests, but also enhance species delimitation and hybrid detection, and enable the characterisation of phylogenetically related but previously underexplored species.

@article{klaminder_perspective_2026,
	title = {Perspective: {The} enigmatic extirpation of {Russian} larch from {Fennoscandia} and its relevance to modern forestry},
	volume = {608},
	issn = {0378-1127},
	shorttitle = {Perspective},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112726000976},
	doi = {10.1016/j.foreco.2026.123599},
	abstract = {For more than two centuries, Russian larch (Larix sibirica; Larix sukaczewii; Larix archangelica) was considered an alien species within Fennoscandia forestry. Findings of ancient alpine macrofossils led the Swedish Forest Agency to a policy shift where the Russian larch became recognized as part of the native flora. Despite the ongoing use of larch within Fennoscandian forestry, we lack a thorough discussion about its historic extirpation from this region and the possibility that it may happen again. In this perspective, we highlight that paleoecological studies indicate that Russian larch existed not only in alpine regions of Fennoscandia as previously suggested, but also in boreal areas of Sweden, Finland and Latvia. We identified a longitudinal trend where larch populations disappeared from western alpine habitats in Early Holocene but lingered until the last millennia in easter part of Finland. Our empirical analyses of forest experiments suggest that Russian larch has a growth advantage against Scots pine (Pinus sylverstris) and Norway spruce (Picea abies) across contemporary cold Fennoscandian climates, making it unlikely that Russian larch was extirpated simply due to negative growth effects from a colder climate occurring after the Early/Mid Holocene thermal optimum. We highlight that the driver(s) behind the enigmatic extirpation of Russian larch remain unresolved but should warrant attention given the current interest for Russian larch within Fennoscandian forestry.},
	urldate = {2026-02-20},
	journal = {Forest Ecology and Management},
	author = {Klaminder, Jonatan and Klingberg, Adam and Jerand, Philip},
	month = may,
	year = {2026},
	keywords = {Finland, Norway, Silviculture, Sweden, Vegetation history},
	pages = {123599},
}

For more than two centuries, Russian larch (Larix sibirica; Larix sukaczewii; Larix archangelica) was considered an alien species within Fennoscandia forestry. Findings of ancient alpine macrofossils led the Swedish Forest Agency to a policy shift where the Russian larch became recognized as part of the native flora. Despite the ongoing use of larch within Fennoscandian forestry, we lack a thorough discussion about its historic extirpation from this region and the possibility that it may happen again. In this perspective, we highlight that paleoecological studies indicate that Russian larch existed not only in alpine regions of Fennoscandia as previously suggested, but also in boreal areas of Sweden, Finland and Latvia. We identified a longitudinal trend where larch populations disappeared from western alpine habitats in Early Holocene but lingered until the last millennia in easter part of Finland. Our empirical analyses of forest experiments suggest that Russian larch has a growth advantage against Scots pine (Pinus sylverstris) and Norway spruce (Picea abies) across contemporary cold Fennoscandian climates, making it unlikely that Russian larch was extirpated simply due to negative growth effects from a colder climate occurring after the Early/Mid Holocene thermal optimum. We highlight that the driver(s) behind the enigmatic extirpation of Russian larch remain unresolved but should warrant attention given the current interest for Russian larch within Fennoscandian forestry.

@article{ko_recruitment_2026,
	title = {Recruitment of bifunctional regulator thermospermine to methylated ribosomes directs xylem fate},
	volume = {391},
	url = {https://www.science.org/doi/10.1126/science.adx2867},
	doi = {10.1126/science.adx2867},
	abstract = {Polyamines are often associated with ribosomes and are thought to stabilize their integrity. In Arabidopsis, the polyamine thermospermine (tSpm) affects xylem cell fate. tSpm induces translation of SUPPRESSOR-OF-ACAULIS51 (SAC51) and SAC51-LIKEs (SACLs), which inhibit heterodimerization of the xylem development proteins LONESOME-HIGHWAY (LHW) and TARGET-OF-MONOPTEROS5. Here, we report a methyltransferase, OVERACHIEVER, that methylates the peptidyl transferase center of the 25S ribosomal RNA (rRNA). Residue m3U2952 promotes functional tSpm binding to a specific site connecting the P-site transfer RNA (tRNA) with rRNA residues in the peptidyl transferase center. This interaction enhances the translation of SACLs but inhibits that of LHW. Our study uncovers the dependency between a conserved rRNA base methylation and a polyamine in orchestrating cell fate decisions, highlighting a role for the ribosome chemical landscape in translational regulation.},
	number = {6786},
	urldate = {2026-02-20},
	journal = {Science},
	publisher = {American Association for the Advancement of Science},
	author = {Ko, Donghwi and Ruonala, Raili and Faille, Alexandre and Hellmann, Eva and Help, Hanna and Liu, Huili and Nielsen, Ronni and Haakonsson, Anders and De Diego, Nuria and Paatero, Anja and Shcherbii, Mariia V. and Stefanowicz, Karolina and Ćavar Zeljković, Sanja and Drud Lundager Rasmussen, Tine and Novak, Ondrej and Bodi, Zsuzsanna and Eswaran, Gugan and Wybouw, Brecht and Bourdon, Matthieu and Urbez, Cristina and Liu, Xiaonan and Salokas, Kari and Öhman, Tiina and Waldie, Tanya and Törönen, Petri and el-Showk, Sedeer and Balcerowicz, Martin and Besnard, Fabrice and Liu, Xiaomin and Perkins, Patrick and Mazzoni-Putman, Serina and Vainonen, Julia P. and Sierla, Maija and Frilander, Mikko J. and Mandrup, Susanne and Vernoux, Teva and Ljung, Karin and Ferrando, Alejandro and Blazquez, Miguel A. and Holm, Liisa and Fray, Rupert and Varjosalo, Markku and Leyser, Ottoline and Paavilainen, Ville O. and Mähönen, Ari Pekka and Stepanova, Anna and Alonso, Jose and Heber, Steffen and Malinowski, Robert and Kirpekar, Finn and Warren, Alan J. and Helariutta, Ykä},
	month = feb,
	year = {2026},
	pages = {694--699},
}

Polyamines are often associated with ribosomes and are thought to stabilize their integrity. In Arabidopsis, the polyamine thermospermine (tSpm) affects xylem cell fate. tSpm induces translation of SUPPRESSOR-OF-ACAULIS51 (SAC51) and SAC51-LIKEs (SACLs), which inhibit heterodimerization of the xylem development proteins LONESOME-HIGHWAY (LHW) and TARGET-OF-MONOPTEROS5. Here, we report a methyltransferase, OVERACHIEVER, that methylates the peptidyl transferase center of the 25S ribosomal RNA (rRNA). Residue m3U2952 promotes functional tSpm binding to a specific site connecting the P-site transfer RNA (tRNA) with rRNA residues in the peptidyl transferase center. This interaction enhances the translation of SACLs but inhibits that of LHW. Our study uncovers the dependency between a conserved rRNA base methylation and a polyamine in orchestrating cell fate decisions, highlighting a role for the ribosome chemical landscape in translational regulation.

@article{ramanathan_effects_2026,
	title = {The {Effects} of {Acorn} {Origin}, {Environmental} {Microbiomes} and {Local} {Adaptation} on the {Leaf} {Metabolome}},
	volume = {52},
	issn = {1573-1561},
	url = {https://doi.org/10.1007/s10886-026-01692-9},
	doi = {10.1007/s10886-026-01692-9},
	abstract = {Plants are associated with microbial communities, which are inherited through the seed and acquired from the environment. These microbiomes influence plant physiology, chemistry, and functioning. Yet, we lack insights into how seed origin and the environmental microbiome jointly influence the leaf metabolome. We used untargeted metabolomics (gas chromatography/mass spectrometry) on leaves of pedunculate oak (Quercus robur) seedlings to examine metabolic responses to different seed origins and environmental microbiomes, as well as home and away environments. For this, acorns were collected from three mother trees and grown in a multifactorial design with soil and canopy microbiomes originating from the local mother tree (i.e., the home treatment) and neighbouring trees (i.e., the away treatment). We also measured two plant traits—plant height and leaf chlorophyll content—to examine relationships between plant traits and the metabolome. The leaf metabolome did not differ significantly between plants growing with different soil and canopy microbiomes. However, the leaf metabolome differed among acorn origins and between seedlings growing in home vs. away treatments. We found no clear link between plant traits and the leaf metabolome. This study is one of the first to disentangle the combined effects of seed origin and environmental microbiomes on plant leaf chemistry, and the home vs. away framework provides novel insights into local adaptation effects on plant metabolomes within forest ecosystems. These findings have practical implications for the use of local genotypes and the development of microorganism-based management practices in sustainable forestry and agriculture.},
	language = {en},
	number = {1},
	urldate = {2026-02-13},
	journal = {Journal of Chemical Ecology},
	author = {Ramanathan, Chandrasekar and Goris, Lisse and Mishra, Arti and Lihavainen-Bag, Jenna and Pawlowski, Katharina and Albrectsen, Benedicte Riber and Tack, Ayco J.M.},
	month = feb,
	year = {2026},
	keywords = {GC-MS, Local adaptation, Metabolomics, Microbiome, Plant-microbe interactions, Quercus robur},
	pages = {18},
}

Plants are associated with microbial communities, which are inherited through the seed and acquired from the environment. These microbiomes influence plant physiology, chemistry, and functioning. Yet, we lack insights into how seed origin and the environmental microbiome jointly influence the leaf metabolome. We used untargeted metabolomics (gas chromatography/mass spectrometry) on leaves of pedunculate oak (Quercus robur) seedlings to examine metabolic responses to different seed origins and environmental microbiomes, as well as home and away environments. For this, acorns were collected from three mother trees and grown in a multifactorial design with soil and canopy microbiomes originating from the local mother tree (i.e., the home treatment) and neighbouring trees (i.e., the away treatment). We also measured two plant traits—plant height and leaf chlorophyll content—to examine relationships between plant traits and the metabolome. The leaf metabolome did not differ significantly between plants growing with different soil and canopy microbiomes. However, the leaf metabolome differed among acorn origins and between seedlings growing in home vs. away treatments. We found no clear link between plant traits and the leaf metabolome. This study is one of the first to disentangle the combined effects of seed origin and environmental microbiomes on plant leaf chemistry, and the home vs. away framework provides novel insights into local adaptation effects on plant metabolomes within forest ecosystems. These findings have practical implications for the use of local genotypes and the development of microorganism-based management practices in sustainable forestry and agriculture.

@article{ma_pangenome_2026,
	title = {A pangenome insight into the genome divergence and flower color diversity among {Rhododendron} species},
	volume = {27},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/s12864-025-12461-5},
	doi = {10.1186/s12864-025-12461-5},
	abstract = {The Rhododendron genus (Rhododendron L.), recognized as the most extensive woody plant genus in the Northern Hemisphere, captivates with its strikingly beautiful corollas and variety of flower colors. In addition, the Rhododendron genus exhibits a complex evolutionary history and substantial species diversification. To comprehensively understand the genomic complexity and flower color diversity within this genus, comparative genomics has emerged as a promising approach, enabling analysis at a super-species level.},
	language = {en},
	number = {1},
	urldate = {2026-02-13},
	journal = {BMC Genomics},
	author = {Ma, Hai-Yao and Nie, Shuai and Liu, Hai-Bo and Shi, Tian-Le and Zhao, Shi-Wei and Chen, Zhao-Yang and Bao, Yu-Tao and Li, Zhi-Chao and Mao, Jian-Feng},
	month = jan,
	year = {2026},
	keywords = {DNA Transposable Elements, Evolution, Molecular, Flower color, Flowers, Gene duplication, Gene loss, Genetic Variation, Genome, Plant, Genomics, Phylogeny, Pigmentation, Retroelements, Rhododendron, Transposable element},
	pages = {101},
}

The Rhododendron genus (Rhododendron L.), recognized as the most extensive woody plant genus in the Northern Hemisphere, captivates with its strikingly beautiful corollas and variety of flower colors. In addition, the Rhododendron genus exhibits a complex evolutionary history and substantial species diversification. To comprehensively understand the genomic complexity and flower color diversity within this genus, comparative genomics has emerged as a promising approach, enabling analysis at a super-species level.

@article{holloway-phillips_rethinking_2026,
	title = {Rethinking the {2H} fingerprint of carbohydrates: a novel proxy for plant metabolism and performance},
	volume = {249},
	issn = {1469-8137},
	shorttitle = {Rethinking the {2H} fingerprint of carbohydrates},
	doi = {10.1111/nph.70845},
	abstract = {The intricate architecture of plant metabolic networks and the dynamic fluxes of elements through these networks are fundamental determinants of how carbon (C) is partitioned among growth, reproduction, storage, respiration and the synthesis of secondary metabolites. While these C fluxes are critical to cellular function and plant life, their routine measurement remains a significant challenge. This review aimed to highlight the substantial potential of hydrogen (H) isotopes of plant carbohydrates to bridge this methodological gap by serving as a flux-based proxy for primary C metabolism. This potential is demonstrated from both a theoretical perspective and by summarising available evidence at the whole-molecule and position-specific levels. The utility of this proxy is significant for understanding species' metabolic plasticity, assessing plant responses to environmental change and selecting superior metabolic phenotypes in agriculture and forestry. However, for this proxy to be fully realised, several fundamental questions remain. This includes the identification of specific metabolic reactions associated with isotopic variation and their relationship to plant performance. We outline several approaches to advance the development of an H-isotope based plant metabolic proxy for plant performance.},
	language = {eng},
	number = {4},
	journal = {The New Phytologist},
	author = {Holloway-Phillips, Meisha and Lehmann, Marco M. and Tcherkez, Guillaume and Werner, Roland A. and Nelson, Daniel B. and Baan, Jochem and Cernusak, Lucas A. and Cormier, Marc-Andre and Diao, Haoyu and Gessler, Arthur and Guidi, Claudia and Hugger, Selina and Ladd, S. Nemiah and Martínez-Sancho, Elisabet and Niittylä, Totte and Saurer, Matthias and Schuler, Philipp and Vitali, Valentina and Wieloch, Thomas and Kahmen, Ansgar},
	month = feb,
	year = {2026},
	keywords = {Carbohydrate Metabolism, Carbon, Deuterium, Plants, carbohydrates, hydrogen stable isotopes, isotope fractionation, metabolic flux analysis, plant C metabolism, plant physiology},
	pages = {1623--1643},
}

The intricate architecture of plant metabolic networks and the dynamic fluxes of elements through these networks are fundamental determinants of how carbon (C) is partitioned among growth, reproduction, storage, respiration and the synthesis of secondary metabolites. While these C fluxes are critical to cellular function and plant life, their routine measurement remains a significant challenge. This review aimed to highlight the substantial potential of hydrogen (H) isotopes of plant carbohydrates to bridge this methodological gap by serving as a flux-based proxy for primary C metabolism. This potential is demonstrated from both a theoretical perspective and by summarising available evidence at the whole-molecule and position-specific levels. The utility of this proxy is significant for understanding species' metabolic plasticity, assessing plant responses to environmental change and selecting superior metabolic phenotypes in agriculture and forestry. However, for this proxy to be fully realised, several fundamental questions remain. This includes the identification of specific metabolic reactions associated with isotopic variation and their relationship to plant performance. We outline several approaches to advance the development of an H-isotope based plant metabolic proxy for plant performance.

@article{karamat_arabidopsis_2026,
	title = {Arabidopsis mutants for {Mediator} {Head}, {Middle}, {Tail}, and {Kinase} modules reveal distinct roles in regulating the transcriptional response to salt stress},
	volume = {19},
	issn = {2667-064X},
	url = {https://www.sciencedirect.com/science/article/pii/S2667064X25004567},
	doi = {10.1016/j.stress.2025.101189},
	abstract = {Environmental changes trigger stress responses in living organisms. Although the underlying mechanisms are only partly understood, they involve intricate signaling pathways and transcription factors (TFs). Mediator is a conserved co-regulator complex required for transcriptional regulation of all eukaryotic protein-encoding genes. However, its function in abiotic stress responses is elusive. Here, we describe global gene expression changes induced by salt stress in Arabidopsis thaliana. To investigate the involvement of Mediator, we analyzed med9, med16, med18, and cdk8 mutants, each representing one of the four Mediator modules. Our results demonstrate that promoters of differentially expressed genes (DEGs) for each mutant are enriched for binding sites of specific TFs. Phenotypic analyses further support the transcriptomic data: med16 and med18, and to a lesser extent cdk8, exhibit defects typical to mutations that affect abscisic acid and anthocyanin metabolism and we identify dysregulated signaling molecules, TFs, and target genes in these pathways. Our results reveal how signals from different stress response pathways are dependent on, and integrated by, Mediator subunits to coordinate a functional response to salt stress.},
	urldate = {2026-01-23},
	journal = {Plant Stress},
	author = {Karamat, Fazeelat and Vergara, Alexander and Blomberg, Jeanette and Crawford, Tim and Lehotai, Nóra and Rentoft, Matilda and Strand, Åsa and Björklund, Stefan},
	month = jan,
	year = {2026},
	keywords = {Mediator, RNAseq, Salt stress},
	pages = {101189},
}

Environmental changes trigger stress responses in living organisms. Although the underlying mechanisms are only partly understood, they involve intricate signaling pathways and transcription factors (TFs). Mediator is a conserved co-regulator complex required for transcriptional regulation of all eukaryotic protein-encoding genes. However, its function in abiotic stress responses is elusive. Here, we describe global gene expression changes induced by salt stress in Arabidopsis thaliana. To investigate the involvement of Mediator, we analyzed med9, med16, med18, and cdk8 mutants, each representing one of the four Mediator modules. Our results demonstrate that promoters of differentially expressed genes (DEGs) for each mutant are enriched for binding sites of specific TFs. Phenotypic analyses further support the transcriptomic data: med16 and med18, and to a lesser extent cdk8, exhibit defects typical to mutations that affect abscisic acid and anthocyanin metabolism and we identify dysregulated signaling molecules, TFs, and target genes in these pathways. Our results reveal how signals from different stress response pathways are dependent on, and integrated by, Mediator subunits to coordinate a functional response to salt stress.

@article{sandehn_bioelectronics_2026,
	title = {Bioelectronics for basic plant science and precision agriculture},
	copyright = {2026 Springer Nature Limited},
	issn = {2948-1201},
	url = {https://www.nature.com/articles/s44287-025-00258-3},
	doi = {10.1038/s44287-025-00258-3},
	abstract = {The rapid growth of the global population and intensified climate challenges make the need for sustainable and efficient food production more urgent than ever. Agriculture is both an important contributor to greenhouse gas emissions and impacted by environmental degradation. Emerging bioelectronic technologies enable real-time monitoring and precise modulation of plant physiology and environmental conditions and have the potential to transform sustainable agriculture. In this Review, we explore the applications of bioelectronics in basic plant science and precision agriculture. In basic research, these technologies can complement or overcome limitations of traditional tools, accelerating efforts to engineer plants that are resistant to environmental stress and have enhanced productivity. In agriculture, bioelectronics offer potential for optimized resource use, enhanced crop yield and early disease detection. While highlighting the interdisciplinary challenges of integrating bioelectronics, from materials and device design through to field deployment and environmental impact, we aim to inform and inspire plant scientists, engineers and agricultural stakeholders.},
	language = {en},
	urldate = {2026-01-23},
	journal = {Nature Reviews Electrical Engineering},
	publisher = {Nature Publishing Group},
	author = {Sandéhn, Alexandra and Vijayarouthu, S. S. V. Prasanna and Costa, Alex and Stavrinidou, Eleni},
	month = jan,
	year = {2026},
	keywords = {Biological techniques, Electrical and electronic engineering, Sensors and biosensors},
	pages = {1--12},
}

The rapid growth of the global population and intensified climate challenges make the need for sustainable and efficient food production more urgent than ever. Agriculture is both an important contributor to greenhouse gas emissions and impacted by environmental degradation. Emerging bioelectronic technologies enable real-time monitoring and precise modulation of plant physiology and environmental conditions and have the potential to transform sustainable agriculture. In this Review, we explore the applications of bioelectronics in basic plant science and precision agriculture. In basic research, these technologies can complement or overcome limitations of traditional tools, accelerating efforts to engineer plants that are resistant to environmental stress and have enhanced productivity. In agriculture, bioelectronics offer potential for optimized resource use, enhanced crop yield and early disease detection. While highlighting the interdisciplinary challenges of integrating bioelectronics, from materials and device design through to field deployment and environmental impact, we aim to inform and inspire plant scientists, engineers and agricultural stakeholders.

@article{bekele_associations_2026,
	title = {Associations between volatile fatty acid profiles, methane emissions, and rumen microbiota in sheep fed {Ethiopian} forage},
	volume = {16},
	issn = {1664-302X},
	url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1731623/full},
	doi = {10.3389/fmicb.2025.1731623},
	abstract = {This study was part of an in vivo investigation of methane (CH4) abatement feed on local Menz breed sheep in Ethiopia, conducted over 90 days period using a randomized complete block design. Sheep were subjected to four dietary treatments: Control, Acacia (Acacia nilotica), BSG (Brewer's Spent Grain), and Ziziphus (Ziziphus spina-christi). The aim of the study was to investigate the rumen microbial community composition, diversity, and their relationships with CH4 intensity. Rumen fluid was collected on days 0 (SD\_0), 45 (SD\_45), and 90 (SD\_90), using an esophageal tube. The dynamics of the bacterial and archaeal domains were assessed by 16S rRNA gene sequencing. The sequencing results showed that 92.9\% of ASVs were Bacteria, and 0.05\% Archaea. At the genus level, Rikenellaceae RC9 gut group (18\%), Prevotella (17\%), and Candidatus Saccharimonas (8.9\%) were the most abundant Bacteria, while Methanobrevibacter (88\%) dominated the Archaeal genera across all treatment groups. Treatment feed significantly altered microbial profiles, notably reducing Methanobrevibacter abundance in CH4 abatement diets and increasing the presence of Methanosphaera. Shannon diversity increased in the abatement diet and decreased when the sheep were fed BSG. CH4 intensity was most strongly associated with the archaeal genus Methanomicrobium, but did not associate strongly with any other Bacteria or Archaea, although Methanobrevibacter and Methanosphaera were correlated negatively (r = –0.97). CH4 intensity also did not covary with volatile fatty acids (VFAs), of which Acacia yielded the highest acetate (772 mmol/mol) and BSG the highest propionate (172 mmol/mol) concentration. The volatile fatty acids (VFAs) showed a strong correlation: a positive correlation between acetate and butyrate (r = 0.80) and a strong negative correlation between acetate and propionate (r = –0.92). These findings highlight the complex relationship between diet, rumen microbiota, and fermentation products, with implications for CH4 mitigation strategies in sheep.},
	language = {English},
	urldate = {2026-01-23},
	journal = {Frontiers in Microbiology},
	publisher = {Frontiers},
	author = {Bekele, Wondimagegne and Mahawar, Lovely and Ramin, Mohammad and Simachew, Addis and Albrectsen, Benedicte Riber and Zegeye, Abiy},
	month = jan,
	year = {2026},
	keywords = {Archaea, Bacteria, CH4 intensity, Illumina sequencing, gut microbiota, metabarcoding, ruminant, volatile fatty acids},
}

This study was part of an in vivo investigation of methane (CH4) abatement feed on local Menz breed sheep in Ethiopia, conducted over 90 days period using a randomized complete block design. Sheep were subjected to four dietary treatments: Control, Acacia (Acacia nilotica), BSG (Brewer's Spent Grain), and Ziziphus (Ziziphus spina-christi). The aim of the study was to investigate the rumen microbial community composition, diversity, and their relationships with CH4 intensity. Rumen fluid was collected on days 0 (SD_0), 45 (SD_45), and 90 (SD_90), using an esophageal tube. The dynamics of the bacterial and archaeal domains were assessed by 16S rRNA gene sequencing. The sequencing results showed that 92.9% of ASVs were Bacteria, and 0.05% Archaea. At the genus level, Rikenellaceae RC9 gut group (18%), Prevotella (17%), and Candidatus Saccharimonas (8.9%) were the most abundant Bacteria, while Methanobrevibacter (88%) dominated the Archaeal genera across all treatment groups. Treatment feed significantly altered microbial profiles, notably reducing Methanobrevibacter abundance in CH4 abatement diets and increasing the presence of Methanosphaera. Shannon diversity increased in the abatement diet and decreased when the sheep were fed BSG. CH4 intensity was most strongly associated with the archaeal genus Methanomicrobium, but did not associate strongly with any other Bacteria or Archaea, although Methanobrevibacter and Methanosphaera were correlated negatively (r = –0.97). CH4 intensity also did not covary with volatile fatty acids (VFAs), of which Acacia yielded the highest acetate (772 mmol/mol) and BSG the highest propionate (172 mmol/mol) concentration. The volatile fatty acids (VFAs) showed a strong correlation: a positive correlation between acetate and butyrate (r = 0.80) and a strong negative correlation between acetate and propionate (r = –0.92). These findings highlight the complex relationship between diet, rumen microbiota, and fermentation products, with implications for CH4 mitigation strategies in sheep.

@article{pandey_variable_2026,
	title = {Variable temperature processing by plasmodesmata regulates robust bud dormancy release},
	volume = {17},
	copyright = {2026 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-67260-z},
	doi = {10.1038/s41467-025-67260-z},
	abstract = {Dormancy is a key mechanism in perennial plants in boreal and temperate regions, protecting buds from winter damage by repressing precocious bud break before spring onset. How plants robustly time dormancy release under fluctuating environments remains unknown. Here, we show that, rather than simply sensing cold duration, buds leverage warm spikes to sense winter progression and time dormancy release. This timing mechanism is mediated by previously unrecognized regulation of plasmodesmata by warm spikes acting through tree ortholog of FLOWERING LOCUS T (FT1) and the gibberellic acid pathway. Our results reveal FT1 as a previously unrecognized, suppressor of callose levels and show that warm spikes repress cold induction of FT1 and GA pathway to suppress PD opening and dormancy release. Importantly, buds exhibit heterogeneity in bud break. This heterogeneity in bud break crucial for bet hedging is amplified under temperature fluctuations and is associated with the thermal responsiveness of plasmodesmata. Altogether, our work reveals dynamic plasmodesmata regulation as a crucial tissue-level mediator of variable temperature processing by buds, enabling robust adaptation of trees to seasonal changes.},
	language = {en},
	number = {1},
	urldate = {2026-01-16},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Pandey, Shashank K. and Moraes, Tatiana S. and Nair, Aswin and Aryal, Bibek and Azeez, Abdul and Miskolczi, Pal and Maucort, Guillaume and Cordelières, Fabrice P. and Brocard, Lysiane and Davis, Gwendolyn V. and Dromiack, Hannah and Khanapurkar, Swanand and Walker, Sara I. and Bassel, George W. and Bayer, Emmanuelle M. and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2026},
	keywords = {Plant molecular biology, Plant physiology, Shoot apical meristem},
	pages = {348},
}

Dormancy is a key mechanism in perennial plants in boreal and temperate regions, protecting buds from winter damage by repressing precocious bud break before spring onset. How plants robustly time dormancy release under fluctuating environments remains unknown. Here, we show that, rather than simply sensing cold duration, buds leverage warm spikes to sense winter progression and time dormancy release. This timing mechanism is mediated by previously unrecognized regulation of plasmodesmata by warm spikes acting through tree ortholog of FLOWERING LOCUS T (FT1) and the gibberellic acid pathway. Our results reveal FT1 as a previously unrecognized, suppressor of callose levels and show that warm spikes repress cold induction of FT1 and GA pathway to suppress PD opening and dormancy release. Importantly, buds exhibit heterogeneity in bud break. This heterogeneity in bud break crucial for bet hedging is amplified under temperature fluctuations and is associated with the thermal responsiveness of plasmodesmata. Altogether, our work reveals dynamic plasmodesmata regulation as a crucial tissue-level mediator of variable temperature processing by buds, enabling robust adaptation of trees to seasonal changes.

@article{parizkova_l-glutamine_2026,
	title = {L-{Glutamine} {Modulates} {Root} {Architecture} and {Hormonal} {Balance} in {Arabidopsis}},
	volume = {178},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70723},
	doi = {10.1111/ppl.70723},
	abstract = {Nitrogen (N) availability is a key determinant of plant growth and development. Here, we investigate how different N sources shape Arabidopsis thaliana root system architecture, metabolism and hormone dynamics. L-glutamine (L-GLN) significantly enhances root biomass compared to nitrate (KNO3) without compromising shoot growth. This effect emerges after 2 weeks and is independent of L-GLN's role as a carbon or ammonium source or of potential L-GLN-induced pH changes due to ammonium release, indicating a specific function of L-GLN as a N source and signaling molecule. A reverse genetic screen identified AMINO ACID PERMEASE 1 (AAP1)-mediated uptake and GLUTAMINE SYNTHETASE (GS)-dependent assimilation as essential for L-GLN-induced root biomass. In contrast, the N-sensing regulators NITRATE TRANSPORTER 1.1 (NRT1.1) and AMMONIUM TRANSPORTER (AMT) family members contribute to the differential root responses between KNO3 and L-GLN. Metabolic profiling revealed distinct amino acid signatures under these N sources, irrespective of genotype. Hormonal analyses showed that L-GLN modulates auxin homeostasis, with auxin supplementation restoring primary root growth and lateral root symmetry under L-GLN conditions. L-GLN also reconfigures cytokinin balance by elevating cZ while reducing tZ, collectively shaping root system architecture through hormone-dependent regulation. Together, these findings establish L-GLN as an integrator of N metabolism and hormone signaling in root development, highlighting its signaling capacity beyond nutrient supply and offering new perspectives for improving N use efficiency.},
	language = {en},
	number = {1},
	urldate = {2026-01-09},
	journal = {Physiologia Plantarum},
	author = {Pařízková, Barbora and Johansson, Annika I. and Juvany, Marta and Šimura, Jan and Ljung, Karin and Antoniadi, Ioanna},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70723},
	keywords = {KNO3, L-GLN, auxin, cytokinin, organic N, root growth, root system architecture},
	pages = {e70723},
}

Nitrogen (N) availability is a key determinant of plant growth and development. Here, we investigate how different N sources shape Arabidopsis thaliana root system architecture, metabolism and hormone dynamics. L-glutamine (L-GLN) significantly enhances root biomass compared to nitrate (KNO3) without compromising shoot growth. This effect emerges after 2 weeks and is independent of L-GLN's role as a carbon or ammonium source or of potential L-GLN-induced pH changes due to ammonium release, indicating a specific function of L-GLN as a N source and signaling molecule. A reverse genetic screen identified AMINO ACID PERMEASE 1 (AAP1)-mediated uptake and GLUTAMINE SYNTHETASE (GS)-dependent assimilation as essential for L-GLN-induced root biomass. In contrast, the N-sensing regulators NITRATE TRANSPORTER 1.1 (NRT1.1) and AMMONIUM TRANSPORTER (AMT) family members contribute to the differential root responses between KNO3 and L-GLN. Metabolic profiling revealed distinct amino acid signatures under these N sources, irrespective of genotype. Hormonal analyses showed that L-GLN modulates auxin homeostasis, with auxin supplementation restoring primary root growth and lateral root symmetry under L-GLN conditions. L-GLN also reconfigures cytokinin balance by elevating cZ while reducing tZ, collectively shaping root system architecture through hormone-dependent regulation. Together, these findings establish L-GLN as an integrator of N metabolism and hormone signaling in root development, highlighting its signaling capacity beyond nutrient supply and offering new perspectives for improving N use efficiency.

@article{marciano_comparative_2026,
	title = {A {Comparative} {Analysis} of {Receptor}-{Like} {Kinases} in {Chlorophyta} {Reveals} the {Presence} of {Putative} {Cell} {Wall} {Integrity} {Sensors}},
	volume = {178},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70703},
	doi = {10.1111/ppl.70703},
	abstract = {Receptor-like kinases (RLKs) detect external and internal signals, triggering responses essential for growth and adaptation. Among internal cues, cell wall integrity (CWI) sensing plays a key role, as changes in cell wall structure activate responses critical for development and defense. While RLKs are well-studied in vascular plants, their diversity and function remain largely unknown in green algae belonging to the Chlorophyta phylum, a group that is relevant for global oxygen production and carbon cycling. Due to their varied cell wall structures, Chlorophyta offer a useful system to study the origins of CWI sensing. In this study, we used advanced bioinformatics and AI-based tools to analyze RLKs in 34 Chlorophyta species, mapping their distribution, structural features, and similarity to plant RLKs. We identified 736 putative RLKs, expanding the known repertoire in green algae. Structural analyses showed a wide range of extracellular domains, including motifs related to plant CWI sensors: domains mediating protein interactions (e.g., Leucine Rich Repeats—LRR, Plasminogen Apple Nematod e-PAN, Armadillo repeat—ARM), cell wall remodeling (e.g., glycosyl hydrolases, lyases), and mechanosensing (e.g., Leucine-Proline-X-Threonine-Glycine motifs—LPXTG, Fibronectin). This diversity suggests that mechanisms for extracellular sensing and CWI monitoring emerged early in evolution. The results provide a basis for future studies on the function of RLKs in algae and their evolutionary links to vascular plant signaling.},
	language = {en},
	number = {1},
	urldate = {2026-01-09},
	journal = {Physiologia Plantarum},
	author = {Marcianò, Demetrio and Dauphin, Bastien G. and Basso, Fabian and Funk, Christiane and Bacete, Laura},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70703},
	keywords = {Chlorella vulgaris, algae-plants evolutionary conservation, microalgae signal transduction, receptor functional divergence},
	pages = {e70703},
}

Receptor-like kinases (RLKs) detect external and internal signals, triggering responses essential for growth and adaptation. Among internal cues, cell wall integrity (CWI) sensing plays a key role, as changes in cell wall structure activate responses critical for development and defense. While RLKs are well-studied in vascular plants, their diversity and function remain largely unknown in green algae belonging to the Chlorophyta phylum, a group that is relevant for global oxygen production and carbon cycling. Due to their varied cell wall structures, Chlorophyta offer a useful system to study the origins of CWI sensing. In this study, we used advanced bioinformatics and AI-based tools to analyze RLKs in 34 Chlorophyta species, mapping their distribution, structural features, and similarity to plant RLKs. We identified 736 putative RLKs, expanding the known repertoire in green algae. Structural analyses showed a wide range of extracellular domains, including motifs related to plant CWI sensors: domains mediating protein interactions (e.g., Leucine Rich Repeats—LRR, Plasminogen Apple Nematod e-PAN, Armadillo repeat—ARM), cell wall remodeling (e.g., glycosyl hydrolases, lyases), and mechanosensing (e.g., Leucine-Proline-X-Threonine-Glycine motifs—LPXTG, Fibronectin). This diversity suggests that mechanisms for extracellular sensing and CWI monitoring emerged early in evolution. The results provide a basis for future studies on the function of RLKs in algae and their evolutionary links to vascular plant signaling.

@article{chanwala_functions_2026,
	title = {The functions of long noncoding {RNAs} in plants},
	volume = {89},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S136952662500144X},
	doi = {10.1016/j.pbi.2025.102830},
	abstract = {Noncoding RNAs are emerging as major regulators in plant development and environmental response. MicroRNAs, small RNAs, and ribosomal RNAs have established mechanisms for generation, maturation, and function. However, long noncoding RNAs (lncRNAs) currently lack a robust classification according to their function. lncRNAs are here defined as noncoding RNAs that are longer than 200 nucleotides and generally transcribed by RNA polymerase II. They often exhibit low expression and limited sequence conservation yet display tissue or stress-specific regulation. Furthermore, lncRNAs are categorized based on their location relative to nearby genes, including sense (overlapping a gene on the same strand), antisense (overlapping on the opposite strand), intronic (located within intron), intergenic (found between genes), and bidirectional (transcribed in the opposite direction from a nearby gene). Here, we summarized the last years of work in the field of lncRNA, but instead of grouping them into the biological processes they are involved in, we attempt to group them into general functions in plants. This will not be an exhaustive grouping of known functions for lncRNA, rather a list of established functions with several characterized cases.},
	urldate = {2025-12-18},
	journal = {Current Opinion in Plant Biology},
	author = {Chanwala, Jeky and Rosenkranz, Isabell and Kindgren, Peter},
	month = feb,
	year = {2026},
	pages = {102830},
}

Noncoding RNAs are emerging as major regulators in plant development and environmental response. MicroRNAs, small RNAs, and ribosomal RNAs have established mechanisms for generation, maturation, and function. However, long noncoding RNAs (lncRNAs) currently lack a robust classification according to their function. lncRNAs are here defined as noncoding RNAs that are longer than 200 nucleotides and generally transcribed by RNA polymerase II. They often exhibit low expression and limited sequence conservation yet display tissue or stress-specific regulation. Furthermore, lncRNAs are categorized based on their location relative to nearby genes, including sense (overlapping a gene on the same strand), antisense (overlapping on the opposite strand), intronic (located within intron), intergenic (found between genes), and bidirectional (transcribed in the opposite direction from a nearby gene). Here, we summarized the last years of work in the field of lncRNA, but instead of grouping them into the biological processes they are involved in, we attempt to group them into general functions in plants. This will not be an exhaustive grouping of known functions for lncRNA, rather a list of established functions with several characterized cases.

@article{vergara_isoformmapper_2026,
	title = {{IsoformMapper}: a web application for protein-level comparison of splice variants through structural community analysis},
	volume = {32},
	issn = {1355-8382, 1469-9001},
	shorttitle = {{IsoformMapper}},
	url = {http://rnajournal.cshlp.org/content/32/1/1},
	doi = {10.1261/rna.080738.125},
	abstract = {Alternative splicing (AS) enables cells to produce multiple protein isoforms from single genes, fine-tuning protein function across numerous cellular processes. However, despite its biological importance, researchers lack effective tools to compare the domain composition of AS-derived protein isoforms because such comparisons require both structural data and specialized methods. Recent advances in AI-driven protein structure prediction, particularly AlphaFold2, now make accurate structural determination of splicing isoforms accessible, enabling functional AS analysis at the protein structure level. Here, we present IsoformMapper, a web resource that analyzes AS through network community analysis of protein structures. This approach captures 3D physical interactions between protein regions often missed by traditional domain analysis, enabling structural comparisons of isoforms across any biological system. We illustrate our tool by analyzing validated human Bcl-X protein isoforms, revealing how AS creates distinct community structures with antagonistic functional roles. As a proof of concept, we apply our tool to investigate how GENOMES UNCOUPLED1 (GUN1)–dependent retrograde signaling regulates plant de-etiolation through alternative splicing in Arabidopsis. In response to light, gun1 shows alterations in spliceosome component expression, suggesting that GUN1 contributes to AS regulation of genes essential for photosynthetic establishment. The gun1 mutant displays altered splice variant ratios for PNSL2, CHAOS, and SIG5. Our tool reveals that these isoforms form distinct protein community structures, demonstrating how AS impacts protein function and validating IsoformMapper's practical value.},
	language = {en},
	number = {1},
	urldate = {2025-12-18},
	journal = {RNA},
	publisher = {Cold Spring Harbor Lab},
	author = {Vergara, Alexander and Hernández-Verdeja, Tamara and Ojeda-May, Pedro and Ramirez, Leonor and Edler, Daniel and Rosvall, Martin and Strand, Åsa},
	month = jan,
	year = {2026},
	note = {Company: Cold Spring Harbor Laboratory Press
Distributor: Cold Spring Harbor Laboratory Press
Institution: Cold Spring Harbor Laboratory Press
Label: Cold Spring Harbor Laboratory Press},
	keywords = {alternative splicing, plastid retrograde signaling},
	pages = {1--20},
}

Alternative splicing (AS) enables cells to produce multiple protein isoforms from single genes, fine-tuning protein function across numerous cellular processes. However, despite its biological importance, researchers lack effective tools to compare the domain composition of AS-derived protein isoforms because such comparisons require both structural data and specialized methods. Recent advances in AI-driven protein structure prediction, particularly AlphaFold2, now make accurate structural determination of splicing isoforms accessible, enabling functional AS analysis at the protein structure level. Here, we present IsoformMapper, a web resource that analyzes AS through network community analysis of protein structures. This approach captures 3D physical interactions between protein regions often missed by traditional domain analysis, enabling structural comparisons of isoforms across any biological system. We illustrate our tool by analyzing validated human Bcl-X protein isoforms, revealing how AS creates distinct community structures with antagonistic functional roles. As a proof of concept, we apply our tool to investigate how GENOMES UNCOUPLED1 (GUN1)–dependent retrograde signaling regulates plant de-etiolation through alternative splicing in Arabidopsis. In response to light, gun1 shows alterations in spliceosome component expression, suggesting that GUN1 contributes to AS regulation of genes essential for photosynthetic establishment. The gun1 mutant displays altered splice variant ratios for PNSL2, CHAOS, and SIG5. Our tool reveals that these isoforms form distinct protein community structures, demonstrating how AS impacts protein function and validating IsoformMapper's practical value.

@article{skalicky_illuminating_2026,
	title = {Illuminating the subcellular maze: fluorescence-activated organelle sorting in plant sciences},
	volume = {77},
	issn = {0022-0957},
	shorttitle = {Illuminating the subcellular maze},
	url = {https://doi.org/10.1093/jxb/eraf490},
	doi = {10.1093/jxb/eraf490},
	abstract = {The isolation of organelles is critical for gaining a deeper understanding of their functions in intracellular processes, not only at the cellular but also at the multicellular, organ, and organism levels. Isolating them into pure fractions allows for the reduction of sample complexity, thereby ensuring high quality downstream analysis, such as in protein localization studies. Since the mid-20th century, new methods of subcellular fractionation have constantly emerged. Conventional fractionation approaches based on (ultra)centrifugation typically focus on isolating only one type of organelle. Moreover, their resolving power may be inadequate for improving the limit of detection of downstream applications. Fluorescence-activated organelle sorting (FAOS) is a versatile and advanced technique that is gaining popularity due to its high efficiency. This efficiency refers to the ability to monitor organelle isolation live and to sort multiple organelle populations simultaneously from a single sample. This review offers an overview of the usage of FAOS and highlights its promising prospects within the realm of plant sciences. FAOS shows great potential for applications in both the functional and structural analysis of plant organelles while serving as a valuable isolation tool for downstream applications, including ‘omics’ studies.},
	number = {1},
	urldate = {2025-12-18},
	journal = {Journal of Experimental Botany},
	author = {Skalický, Vladimír and Antoniadi, Ioanna and Ljung, Karin and Novák, Ondřej},
	month = jan,
	year = {2026},
	pages = {120--133},
}

The isolation of organelles is critical for gaining a deeper understanding of their functions in intracellular processes, not only at the cellular but also at the multicellular, organ, and organism levels. Isolating them into pure fractions allows for the reduction of sample complexity, thereby ensuring high quality downstream analysis, such as in protein localization studies. Since the mid-20th century, new methods of subcellular fractionation have constantly emerged. Conventional fractionation approaches based on (ultra)centrifugation typically focus on isolating only one type of organelle. Moreover, their resolving power may be inadequate for improving the limit of detection of downstream applications. Fluorescence-activated organelle sorting (FAOS) is a versatile and advanced technique that is gaining popularity due to its high efficiency. This efficiency refers to the ability to monitor organelle isolation live and to sort multiple organelle populations simultaneously from a single sample. This review offers an overview of the usage of FAOS and highlights its promising prospects within the realm of plant sciences. FAOS shows great potential for applications in both the functional and structural analysis of plant organelles while serving as a valuable isolation tool for downstream applications, including ‘omics’ studies.

@incollection{shankar_microproteins_2026,
	address = {New York, NY},
	title = {Microproteins: {Uncovering} {Hidden} {Layers} of the {Proteome}},
	isbn = {978-1-0716-5013-4},
	shorttitle = {Microproteins},
	url = {https://doi.org/10.1007/978-1-0716-5013-4_1},
	doi = {10.1007/978-1-0716-5013-4_1},
	abstract = {Once dismissed as nonfunctional transcriptional noise, small open reading frames (sORFs) and their encoded microproteins have rapidly emerged as key players in diverse biological processes. Ranging from just a few to about 150 amino acids in length, microproteins are now recognized for their ability to modulate cellular functions, often acting as dominant-negative regulators, scaffolds, or signaling intermediates. Initially overlooked due to technical and conceptual limitations, they are increasingly being detected thanks to advances in high-resolution proteomics, ribosome profiling, and integrative bioinformatics. In this chapter, we provide a concise overview of the discovery, origins, functions, and biological significance of microproteins. We also introduce the structure of this methods book, which captures the latest experimental and computational tools used to identify, characterize, and functionally dissect microproteins across a wide range of organisms and research disciplines. This emerging field exemplifies the power of cross-disciplinary collaboration, and we hope this volume will support and inspire further research in this exciting and rapidly expanding area.},
	language = {en},
	urldate = {2025-11-21},
	booktitle = {Microproteins: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Shankar, Naveen and Wenkel, Stephan},
	editor = {Wenkel, Stephan},
	year = {2026},
	keywords = {Evolution, Microproteins, Protein structure, lncRNAs, sORFs},
	pages = {3--18},
}

Once dismissed as nonfunctional transcriptional noise, small open reading frames (sORFs) and their encoded microproteins have rapidly emerged as key players in diverse biological processes. Ranging from just a few to about 150 amino acids in length, microproteins are now recognized for their ability to modulate cellular functions, often acting as dominant-negative regulators, scaffolds, or signaling intermediates. Initially overlooked due to technical and conceptual limitations, they are increasingly being detected thanks to advances in high-resolution proteomics, ribosome profiling, and integrative bioinformatics. In this chapter, we provide a concise overview of the discovery, origins, functions, and biological significance of microproteins. We also introduce the structure of this methods book, which captures the latest experimental and computational tools used to identify, characterize, and functionally dissect microproteins across a wide range of organisms and research disciplines. This emerging field exemplifies the power of cross-disciplinary collaboration, and we hope this volume will support and inspire further research in this exciting and rapidly expanding area.

@article{munoz_lysine_2026,
	title = {Lysine potentiates insulin secretion via {AASS}-dependent catabolism and regulation of {GABA} content and signaling},
	volume = {174},
	issn = {0026-0495},
	url = {https://www.sciencedirect.com/science/article/pii/S0026049525002926},
	doi = {10.1016/j.metabol.2025.156423},
	abstract = {Lysine is an essential amino acid with insulinotropic effects in humans. In vitro, it enhances glucose-stimulated insulin secretion (GSIS) in β-cell lines and rodent islets. While lysine is thought to act via membrane depolarization similar to arginine, the role of its intracellular metabolism in β-cell function remains unexplored. Here, we show that lysine acutely potentiates GSIS and that genes encoding enzymes in the lysine degradation pathway, including AminoAdipate-Semialdehyde Synthase (AASS), a key mitochondrial enzyme catalysing the first two steps of lysine catabolism, were present in human pancreatic islets and INS1 832/13 β cells. Some of these genes including AASS, ALDH7A1, DHTKD1, and HADH, were downregulated in pancreatic islets from type 2 diabetes (T2D) versus non-diabetic (ND) donors. Silencing AASS in human islets and INS1 832/13 β cells led to reduced GSIS. Integrated transcriptomics and metabolomics revealed altered expression of GABA metabolism genes, reduced GABA content and accumulation of glutamate in Aass-KD cells. Mitochondrial TCA cycle and OXPHOS function was impaired, evidenced by decreased ATP/ADP ratio, diminished glucose-stimulated mitochondrial respiration, and elevated lactate/pyruvate ratio. Cytosolic calcium responses to glucose and GABA were also disrupted. Pharmacological analyses demonstrated that inhibition of GABA synthesis or degradation did not account for the reduced GSIS, but providing substrates and activation of GDH partially restored insulin secretion, pointing to a diminished glutamate supply as a contributing factor. Remarkably, exogenous GABA restored insulin secretion in β cells and human islets with suppressed AASS-dependent lysine catabolism, supporting a role for GABA as both a metabolic substrate and signaling effector. Together, these findings identify AASS-mediated lysine catabolism as a critical regulator of β-cell metabolic integrity, linking impaired lysine metabolism to GABA depletion, mitochondrial dysfunction, and secretory failure in T2D islets. They also underscore the nutritional importance of essential amino acids such as lysine in sustaining GSIS and glucose homeostasis, and support therapeutic strategies aimed at restoring lysine catabolism or GABA/glutamate balance to maintain β-cell function.},
	urldate = {2025-11-07},
	journal = {Metabolism},
	author = {Muñoz, Felipe and Gao, Qian and Mattanovich, Matthias and Trost, Kajetan and Hodek, Ondřej and Lindqvist, Andreas and Wierup, Nils and Fex, Malin and Moritz, Thomas and Mulder, Hindrik and Cataldo, Luis Rodrigo},
	month = jan,
	year = {2026},
	keywords = {AASS, Amino acids, GABA, GABA shunt, GDH, Glutamate, Insulin secretion, Lysine, Mitochondrial metabolism, TCA cycle, Type 2 diabetes},
	pages = {156423},
}

Lysine is an essential amino acid with insulinotropic effects in humans. In vitro, it enhances glucose-stimulated insulin secretion (GSIS) in β-cell lines and rodent islets. While lysine is thought to act via membrane depolarization similar to arginine, the role of its intracellular metabolism in β-cell function remains unexplored. Here, we show that lysine acutely potentiates GSIS and that genes encoding enzymes in the lysine degradation pathway, including AminoAdipate-Semialdehyde Synthase (AASS), a key mitochondrial enzyme catalysing the first two steps of lysine catabolism, were present in human pancreatic islets and INS1 832/13 β cells. Some of these genes including AASS, ALDH7A1, DHTKD1, and HADH, were downregulated in pancreatic islets from type 2 diabetes (T2D) versus non-diabetic (ND) donors. Silencing AASS in human islets and INS1 832/13 β cells led to reduced GSIS. Integrated transcriptomics and metabolomics revealed altered expression of GABA metabolism genes, reduced GABA content and accumulation of glutamate in Aass-KD cells. Mitochondrial TCA cycle and OXPHOS function was impaired, evidenced by decreased ATP/ADP ratio, diminished glucose-stimulated mitochondrial respiration, and elevated lactate/pyruvate ratio. Cytosolic calcium responses to glucose and GABA were also disrupted. Pharmacological analyses demonstrated that inhibition of GABA synthesis or degradation did not account for the reduced GSIS, but providing substrates and activation of GDH partially restored insulin secretion, pointing to a diminished glutamate supply as a contributing factor. Remarkably, exogenous GABA restored insulin secretion in β cells and human islets with suppressed AASS-dependent lysine catabolism, supporting a role for GABA as both a metabolic substrate and signaling effector. Together, these findings identify AASS-mediated lysine catabolism as a critical regulator of β-cell metabolic integrity, linking impaired lysine metabolism to GABA depletion, mitochondrial dysfunction, and secretory failure in T2D islets. They also underscore the nutritional importance of essential amino acids such as lysine in sustaining GSIS and glucose homeostasis, and support therapeutic strategies aimed at restoring lysine catabolism or GABA/glutamate balance to maintain β-cell function.

@article{kareem_tmo5_2025,
	title = {{TMO5} regulates {PIN1} polarity convergence and organogenesis downstream of {MONOPTEROS} in the {Arabidopsis} shoot},
	volume = {152},
	issn = {0950-1991},
	url = {https://doi.org/10.1242/dev.205255},
	doi = {10.1242/dev.205255},
	abstract = {Plants continuously produce lateral organs, such as leaves and flowers, from the shoot apical meristem (SAM). This process is guided by the accumulation of the plant hormone auxin and the polar localization of the efflux protein PIN-FORMED1 (PIN1). The transcription factor MONOPTEROS (MP) plays a crucial role in orienting PIN1 polarity, thereby facilitating auxin-driven organogenesis. In this study, we investigate genes downstream of MP that may regulate PIN1 polarity and organogenesis, discovering that the downstream vascular transcription factor TMO5 can promote PIN1 polarity convergence non-cell-autonomously and that TMO5 and its family members promote organ initiation in the SAM. By examining the role of auxin and cytokinin downstream of these genes, we provide evidence that the TMO5-like genes control PIN1 polarity and drive organogenesis by coordinating multiple hormonal signalling pathways.},
	number = {24},
	urldate = {2026-09-07},
	journal = {Development},
	author = {Kareem, Abdul and Ohno, Carolyn and Heisler, Marcus G.},
	month = dec,
	year = {2025},
	pages = {dev205255},
}

Plants continuously produce lateral organs, such as leaves and flowers, from the shoot apical meristem (SAM). This process is guided by the accumulation of the plant hormone auxin and the polar localization of the efflux protein PIN-FORMED1 (PIN1). The transcription factor MONOPTEROS (MP) plays a crucial role in orienting PIN1 polarity, thereby facilitating auxin-driven organogenesis. In this study, we investigate genes downstream of MP that may regulate PIN1 polarity and organogenesis, discovering that the downstream vascular transcription factor TMO5 can promote PIN1 polarity convergence non-cell-autonomously and that TMO5 and its family members promote organ initiation in the SAM. By examining the role of auxin and cytokinin downstream of these genes, we provide evidence that the TMO5-like genes control PIN1 polarity and drive organogenesis by coordinating multiple hormonal signalling pathways.

@article{kareem_water_2025,
	title = {Water availability positions auxin response maxima to determine plant regeneration fates},
	volume = {11},
	copyright = {2025 The Author(s)},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-025-02029-2},
	doi = {10.1038/s41477-025-02029-2},
	abstract = {Wounding and hormones serve as diverse triggers for regeneration in animals and plants. Despite important advances in understanding various types of regeneration, the mechanism by which plants determine regeneration outcomes remains largely unknown. Here we demonstrate in Arabidopsis that a trade-off between two regeneration fates, wound-induced callus and root regeneration, was driven by distinct molecular pathways related to cambium and root development, respectively. We discovered that local water availability near the wound site determined the early stages of regeneration fates in Arabidopsis and tomato, with high water triggering root fate and low water initiating callus fate. Distinct spatial distributions of auxin response maxima around the wound, shaped by water availability, were critical for determining root or callus fates. We found that, by perturbing auxin response or auxin transport dynamics, we could change regeneration outcomes. Moreover, high water availability enhanced ethylene and jasmonic acid responses, whereas treatments with these hormones could modify auxin transport dynamics or the location of auxin response maxima, thus influencing regeneration fates. We propose that, through stress hormones, water availability modifies the auxin response distribution to control regeneration outcomes, thus allowing environmental control of regeneration and providing a means to improve in vitro regeneration by changing the water potential.},
	language = {en},
	number = {7},
	urldate = {2026-09-07},
	journal = {Nature Plants},
	publisher = {Nature Publishing Group},
	author = {Kareem, Abdul and van Wüllen, Anna K. and Zhang, Ai and Walckiers, Gabriel and Fasth, Ellen and Melnyk, Charles W.},
	month = jul,
	year = {2025},
	keywords = {Cell fate, Plant regeneration},
	pages = {1367--1379},
}

Wounding and hormones serve as diverse triggers for regeneration in animals and plants. Despite important advances in understanding various types of regeneration, the mechanism by which plants determine regeneration outcomes remains largely unknown. Here we demonstrate in Arabidopsis that a trade-off between two regeneration fates, wound-induced callus and root regeneration, was driven by distinct molecular pathways related to cambium and root development, respectively. We discovered that local water availability near the wound site determined the early stages of regeneration fates in Arabidopsis and tomato, with high water triggering root fate and low water initiating callus fate. Distinct spatial distributions of auxin response maxima around the wound, shaped by water availability, were critical for determining root or callus fates. We found that, by perturbing auxin response or auxin transport dynamics, we could change regeneration outcomes. Moreover, high water availability enhanced ethylene and jasmonic acid responses, whereas treatments with these hormones could modify auxin transport dynamics or the location of auxin response maxima, thus influencing regeneration fates. We propose that, through stress hormones, water availability modifies the auxin response distribution to control regeneration outcomes, thus allowing environmental control of regeneration and providing a means to improve in vitro regeneration by changing the water potential.

@article{urbancsok_wood-specific_2025,
	title = {Wood-specific modification of glucuronoxylan can enhance growth in {Populus}},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/eraf364},
	doi = {10.1093/jxb/eraf364},
	abstract = {Xylem cells are surrounded by primary and secondary cell walls. Formation of primary walls is regulated by the cell wall integrity surveillance system, but it is unclear if the deposition of secondary walls is similarly regulated. To study this question, we introduced to aspen three different enzymes cleaving cell wall-localized xylan and we suppressed xylan synthase components either ubiquitously or specifically during secondary wall formation using Populus trichocarpa GT43B promoter. When xylan was ubiquitously altered, 95\% of lines showed reduced growth, whereas when it was altered during secondary wall deposition, 30\% of lines grew better with the rest having no growth impairment, suggesting opposite effects of primary and secondary wall disturbances. To detect mechanism of growth stimulation by disturbed deposition of secondary wall, we analyzed changes in wood quality traits, chemistry, transcriptomics, metabolomics and hormonomics in transgenic lines. We found increased tension wood production, reduced S- and H-lignin, and changes in several metabolites in common in these lines. Remorin REM1.3 and NRL2 (NPH3 family) transcripts increased and changes in jasmonates, ABA and SA occurred in secondary wall-forming xylem suggesting their involvement in secondary wall integrity surveyance and signaling. The data indicate that a unique program mediates responses to secondary wall impairment that induces growth.},
	urldate = {2025-08-29},
	journal = {Journal of Experimental Botany},
	author = {Urbancsok, János and Donev, Evgeniy N and Derba-Maceluch, Marta and Sivan, Pramod and Barbut, Félix R and Mitra, Madhusree and Yassin, Zakiya and Cermanová, Kateřina and Šimura, Jan and Karady, Michal and Scheepers, Gerhard and Mellerowicz, Ewa J},
	month = aug,
	year = {2025},
	pages = {eraf364},
}

Xylem cells are surrounded by primary and secondary cell walls. Formation of primary walls is regulated by the cell wall integrity surveillance system, but it is unclear if the deposition of secondary walls is similarly regulated. To study this question, we introduced to aspen three different enzymes cleaving cell wall-localized xylan and we suppressed xylan synthase components either ubiquitously or specifically during secondary wall formation using Populus trichocarpa GT43B promoter. When xylan was ubiquitously altered, 95% of lines showed reduced growth, whereas when it was altered during secondary wall deposition, 30% of lines grew better with the rest having no growth impairment, suggesting opposite effects of primary and secondary wall disturbances. To detect mechanism of growth stimulation by disturbed deposition of secondary wall, we analyzed changes in wood quality traits, chemistry, transcriptomics, metabolomics and hormonomics in transgenic lines. We found increased tension wood production, reduced S- and H-lignin, and changes in several metabolites in common in these lines. Remorin REM1.3 and NRL2 (NPH3 family) transcripts increased and changes in jasmonates, ABA and SA occurred in secondary wall-forming xylem suggesting their involvement in secondary wall integrity surveyance and signaling. The data indicate that a unique program mediates responses to secondary wall impairment that induces growth.

@article{han_easyomics_2025,
	title = {{EasyOmics}: {A} graphical interface for population-scale omics data association, integration, and visualization},
	volume = {6},
	issn = {2590-3462},
	shorttitle = {{EasyOmics}},
	url = {https://www.sciencedirect.com/science/article/pii/S2590346225000550},
	doi = {10.1016/j.xplc.2025.101293},
	abstract = {The rapid growth of population-scale whole-genome resequencing, RNA sequencing, bisulfite sequencing, and metabolomic and proteomic profiling has led quantitative genetics into the era of big omics data. Association analyses of omics data, such as genome-, transcriptome-, proteome-, and methylome-wide association studies, along with integrative analyses of multiple omics datasets, require various bioinformatics tools, which rely on advanced programming skills and command-line interfaces and thus pose challenges for wet-lab biologists. Here, we present EasyOmics, a stand-alone R Shiny application with a user-friendly interface that enables wet-lab biologists to perform population-scale omics data association, integration, and visualization. The toolkit incorporates multiple functions designed to meet the increasing demand for population-scale omics data analyses, including data quality control, heritability estimation, genome-wide association analysis, conditional association analysis, omics quantitative trait locus mapping, omics-wide association analysis, omics data integration, and visualization. A wide range of publication-quality graphs can be prepared in EasyOmics by pointing and clicking. EasyOmics is a platform-independent software that can be run under all operating systems, with a docker container for quick installation. It is freely available to non-commercial users at Docker Hub https://hub.docker.com/r/yuhan2000/easyomics.},
	number = {5},
	urldate = {2026-05-19},
	journal = {Plant Communications},
	author = {Han, Yu and Du, Qiao and Dai, Yifei and Gu, Shaobo and Lei, Mengyu and Liu, Wei and Zhang, Wenjia and Zhu, Mingjia and Feng, Landi and Si, Huan and Liu, Jianquan and Zan, Yanjun},
	month = may,
	year = {2025},
	keywords = {association analysis, bioinformatics, data visualization, omics data},
	pages = {101293},
}

The rapid growth of population-scale whole-genome resequencing, RNA sequencing, bisulfite sequencing, and metabolomic and proteomic profiling has led quantitative genetics into the era of big omics data. Association analyses of omics data, such as genome-, transcriptome-, proteome-, and methylome-wide association studies, along with integrative analyses of multiple omics datasets, require various bioinformatics tools, which rely on advanced programming skills and command-line interfaces and thus pose challenges for wet-lab biologists. Here, we present EasyOmics, a stand-alone R Shiny application with a user-friendly interface that enables wet-lab biologists to perform population-scale omics data association, integration, and visualization. The toolkit incorporates multiple functions designed to meet the increasing demand for population-scale omics data analyses, including data quality control, heritability estimation, genome-wide association analysis, conditional association analysis, omics quantitative trait locus mapping, omics-wide association analysis, omics data integration, and visualization. A wide range of publication-quality graphs can be prepared in EasyOmics by pointing and clicking. EasyOmics is a platform-independent software that can be run under all operating systems, with a docker container for quick installation. It is freely available to non-commercial users at Docker Hub https://hub.docker.com/r/yuhan2000/easyomics.

@article{wang_identification_2025,
	title = {Identification, {Characterization}, {Expression} {Profiling} and {Functional} {Analysis} of {Tobacco} {CalS} {Gene} {Family}},
	volume = {15},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2073-4395},
	url = {https://www.mdpi.com/2073-4395/15/4/884},
	doi = {10.3390/agronomy15040884},
	abstract = {Callose plays an important role in plant development and in response to a wide range of biotic and abiotic stresses. However, the systematic identification of callose synthase (CalS), the major enzyme for callose biosynthesis, has been delayed in crops, especially in Solanaceae. In the current research, 18 CalS genes (NtCalS1–NtCalS18) were identified in Nicotiana tabacum and classified into four subfamilies. A comprehensive analysis of their physicochemical properties, gene structure, and evolutionary history highlighted their evolutionary conservation. We also identified a number of NtCalSs that responded to the infection with Phytophthora nicotianae and Ralstonia solanacearum, as well as to drought and cold treatments, by analyzing RNA-seq data. NtCalS1 and NtCalS12, a highly homologous gene pair, were selected to create mutants using the CRISPR-Cas9 technology for their drastic response to Phytophthora nicotianae infection as well as the strong expression levels in roots. The mutants with the simultaneous knockout of NtCalS1 and NtCalS12, compared with the control plants, displayed more resistance to tobacco black shank caused by Phytophthora nicotianae. Furthermore, the real-time quantitative PCR (qRT-PCR) assay showed that the knockout of NtCalS1 and NtCalS12 activated the signaling pathways mediated by plant hormones salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) before and after the infection of Phytophthora nicotianae and thus may have contributed to tobacco immunity against black shank. These findings contribute valuable information for further understanding the roles of CalS genes in tobacco stress responses and provide alternative genes for resistance improvement.},
	language = {en},
	number = {4},
	urldate = {2026-05-19},
	journal = {Agronomy},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Wang, Hong and Meng, He and Qi, Xiaohan and Pan, Yi and Ji, Bailu and Wen, Liuying and Zan, Yanjun and Si, Huan and Wang, Yuanying and Liu, Dan and Yang, Aiguo and Liu, Zhengwen and Cheng, Lirui},
	month = apr,
	year = {2025},
	keywords = {\textit{CalS} gene family, \textit{Nicotiana tabacum}, callose synthase, expression analysis, gene editing, stress response},
	pages = {884},
}

Callose plays an important role in plant development and in response to a wide range of biotic and abiotic stresses. However, the systematic identification of callose synthase (CalS), the major enzyme for callose biosynthesis, has been delayed in crops, especially in Solanaceae. In the current research, 18 CalS genes (NtCalS1–NtCalS18) were identified in Nicotiana tabacum and classified into four subfamilies. A comprehensive analysis of their physicochemical properties, gene structure, and evolutionary history highlighted their evolutionary conservation. We also identified a number of NtCalSs that responded to the infection with Phytophthora nicotianae and Ralstonia solanacearum, as well as to drought and cold treatments, by analyzing RNA-seq data. NtCalS1 and NtCalS12, a highly homologous gene pair, were selected to create mutants using the CRISPR-Cas9 technology for their drastic response to Phytophthora nicotianae infection as well as the strong expression levels in roots. The mutants with the simultaneous knockout of NtCalS1 and NtCalS12, compared with the control plants, displayed more resistance to tobacco black shank caused by Phytophthora nicotianae. Furthermore, the real-time quantitative PCR (qRT-PCR) assay showed that the knockout of NtCalS1 and NtCalS12 activated the signaling pathways mediated by plant hormones salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) before and after the infection of Phytophthora nicotianae and thus may have contributed to tobacco immunity against black shank. These findings contribute valuable information for further understanding the roles of CalS genes in tobacco stress responses and provide alternative genes for resistance improvement.

@article{si_development_2025,
	title = {Development of two sets of tobacco chromosome segment substitution lines and {QTL} mapping for agronomic and disease resistance traits},
	volume = {226},
	issn = {0926-6690},
	url = {https://www.sciencedirect.com/science/article/pii/S0926669025001682},
	doi = {10.1016/j.indcrop.2025.120622},
	abstract = {Chromosome segment substitution lines (CSSLs) represent a powerful genetic resource for quantitative trait loci (QTL) mapping, gene cloning and breeding. Here, we developed two sets of CSSLs consisting of 245 and 128 unique lines, which derived from OX2028 × K326 and Samsun × K326 crosses. On average, each CSSL carried 1.8 and 2.9 introgressed segments in the two sets, with an average physical segment length of approximately 34.3 Mb and 27.6 Mb, respectively. These CSSLs covered ∼97 \% and ∼77 \% of the genomes of OX2028 and Samsun, respectively. By performing QTL mapping based on best linear unbiased prediction (BLUP) of phenotypic traits, we identified a total of 64 QTLs associated with six agronomic traits and three disease resistance traits. These QTLs explained phenotypic variation ranging from 1.5 \% to 50.8 \%. Among them, 22 QTLs detected in OX2028 derived population and 42 detected in Samsun derived CSSLs. Notably, a new QTL for tobacco leaf width, qLW1–1 was narrowed down to an 8-Mb interval on chromosome 1, and NtZY01G00114, encoding an auxin-response factor protein, was considered as the candidate gene. Our study provides valuable genetic resources for tobacco breeding and enhances our understanding of the genetic basis of complex traits in tobacco.},
	urldate = {2026-05-19},
	journal = {Industrial Crops and Products},
	author = {Si, Huan and Wang, Dong and Zan, Yanjun and Liu, Wanfeng and Pu, Wenxuan and Li, Xiaoxu and Mao, Hui and Yang, Xingyou and Song, Shiyang and Wang, Yongda and Jiang, Caihong and Pan, Xuhao and Xiao, Zhiliang and Wen, Liuying and Sun, Yiwen and Liu, Dan and Cheng, Lirui and Yang, Aiguo},
	month = apr,
	year = {2025},
	keywords = {Agronomic traits, CSSLs, Disease resistance, QTL mapping, Tobacco},
	pages = {120622},
}

Chromosome segment substitution lines (CSSLs) represent a powerful genetic resource for quantitative trait loci (QTL) mapping, gene cloning and breeding. Here, we developed two sets of CSSLs consisting of 245 and 128 unique lines, which derived from OX2028 × K326 and Samsun × K326 crosses. On average, each CSSL carried 1.8 and 2.9 introgressed segments in the two sets, with an average physical segment length of approximately 34.3 Mb and 27.6 Mb, respectively. These CSSLs covered ∼97 % and ∼77 % of the genomes of OX2028 and Samsun, respectively. By performing QTL mapping based on best linear unbiased prediction (BLUP) of phenotypic traits, we identified a total of 64 QTLs associated with six agronomic traits and three disease resistance traits. These QTLs explained phenotypic variation ranging from 1.5 % to 50.8 %. Among them, 22 QTLs detected in OX2028 derived population and 42 detected in Samsun derived CSSLs. Notably, a new QTL for tobacco leaf width, qLW1–1 was narrowed down to an 8-Mb interval on chromosome 1, and NtZY01G00114, encoding an auxin-response factor protein, was considered as the candidate gene. Our study provides valuable genetic resources for tobacco breeding and enhances our understanding of the genetic basis of complex traits in tobacco.

@article{liu_origin_2025,
	title = {Origin and de novo domestication of sweet orange},
	volume = {57},
	copyright = {2025 The Author(s)},
	issn = {1546-1718},
	url = {https://www.nature.com/articles/s41588-025-02122-4},
	doi = {10.1038/s41588-025-02122-4},
	abstract = {Sweet orange is cultivated worldwide but suffers from various devastating diseases because of its monogenetic background. The elucidation of the origin of a crop facilitates the domestication of new crops that may better cope with new challenges. Here we collected and sequenced 226 citrus accessions and assembled telomere-to-telomere phased diploid genomes of sweet orange and sour orange. On the basis of a high-resolution haplotype-resolved genome analysis, we inferred that sweet orange originated from a sour orange × mandarin cross and confirmed this model using artificial hybridization experiments. We identified defense-related metabolites that potently inhibited the growth of multiple industrially important pathogenic bacteria. We introduced diversity to sweet orange, which showed wide segregation in fruit flavor and disease resistance and produced canker-resistant sweet orange by selecting defense-related metabolites. Our findings elucidate the origin of sweet orange and de novo domesticated disease-resistant sweet oranges, illuminating a strategy for the rapid domestication of perennial crops.},
	language = {en},
	number = {3},
	urldate = {2026-05-19},
	journal = {Nature Genetics},
	publisher = {Nature Publishing Group},
	author = {Liu, Shengjun and Xu, Yuantao and Yang, Kun and Huang, Yue and Lu, Zhihao and Chen, Shulin and Gao, Xiang and Xiao, Gongao and Chen, Peng and Zeng, Xiuli and Wang, Lun and Zheng, Weikang and Liu, Zishuang and Liao, Guanglian and He, Fa and Liu, Junjie and Wan, Pengfei and Ding, Fang and Ye, Junli and Jiao, Wenbiao and Chai, Lijun and Pan, Zhiyong and Zhang, Fei and Lin, Zongcheng and Zan, Yanjun and Guo, Wenwu and Larkin, Robert M. and Xie, Zongzhou and Wang, Xia and Deng, Xiuxin and Xu, Qiang},
	month = mar,
	year = {2025},
	keywords = {Plant breeding, Plant genetics, Plant molecular biology},
	pages = {754--762},
}

Sweet orange is cultivated worldwide but suffers from various devastating diseases because of its monogenetic background. The elucidation of the origin of a crop facilitates the domestication of new crops that may better cope with new challenges. Here we collected and sequenced 226 citrus accessions and assembled telomere-to-telomere phased diploid genomes of sweet orange and sour orange. On the basis of a high-resolution haplotype-resolved genome analysis, we inferred that sweet orange originated from a sour orange × mandarin cross and confirmed this model using artificial hybridization experiments. We identified defense-related metabolites that potently inhibited the growth of multiple industrially important pathogenic bacteria. We introduced diversity to sweet orange, which showed wide segregation in fruit flavor and disease resistance and produced canker-resistant sweet orange by selecting defense-related metabolites. Our findings elucidate the origin of sweet orange and de novo domesticated disease-resistant sweet oranges, illuminating a strategy for the rapid domestication of perennial crops.

@article{zan_genome_2025,
	title = {The genome and {GeneBank} genomics of allotetraploid {Nicotiana} tabacum provide insights into genome evolution and complex trait regulation},
	volume = {57},
	copyright = {2025 The Author(s)},
	issn = {1546-1718},
	url = {https://www.nature.com/articles/s41588-025-02126-0},
	doi = {10.1038/s41588-025-02126-0},
	abstract = {Nicotiana tabacum is an allotetraploid hybrid of Nicotiana sylvestris and Nicotiana tomentosiformis and a model organism in genetics. However, features of subgenome evolution, expression coordination, genetic diversity and complex traits regulation of N. tabacum remain unresolved. Here we present chromosome-scale assemblies for all three species, and genotype and phenotypic data for 5,196 N. tabacum germplasms. Chromosome rearrangements and epigenetic modifications are associated with genome evolution and expression coordination following polyploidization. Two subgenomes and genes biased toward one subgenome contributed unevenly to complex trait variation. Using 178 marker–trait associations, a reference genotype-to-phenotype map was built for 39 morphological, developmental and disease resistance traits, and a novel gene regulating leaf width was validated. Signatures of positive and polygenic selection during the process of selective breeding were detected. Our study provides insights into genome evolution, complex traits regulation in allotetraploid N. tabacum and the use of GeneBank-scale resources for advancing genetic and genomic research.},
	language = {en},
	number = {4},
	urldate = {2026-05-19},
	journal = {Nature Genetics},
	publisher = {Nature Publishing Group},
	author = {Zan, Yanjun and Chen, Shuai and Ren, Min and Liu, Guoxiang and Liu, Yutong and Han, Yu and Dong, Yang and Zhang, Yao and Si, Huan and Liu, Zhengwen and Liu, Dan and Zhang, Xingwei and Tong, Ying and Li, Yuan and Jiang, Caihong and Wen, Liuying and Xiao, Zhiliang and Sun, Yangyang and Geng, Ruimei and Ji, Yan and Feng, Quanfu and Wang, Yuanying and Ye, Guoyou and Fang, Lingzhao and Chen, Yong and Cheng, Lirui and Yang, Aiguo},
	month = apr,
	year = {2025},
	keywords = {Plant genetics, Plant sciences},
	pages = {986--996},
}

Nicotiana tabacum is an allotetraploid hybrid of Nicotiana sylvestris and Nicotiana tomentosiformis and a model organism in genetics. However, features of subgenome evolution, expression coordination, genetic diversity and complex traits regulation of N. tabacum remain unresolved. Here we present chromosome-scale assemblies for all three species, and genotype and phenotypic data for 5,196 N. tabacum germplasms. Chromosome rearrangements and epigenetic modifications are associated with genome evolution and expression coordination following polyploidization. Two subgenomes and genes biased toward one subgenome contributed unevenly to complex trait variation. Using 178 marker–trait associations, a reference genotype-to-phenotype map was built for 39 morphological, developmental and disease resistance traits, and a novel gene regulating leaf width was validated. Signatures of positive and polygenic selection during the process of selective breeding were detected. Our study provides insights into genome evolution, complex traits regulation in allotetraploid N. tabacum and the use of GeneBank-scale resources for advancing genetic and genomic research.

@article{han_divergent_2025,
	title = {Divergent {Flowering} {Time} {Responses} to {Increasing} {Temperatures} {Are} {Associated} {With} {Transcriptome} {Plasticity} and {Epigenetic} {Modification} {Differences} at {FLC} {Promoter} {Region} of {Arabidopsis} thaliana},
	volume = {34},
	copyright = {© 2024 John Wiley \& Sons Ltd.},
	issn = {1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.17544},
	doi = {10.1111/mec.17544},
	abstract = {Understanding the genetic, and transcriptomic changes that drive the phenotypic plasticity of fitness traits is a central question in evolutionary biology. In this study, we utilised 152 natural Swedish Arabidopsis thaliana accessions with re-sequenced genomes, transcriptomes and methylomes and measured flowering times (FTs) under two temperature conditions (10°C and 16°C) to address this question. We revealed that the northern accessions exhibited advanced flowering in response to decreased temperature, whereas the southern accessions delayed their flowering, indicating a divergent flowering response. This contrast in flowering responses was associated with the isothermality of their native ranges, which potentially enables the northern accessions to complete their life cycle more rapidly in years with shorter growth seasons. At the transcriptome level, we observed extensive rewiring of gene co-expression networks, with the expression of 25 core genes being associated with the mean FT and its plastic variation. Notably, variations in FLC expression sensitivity between northern and southern accessions were found to be associated with the divergence FT response. Further analysis suggests that FLC expression sensitivity is associated with differences in CG, CHG and CHH methylation at the promoter region. Overall, our study revealed the association between transcriptome plasticity and flowering time plasticity among different accessions, providing evidence for its relevance in ecological adaptation. These findings offer deeper insights into the genetics of rapid responses to environmental changes and ecological adaptation.},
	language = {en},
	number = {15},
	urldate = {2026-05-19},
	journal = {Molecular Ecology},
	author = {Han, Yu and Liu, Li and Lei, Mengyu and Liu, Wei and Si, Huan and Ji, Yan and Du, Qiao and Zhu, Mingjia and Zhang, Wenjia and Dai, Yifei and Liu, Jianquan and Zan, Yanjun},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.17544},
	keywords = {ecological adaptation, flowering time, gene co-expression network, plasticity},
	pages = {e17544},
}

Understanding the genetic, and transcriptomic changes that drive the phenotypic plasticity of fitness traits is a central question in evolutionary biology. In this study, we utilised 152 natural Swedish Arabidopsis thaliana accessions with re-sequenced genomes, transcriptomes and methylomes and measured flowering times (FTs) under two temperature conditions (10°C and 16°C) to address this question. We revealed that the northern accessions exhibited advanced flowering in response to decreased temperature, whereas the southern accessions delayed their flowering, indicating a divergent flowering response. This contrast in flowering responses was associated with the isothermality of their native ranges, which potentially enables the northern accessions to complete their life cycle more rapidly in years with shorter growth seasons. At the transcriptome level, we observed extensive rewiring of gene co-expression networks, with the expression of 25 core genes being associated with the mean FT and its plastic variation. Notably, variations in FLC expression sensitivity between northern and southern accessions were found to be associated with the divergence FT response. Further analysis suggests that FLC expression sensitivity is associated with differences in CG, CHG and CHH methylation at the promoter region. Overall, our study revealed the association between transcriptome plasticity and flowering time plasticity among different accessions, providing evidence for its relevance in ecological adaptation. These findings offer deeper insights into the genetics of rapid responses to environmental changes and ecological adaptation.

@article{aguilar-trigueros_connecting_2025,
	title = {Connecting the dots: {Network} structure as a functional trait in arbuscular mycorrhizal fungi},
	issn = {2572-2611},
	shorttitle = {Connecting the dots},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ppp3.70058},
	doi = {10.1002/ppp3.70058},
	abstract = {Societal Impact Statement Soil health and sustainable land management are critical to addressing global challenges such as food security, climate resilience, and biodiversity loss. Arbuscular mycorrhizal (AM) fungi form underground networks that enhance plant nutrient uptake and improve soil structure, yet their functional diversity remains poorly understood, limiting their application in agriculture and ecosystem restoration. By proposing potential fungal transport strategies, we provide a framework for predicting AM fungal contributions across different environments. This knowledge can inform agricultural practices, conservation strategies, and land-use policies, ultimately supporting efforts to harness beneficial microbes for resilient and sustainable ecosystems. Summary Arbuscular mycorrhizal (AM) fungi construct extensive mycelial networks in soil, serving as critical mediators of plant–soil interactions and nutrient exchange. However, the ability to harness AM fungal diversity for ecosystem management remains constrained by gaps in functional understanding. Trait-based frameworks offer a promising approach to overcoming these limitations, yet their development has been hindered by methodological challenges and the complexity of AM fungal symbioses. Here, we propose that mycelial network connectivity, a structural trait reflecting the organization of fungal hyphae for nutrient transport, provides a mechanistic basis for distinguishing AM fungal functional groups. Drawing on network theory, we identify two key trade-offs that shape AM fungal transport strategies: (1) a trade-off between transport efficiency and resilience to structural disruption and (2) a positive correlation between network heterogeneity and soil heterogeneity. Based on these relationships, we classify AM fungi into potential functional groups and argue that these connectivity-based classifications provide a predictive framework for understanding AM fungal ecological strategies across environmental gradients, with implications for sustainable land management. Future research should integrate experimental measurements of fungal carbon allocation, network plasticity, and species-specific responses to environmental change to refine this framework further. By linking mycelial architecture to functional diversity, this approach enhances our ability to predict AM fungal contributions to ecosystem processes and optimize their use in applied contexts.},
	language = {en},
	urldate = {2026-03-17},
	journal = {PLANTS, PEOPLE, PLANET},
	author = {Aguilar-Trigueros, Carlos A. and Frew, Adam},
	month = jun,
	year = {2025},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1002/ppp3.70058},
	pages = {1--10},
}

Societal Impact Statement Soil health and sustainable land management are critical to addressing global challenges such as food security, climate resilience, and biodiversity loss. Arbuscular mycorrhizal (AM) fungi form underground networks that enhance plant nutrient uptake and improve soil structure, yet their functional diversity remains poorly understood, limiting their application in agriculture and ecosystem restoration. By proposing potential fungal transport strategies, we provide a framework for predicting AM fungal contributions across different environments. This knowledge can inform agricultural practices, conservation strategies, and land-use policies, ultimately supporting efforts to harness beneficial microbes for resilient and sustainable ecosystems. Summary Arbuscular mycorrhizal (AM) fungi construct extensive mycelial networks in soil, serving as critical mediators of plant–soil interactions and nutrient exchange. However, the ability to harness AM fungal diversity for ecosystem management remains constrained by gaps in functional understanding. Trait-based frameworks offer a promising approach to overcoming these limitations, yet their development has been hindered by methodological challenges and the complexity of AM fungal symbioses. Here, we propose that mycelial network connectivity, a structural trait reflecting the organization of fungal hyphae for nutrient transport, provides a mechanistic basis for distinguishing AM fungal functional groups. Drawing on network theory, we identify two key trade-offs that shape AM fungal transport strategies: (1) a trade-off between transport efficiency and resilience to structural disruption and (2) a positive correlation between network heterogeneity and soil heterogeneity. Based on these relationships, we classify AM fungi into potential functional groups and argue that these connectivity-based classifications provide a predictive framework for understanding AM fungal ecological strategies across environmental gradients, with implications for sustainable land management. Future research should integrate experimental measurements of fungal carbon allocation, network plasticity, and species-specific responses to environmental change to refine this framework further. By linking mycelial architecture to functional diversity, this approach enhances our ability to predict AM fungal contributions to ecosystem processes and optimize their use in applied contexts.

@article{frew_what_2025,
	title = {What does colonisation tell us? {Revisiting} the functional outcomes of root colonisation by arbuscular mycorrhizal fungi},
	volume = {247},
	issn = {0028-646X},
	shorttitle = {What does colonisation tell us?},
	url = {https://pmc.ncbi.nlm.nih.gov/articles/PMC12267904/},
	doi = {10.1111/nph.70284},
	number = {4},
	urldate = {2026-03-18},
	journal = {The New Phytologist},
	author = {Frew, Adam},
	month = aug,
	year = {2025},
	pages = {1572--1578},
}

@article{liu_mycorrhizae-associated_2025,
	title = {Mycorrhizae-associated belowground economics mediate microbial life history strategy in temperate forests},
	volume = {463},
	issn = {0016-7061},
	url = {https://www.sciencedirect.com/science/article/pii/S001670612500415X},
	doi = {10.1016/j.geoderma.2025.117574},
	abstract = {The co-evolution of plant roots, mycorrhizal fungi, and soil saprotrophic microorganisms shapes underground resource acquisition strategies of plants. However, the knowledge of how mycorrhizal associations affect plant belowground economics strategy and rhizosphere microbial community is not well established. Here we sampled leaves, roots and rhizosphere soils from five arbuscular mycorrhizal (AM) and seven ectomycorrhizal (EcM) tree species in a mixed temperate forest to explore the impacts of mycorrhizal associations on plant above- and belowground functional traits and rhizosphere microbial community composition. Mycorrhizal associations regulate soil fungal community composition, root functional traits, and economics space, but do not impact leaf traits. AM trees adopt a more aggressive strategy for nutrient acquirement with higher specific root length and root nitrogen concentration and support greater abundance of fungal community with nutrient acquirement strategy compared to EcM trees. The mycorrhizal-associated belowground economics spectrum, which ranges from conservative to aggressive nutrient acquisition strategies, was positively correlated with the relative abundance of the aggressive-strategy saprotrophic fungi (Ascomycota), while the conservative-strategy fungi (Rozellomycota) were associated with the opposite end of the spectrum. Our study highlights the importance of the mycorrhizal-associated belowground economics spectrum in mediating microbial functional groups and ecological strategies. Integrating mycorrhizal-mediated interactions into root economics framework could improve predictions of nutrient cycling and ecosystem functioning in temperate forests.},
	urldate = {2026-03-17},
	journal = {Geoderma},
	author = {Liu, Ruiqiang and Du, Wenya and Frew, Adam and He, Yanghui and Guo, Liqi and Yan, Xiaolei and Zhou, Guiyao and Zhai, Kaiyan and Xiang, Guangzhen and Zhu, Yimin and Zhou, Xuhui},
	month = nov,
	year = {2025},
	keywords = {Microbial strategy, Mycorrhizal type, Root economics, Root traits, Soil nutrient cycles},
	pages = {117574},
}

The co-evolution of plant roots, mycorrhizal fungi, and soil saprotrophic microorganisms shapes underground resource acquisition strategies of plants. However, the knowledge of how mycorrhizal associations affect plant belowground economics strategy and rhizosphere microbial community is not well established. Here we sampled leaves, roots and rhizosphere soils from five arbuscular mycorrhizal (AM) and seven ectomycorrhizal (EcM) tree species in a mixed temperate forest to explore the impacts of mycorrhizal associations on plant above- and belowground functional traits and rhizosphere microbial community composition. Mycorrhizal associations regulate soil fungal community composition, root functional traits, and economics space, but do not impact leaf traits. AM trees adopt a more aggressive strategy for nutrient acquirement with higher specific root length and root nitrogen concentration and support greater abundance of fungal community with nutrient acquirement strategy compared to EcM trees. The mycorrhizal-associated belowground economics spectrum, which ranges from conservative to aggressive nutrient acquisition strategies, was positively correlated with the relative abundance of the aggressive-strategy saprotrophic fungi (Ascomycota), while the conservative-strategy fungi (Rozellomycota) were associated with the opposite end of the spectrum. Our study highlights the importance of the mycorrhizal-associated belowground economics spectrum in mediating microbial functional groups and ecological strategies. Integrating mycorrhizal-mediated interactions into root economics framework could improve predictions of nutrient cycling and ecosystem functioning in temperate forests.

@article{zheng_tree_2025,
	title = {Tree functional group mediates the effects of nutrient addition on soil nutrients and fungal communities beneath decomposing wood},
	volume = {510},
	issn = {0032-079X, 1573-5036},
	url = {https://link.springer.com/10.1007/s11104-024-06959-2},
	doi = {10.1007/s11104-024-06959-2},
	language = {en},
	number = {1-2},
	urldate = {2026-03-17},
	journal = {Plant and Soil},
	author = {Zheng, Yuxiong and Hu, Zhenhong and Jian, Jinshi and Chen, Ji and Osborne, Brooke B. and Zhou, Guiyao and Xu, Qian and Zheng, Zemei and Ma, Longlong and He, Xian and Bell, Stephen M. and Frew, Adam},
	month = may,
	year = {2025},
	keywords = {Carbon cycling, Nutrient addition experiment, Saprotrophic fungi, Soil nutrient concentrations, Tree functional group, Wood decomposition},
	pages = {797--813},
}

@article{frew_causal_2025,
	title = {Causal determinism by plant host identity in arbuscular mycorrhizal fungal community assembly},
	volume = {39},
	issn = {1365-2435},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2435.14715},
	doi = {10.1111/1365-2435.14715},
	abstract = {An assumption in ecology is that plant identity plays a central role in the assembly of root-colonising arbuscular mycorrhizal (AM) fungal communities. While numerous correlational studies support this notion, with evidence of host selectivity among fungal taxa and host-specific responses to different AM fungi, empirical demonstrations of host-driven AM fungal community assembly remain surprisingly limited. We conducted a factorial experiment growing two globally significant crop species, wheat (Triticum aestivum) and sorghum (Sorghum bicolor), with a common pool of AM fungal species, or without AM fungi. We hypothesised strong differences in AM fungal community structure between the two species driven by strong habitat filtering. Plants were harvested at two time points in which we analysed the community structure of AM fungi in the roots, the phylogenetic diversity, and interactions with plant physiological responses. As we expected, there were distinct trajectories in both the composition and phylogenetic diversity of AM fungal communities between the two host plants through time. However, the effect of habitat filtering during community assembly differed between the two species. In sorghum roots, AM fungal communities exhibited increased richness and became more phylogenetically clustered over time. This shift suggests that community assembly was primarily driven by habitat filtering, or selectivity, imposed by the host which was accompanied by significant increases in plant mycorrhizal growth (from 11.83\% to 43.67\%) and phosphorus responses (from −0.6\% to 43.3\%). In contrast, AM fungal communities in wheat displayed little change in diversity, remained phylogenetically unstructured, and provided minimal benefits to the host, indicating a more stochastic assembly process with a stronger influence of competitive interactions. As the field looks to understand what determines the distribution of AM fungi and their community composition while simultaneously seeking to utilise AM fungi for ecosystem benefits, it is important to know the extent to which host identity can influence fungal assembly within plant roots. Our results provide empirical support of host-determinism in AM fungal community assembly and suggest that this determinism is associated with the growth and nutrient benefits provided by the symbiosis to plants. Read the free Plain Language Summary for this article on the Journal blog.},
	language = {en},
	number = {2},
	urldate = {2026-03-17},
	journal = {Functional Ecology},
	author = {Frew, Adam and Zheng, Yuxiong and Wang, Zhenyu and Fu, Yanrong and Aguilar-Trigueros, Carlos A.},
	year = {2025},
	note = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2435.14715},
	keywords = {arbuscular mycorrhiza, environmental filtering, fungal community, host selection, plant roots, symbiosis},
	pages = {390--402},
}

An assumption in ecology is that plant identity plays a central role in the assembly of root-colonising arbuscular mycorrhizal (AM) fungal communities. While numerous correlational studies support this notion, with evidence of host selectivity among fungal taxa and host-specific responses to different AM fungi, empirical demonstrations of host-driven AM fungal community assembly remain surprisingly limited. We conducted a factorial experiment growing two globally significant crop species, wheat (Triticum aestivum) and sorghum (Sorghum bicolor), with a common pool of AM fungal species, or without AM fungi. We hypothesised strong differences in AM fungal community structure between the two species driven by strong habitat filtering. Plants were harvested at two time points in which we analysed the community structure of AM fungi in the roots, the phylogenetic diversity, and interactions with plant physiological responses. As we expected, there were distinct trajectories in both the composition and phylogenetic diversity of AM fungal communities between the two host plants through time. However, the effect of habitat filtering during community assembly differed between the two species. In sorghum roots, AM fungal communities exhibited increased richness and became more phylogenetically clustered over time. This shift suggests that community assembly was primarily driven by habitat filtering, or selectivity, imposed by the host which was accompanied by significant increases in plant mycorrhizal growth (from 11.83% to 43.67%) and phosphorus responses (from −0.6% to 43.3%). In contrast, AM fungal communities in wheat displayed little change in diversity, remained phylogenetically unstructured, and provided minimal benefits to the host, indicating a more stochastic assembly process with a stronger influence of competitive interactions. As the field looks to understand what determines the distribution of AM fungi and their community composition while simultaneously seeking to utilise AM fungi for ecosystem benefits, it is important to know the extent to which host identity can influence fungal assembly within plant roots. Our results provide empirical support of host-determinism in AM fungal community assembly and suggest that this determinism is associated with the growth and nutrient benefits provided by the symbiosis to plants. Read the free Plain Language Summary for this article on the Journal blog.

@article{xiao_microplastics_2025,
	title = {Microplastics aggravate zinc deficiency-induced inhibition of physiological-biochemical characteristics in apple rootstock \textit{{Malus} hupehensis} ({Pamp}.) {Rehd} seedlings},
	volume = {11},
	issn = {2405-6650},
	url = {https://www.sciencedirect.com/science/article/pii/S2405665024001227},
	doi = {10.1016/j.emcon.2024.100421},
	abstract = {Both microplastic (MP) pollution and zinc (Zn) deficiency have adverse effects on terrestrial plants. However, the combined effect of MPs and Zn deficiency on plant physiology remains unexplored. In this study, a pot-culture experiment and 13C stable isotope tracing technology were employed to investigate the combined effects of MPs and Zn deficiency on the growth, photosynthetic physiology and chlorophyll fluorescence characteristics, as well as synthesis and distribution of photosynthetic products in Malus hupehensis (Pamp.) Rehd seedlings. The results revealed significant reductions in biomass, gas exchange parameters, carbohydrate metabolism enzyme activities, and photosynthetic parameters including Fv/Fm, ΦPSII, ETR and qp in seedlings subjected to both individual and joint treatments of MPs and Zn deficiency compared to the control group. Notably, the combined Zn deficiency and MPs exhibited a more pronounced inhibitory effect on root biomass (RR = −0.42) compared to the single Zn deficiency (RR = −0.37) and MP (RR = −0.26) treatments. Random forest analysis indicated that chlorophyll fluorescence characteristics (37.5 \%) had the greatest impact on biomass variation in seedlings, followed by 13C accumulation in various organs (26.7 \%). MPs exacerbated the inhibition of photosynthesis (Pn and Gs) under Zn deficiency by suppressing chlorophyll fluorescence parameters (Fv/Fm and ΦPSII), further reducing 13C accumulation in roots. In conclusion, the addition of MPs intensified the suppression of photosynthetic parameters caused by Zn deficiency, weakened the carbon assimilation capacity of leaves, and hindered the synthesis of photosynthetic products in leaves and their transport to roots, thereby further inhibiting root growth. This study reveals the combined stress of MP pollution and Zn deficiency on terrestrial plants, deepens our understanding of potential ecological risks, and provides scientific basis for the development of effective mitigation measures to protect plant ecosystems.},
	number = {1},
	urldate = {2026-03-17},
	journal = {Emerging Contaminants},
	author = {Xiao, Haoyan and Yu, Hanxia and Frew, Adam and Jiang, Wei and Wu, Yusen and Wang, Cheng and Xi, Beidou and Tan, Wenbing},
	month = mar,
	year = {2025},
	keywords = {(Pamp.) Rehd, C photosynthate accumulation, Combined effect, Microplastics, Photosynthesis, Zinc deficiency},
	pages = {100421},
}

Both microplastic (MP) pollution and zinc (Zn) deficiency have adverse effects on terrestrial plants. However, the combined effect of MPs and Zn deficiency on plant physiology remains unexplored. In this study, a pot-culture experiment and 13C stable isotope tracing technology were employed to investigate the combined effects of MPs and Zn deficiency on the growth, photosynthetic physiology and chlorophyll fluorescence characteristics, as well as synthesis and distribution of photosynthetic products in Malus hupehensis (Pamp.) Rehd seedlings. The results revealed significant reductions in biomass, gas exchange parameters, carbohydrate metabolism enzyme activities, and photosynthetic parameters including Fv/Fm, ΦPSII, ETR and qp in seedlings subjected to both individual and joint treatments of MPs and Zn deficiency compared to the control group. Notably, the combined Zn deficiency and MPs exhibited a more pronounced inhibitory effect on root biomass (RR = −0.42) compared to the single Zn deficiency (RR = −0.37) and MP (RR = −0.26) treatments. Random forest analysis indicated that chlorophyll fluorescence characteristics (37.5 %) had the greatest impact on biomass variation in seedlings, followed by 13C accumulation in various organs (26.7 %). MPs exacerbated the inhibition of photosynthesis (Pn and Gs) under Zn deficiency by suppressing chlorophyll fluorescence parameters (Fv/Fm and ΦPSII), further reducing 13C accumulation in roots. In conclusion, the addition of MPs intensified the suppression of photosynthetic parameters caused by Zn deficiency, weakened the carbon assimilation capacity of leaves, and hindered the synthesis of photosynthetic products in leaves and their transport to roots, thereby further inhibiting root growth. This study reveals the combined stress of MP pollution and Zn deficiency on terrestrial plants, deepens our understanding of potential ecological risks, and provides scientific basis for the development of effective mitigation measures to protect plant ecosystems.

@inproceedings{heuck_seasonality_2025,
	title = {Seasonality drives arbuscular mycorrhizal ({AM}) fungal community responses while future climate alters {AM} fungi-mediated phosphorus uptake in plant functional groups},
	url = {https://ui.adsabs.harvard.edu/abs/2025EGUGA..2710089H},
	doi = {10.5194/egusphere-egu25-10089},
	abstract = {Arbuscular mycorrhizal (AM) fungi form symbiosis with most terrestrial plants, facilitating nutrient and water uptake while contributing to ecosystem services such as nutrient cycling, soil carbon sequestration, and plant resilience to abiotic stressors. As such, these fungi hold significant potential in advancing climate-change-resilient agriculture. However, their effectiveness in supporting agricultural resilience depends on their own responses to global change, which remain poorly understood due to species-specific and context-dependent variability across agricultural systems and climate scenarios.To address this knowledge gap, we investigated AM fungal community responses at the Global Change Experimental Facility (GCEF) in Bad Lauchstädt, Germany. Established in 2014, the experiment consists of 5 blocks assigned to ambient climate and 5 to a future climate scenario, simulating the expected climate in Central Germany for 2070-2100, based on the consensus of several climate models. The future climate scenario simulates changes in temperature and precipitation patterns. Within each block, we focused on two distinct land-use types, extensive mowing or grazing, typically used for supporting livestock production. The meadows were mown or grazed one to three times annually, depending on plant biomass production. AM fungal community data from 160 soil samples, collected across eight time points spanning two years (mid-2020 to mid-2022) and differentiated by the two land-use types, were analysed using DNA metabarcoding. Additionally, plant biomass and nutrient concentrations were assessed.Hierarchical Modelling of Species Communities (HMSC) revealed that, across land-use types and climate scenarios, seasonality was the dominant driver of AM fungal variance in the abundance and occurrence model. Plant growing season spring was the primary influence on AM fungal responses, particularly regarding alpha indices and phylogeny. In addition, Glomeraceae abundance increased in spring (p: 0.043), potentially highlighting its role in providing fast nutrient supply for host plants. However, future climate scenarios dampened these seasonal patterns, particularly in mowed systems, suggesting a shift in the dynamics of AM symbiosis. Additionally, we observed plant functional group-specific effects: under future climate, phosphorus uptake by grasses (p: 0.11) and forbs (p: 0.027) correlated with AM fungal phylogenetic clustering, while legumes exhibited an opposite pattern, with phosphorus uptake correlating with phylogenetic dispersion (p: 0.021). We speculate that this might be due to the dual symbiosis of legumes with AM fungi and nitrogen-fixing bacteria. Thus, these findings contribute to providing insight into the functional roles of AM fungal communities under future climate and suggest that considering plant functional group composition may become more critical for managing these systems in the future.},
	urldate = {2026-03-17},
	author = {Heuck, Meike Katharina and Reitz, Thomas and Rioscher, Christiane and Powell, Jeff R. and Birnbaum, Christina and Kath, Jarrod and Philipp, Lena and Stoltenburg, Regina and Hoffmann, Petra and Harpole, W. Stanley and Frew, Adam},
	month = apr,
	year = {2025},
	note = {ADS Bibcode: 2025EGUGA..2710089H},
	pages = {EGU25--10089},
}

Arbuscular mycorrhizal (AM) fungi form symbiosis with most terrestrial plants, facilitating nutrient and water uptake while contributing to ecosystem services such as nutrient cycling, soil carbon sequestration, and plant resilience to abiotic stressors. As such, these fungi hold significant potential in advancing climate-change-resilient agriculture. However, their effectiveness in supporting agricultural resilience depends on their own responses to global change, which remain poorly understood due to species-specific and context-dependent variability across agricultural systems and climate scenarios.To address this knowledge gap, we investigated AM fungal community responses at the Global Change Experimental Facility (GCEF) in Bad Lauchstädt, Germany. Established in 2014, the experiment consists of 5 blocks assigned to ambient climate and 5 to a future climate scenario, simulating the expected climate in Central Germany for 2070-2100, based on the consensus of several climate models. The future climate scenario simulates changes in temperature and precipitation patterns. Within each block, we focused on two distinct land-use types, extensive mowing or grazing, typically used for supporting livestock production. The meadows were mown or grazed one to three times annually, depending on plant biomass production. AM fungal community data from 160 soil samples, collected across eight time points spanning two years (mid-2020 to mid-2022) and differentiated by the two land-use types, were analysed using DNA metabarcoding. Additionally, plant biomass and nutrient concentrations were assessed.Hierarchical Modelling of Species Communities (HMSC) revealed that, across land-use types and climate scenarios, seasonality was the dominant driver of AM fungal variance in the abundance and occurrence model. Plant growing season spring was the primary influence on AM fungal responses, particularly regarding alpha indices and phylogeny. In addition, Glomeraceae abundance increased in spring (p: 0.043), potentially highlighting its role in providing fast nutrient supply for host plants. However, future climate scenarios dampened these seasonal patterns, particularly in mowed systems, suggesting a shift in the dynamics of AM symbiosis. Additionally, we observed plant functional group-specific effects: under future climate, phosphorus uptake by grasses (p: 0.11) and forbs (p: 0.027) correlated with AM fungal phylogenetic clustering, while legumes exhibited an opposite pattern, with phosphorus uptake correlating with phylogenetic dispersion (p: 0.021). We speculate that this might be due to the dual symbiosis of legumes with AM fungi and nitrogen-fixing bacteria. Thus, these findings contribute to providing insight into the functional roles of AM fungal communities under future climate and suggest that considering plant functional group composition may become more critical for managing these systems in the future.

@inproceedings{maerowitz-mcmahan_ashes_2025,
	title = {From {Ashes} to {Insights}: {Mycorrhizal} {Fungi} {Functions} in {Post}-{Fire} {Landscapes}},
	shorttitle = {From {Ashes} to {Insights}},
	url = {https://ui.adsabs.harvard.edu/abs/2025EGUGA..2715087M},
	doi = {10.5194/egusphere-egu25-15087},
	abstract = {Communities in fire-affected ecosystems possess unique traits that aid survival and ecosystem recovery post-fire. As fires increase in frequency and intensity due to climate change, we enter a time increasingly influenced by fire therefore understanding the functions of these communities in forested systems is essential. While previous work has been done on the presence or absence of mycorrhizal fungi post-fire, generally using DNA-based approaches, there is limited knowledge about the functions they serve. This work aimed to identify functional traits of mycorrhizal fungi that correlate with fire regime and vegetative composition.Thirty dry sclerophyll forest sites surrounding the Sydney basin that burned in the 2019-2020 black summer fires of Australia were selected based on historical gradients in fire severity and interval. Vegetative composition, fungal communities as well as soil carbon and nutrient availability were analysed from each site, from these, a subset of sites were selected for further study to distinguish direct (via effects on fire regimes) and indirect (via effects on nutrient availability) on mycorrhizal fungal functional traits associated with biomass production, hyphal chemistry (carbon, nitrogen, and phosphorus concentrations). For this, we harvested mycorrhizal fungal biomass using mesh in-growth bags filled with plastic resin-beads that absorb mineralized nutrients.Available nutrients influenced mycorrhizal fungal community structure and biomass production in material collected from in-growth bags, whereas fire regime and vegetative structure had no effect. Hyphal chemistry was not significantly associated with nutrient availability, vegetative structure, or fire regime. In contrast, soil-derived data revealed significant effects of fire frequency on community structure, but no influence of nutrient availability or vegetative structure.By integrating responses related to functional traits, fungal community composition, vegetation structure, and environmental factors, we aim to understand not only the functions that individual fungi provide in forested systems but also how these communities function collectively. We highlight the contrasting effects of fire frequency and nutrient availability on mycorrhizal communities in soil compared to those collected with mesh in-growth bags. These differences in community structure across sites likely reflect fungal growth strategies and their sensitivity to nutrient availability.},
	urldate = {2026-03-17},
	author = {Maerowitz-McMahan, Solomon and Frew, Adam and Gordon, Chris and Nolan, Rachael and Powell, Jeff},
	month = apr,
	year = {2025},
	note = {ADS Bibcode: 2025EGUGA..2715087M},
	pages = {EGU25--15087},
}

Communities in fire-affected ecosystems possess unique traits that aid survival and ecosystem recovery post-fire. As fires increase in frequency and intensity due to climate change, we enter a time increasingly influenced by fire therefore understanding the functions of these communities in forested systems is essential. While previous work has been done on the presence or absence of mycorrhizal fungi post-fire, generally using DNA-based approaches, there is limited knowledge about the functions they serve. This work aimed to identify functional traits of mycorrhizal fungi that correlate with fire regime and vegetative composition.Thirty dry sclerophyll forest sites surrounding the Sydney basin that burned in the 2019-2020 black summer fires of Australia were selected based on historical gradients in fire severity and interval. Vegetative composition, fungal communities as well as soil carbon and nutrient availability were analysed from each site, from these, a subset of sites were selected for further study to distinguish direct (via effects on fire regimes) and indirect (via effects on nutrient availability) on mycorrhizal fungal functional traits associated with biomass production, hyphal chemistry (carbon, nitrogen, and phosphorus concentrations). For this, we harvested mycorrhizal fungal biomass using mesh in-growth bags filled with plastic resin-beads that absorb mineralized nutrients.Available nutrients influenced mycorrhizal fungal community structure and biomass production in material collected from in-growth bags, whereas fire regime and vegetative structure had no effect. Hyphal chemistry was not significantly associated with nutrient availability, vegetative structure, or fire regime. In contrast, soil-derived data revealed significant effects of fire frequency on community structure, but no influence of nutrient availability or vegetative structure.By integrating responses related to functional traits, fungal community composition, vegetation structure, and environmental factors, we aim to understand not only the functions that individual fungi provide in forested systems but also how these communities function collectively. We highlight the contrasting effects of fire frequency and nutrient availability on mycorrhizal communities in soil compared to those collected with mesh in-growth bags. These differences in community structure across sites likely reflect fungal growth strategies and their sensitivity to nutrient availability.

@article{heuck_organic_2025,
	title = {Organic management shapes {AM} fungal community structure and function, partially mitigating the negative effects of conventional agriculture},
	volume = {39},
	copyright = {© 2024 The Author(s). Functional Ecology published by John Wiley \& Sons Ltd on behalf of British Ecological Society.},
	issn = {1365-2435},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2435.14732},
	doi = {10.1111/1365-2435.14732},
	abstract = {Arbuscular mycorrhizal (AM) fungi are important plant symbionts that provide plants with nutrients and water as well as support plant defences against pests and disease. Consequently, they present a promising alternative to using environmentally damaging and costly fertilisers and pesticides in agricultural systems. However, our limited understanding of how agricultural practices impact AM fungal diversity and functions is a key impediment to using them effectively in agriculture. We assessed how organic and conventional agricultural management systems shaped AM fungal communities. We also investigated how AM fungal communities derived from these agricultural management systems affected crop biomass and development. Six soil samples from five organically and five conventionally managed agricultural sites were used to cultivate Sorghum bicolor. Plant growth, plant nutrient concentrations and AM fungal colonisation rates were analysed alongside DNA metabarcoding of community composition. We observed that soil from conventional agricultural fields resulted in a pronounced reduction in sorghum biomass (−53.6\%) and a significant delay in flowering compared to plants grown without AM fungi. Sorghum biomass was also reduced with soil from the organic system, but to a lesser extent (−30\%) and without a delay in flowering. Organic systems were associated with a large proportion of AM fungal taxa (50.5\% of VTs) not found in conventional systems, including Diversispora (r2 = 0.09, p {\textless} 0.001), Archaeospora (r2 = 0.07, p {\textless} 0.001) and Glomus (r2 = 0.25, p {\textless} 0.001) spp., but also shared a large proportion of taxa with conventional systems (42.3\% of VTs). Conventional systems had relatively few unique taxa (7.2\% of VTs). Our results suggest that conventional agricultural practices selected against AM fungi that were, in this context, more beneficial for host plants. In contrast, organic management practices mitigate this negative effect, likely due to the presence of specific key AM fungal taxa. However, this mitigation is only partial, as less beneficial AM fungal taxa still persist, probably due to abiotic factors associated with agricultural management and the sensitivity of AM fungi to these factors. This persistence explains why the effect is not entirely eradicated. Read the free Plain Language Summary for this article on the Journal blog.},
	language = {en},
	number = {6},
	urldate = {2026-03-17},
	journal = {Functional Ecology},
	author = {Heuck, Meike Katharina and Powell, Jeff R. and Kath, Jarrod and Birnbaum, Christina and Frew, Adam},
	year = {2025},
	note = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2435.14732},
	keywords = {arbuscular mycorrhizal fungi, biological soil fertility, community composition, food security, sustainable agriculture},
	pages = {1328--1342},
}

Arbuscular mycorrhizal (AM) fungi are important plant symbionts that provide plants with nutrients and water as well as support plant defences against pests and disease. Consequently, they present a promising alternative to using environmentally damaging and costly fertilisers and pesticides in agricultural systems. However, our limited understanding of how agricultural practices impact AM fungal diversity and functions is a key impediment to using them effectively in agriculture. We assessed how organic and conventional agricultural management systems shaped AM fungal communities. We also investigated how AM fungal communities derived from these agricultural management systems affected crop biomass and development. Six soil samples from five organically and five conventionally managed agricultural sites were used to cultivate Sorghum bicolor. Plant growth, plant nutrient concentrations and AM fungal colonisation rates were analysed alongside DNA metabarcoding of community composition. We observed that soil from conventional agricultural fields resulted in a pronounced reduction in sorghum biomass (−53.6%) and a significant delay in flowering compared to plants grown without AM fungi. Sorghum biomass was also reduced with soil from the organic system, but to a lesser extent (−30%) and without a delay in flowering. Organic systems were associated with a large proportion of AM fungal taxa (50.5% of VTs) not found in conventional systems, including Diversispora (r2 = 0.09, p \textless 0.001), Archaeospora (r2 = 0.07, p \textless 0.001) and Glomus (r2 = 0.25, p \textless 0.001) spp., but also shared a large proportion of taxa with conventional systems (42.3% of VTs). Conventional systems had relatively few unique taxa (7.2% of VTs). Our results suggest that conventional agricultural practices selected against AM fungi that were, in this context, more beneficial for host plants. In contrast, organic management practices mitigate this negative effect, likely due to the presence of specific key AM fungal taxa. However, this mitigation is only partial, as less beneficial AM fungal taxa still persist, probably due to abiotic factors associated with agricultural management and the sensitivity of AM fungi to these factors. This persistence explains why the effect is not entirely eradicated. Read the free Plain Language Summary for this article on the Journal blog.

@article{frew_mycorrhizal_2025,
	title = {Mycorrhizal networks: {Understanding} hidden complexity},
	volume = {39},
	copyright = {© 2025 The Author(s). Functional Ecology published by John Wiley \& Sons Ltd on behalf of British Ecological Society.},
	issn = {1365-2435},
	shorttitle = {Mycorrhizal networks},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2435.70063},
	doi = {10.1111/1365-2435.70063},
	abstract = {The symbiotic relationship between mycorrhizal fungi and plants predates the origin of roots and has played a key role in shaping ecosystems for hundreds of millions of years. In associating with multiple plants simultaneously, mycorrhizal fungi can form complex below-ground networks that directly—and indirectly—influence plant communities, plant and soil resource dynamics, and broader ecosystem processes. Research has provided increasing insight into the structure and function of these networks, including the movement and exchange of resources between symbionts, the mechanisms governing fungal and plant community assembly, and their potential applications in land management. As public interest in mycorrhizal networks has grown, so too have calls within the scientific community for greater clarity regarding their ecological functionality and broader significance. This Special Focus brings together research that advances our understanding of these networks from multiple perspectives. Contributions explore the hierarchical complexity of fungal-plant associations, the ecological and functional implications of mycorrhizal selectivity, the resource exchange dynamics, and their relevance in applied contexts, such as agriculture. By synthesising emerging evidence, this collection highlights key advances while also identifying unresolved questions and the future research directions necessary for disentangling the ecological roles of mycorrhizal networks. Read the free Plain Language Summary for this article on the Journal blog.},
	language = {en},
	number = {6},
	urldate = {2026-03-17},
	journal = {Functional Ecology},
	author = {Frew, Adam and Varga, Sandra and Klein, Tamir},
	year = {2025},
	note = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2435.70063},
	keywords = {below-ground networks, community assembly, mycorrhizal fungi, mycorrhizal selectivity, plant communities, resource exchange},
	pages = {1322--1327},
}

The symbiotic relationship between mycorrhizal fungi and plants predates the origin of roots and has played a key role in shaping ecosystems for hundreds of millions of years. In associating with multiple plants simultaneously, mycorrhizal fungi can form complex below-ground networks that directly—and indirectly—influence plant communities, plant and soil resource dynamics, and broader ecosystem processes. Research has provided increasing insight into the structure and function of these networks, including the movement and exchange of resources between symbionts, the mechanisms governing fungal and plant community assembly, and their potential applications in land management. As public interest in mycorrhizal networks has grown, so too have calls within the scientific community for greater clarity regarding their ecological functionality and broader significance. This Special Focus brings together research that advances our understanding of these networks from multiple perspectives. Contributions explore the hierarchical complexity of fungal-plant associations, the ecological and functional implications of mycorrhizal selectivity, the resource exchange dynamics, and their relevance in applied contexts, such as agriculture. By synthesising emerging evidence, this collection highlights key advances while also identifying unresolved questions and the future research directions necessary for disentangling the ecological roles of mycorrhizal networks. Read the free Plain Language Summary for this article on the Journal blog.

@article{frew_ausamf_2025,
	title = {{AusAMF}: {The} {Database} of {Arbuscular} {Mycorrhizal} {Fungal} {Communities} in {Australia}},
	volume = {34},
	copyright = {© 2025 The Author(s). Global Ecology and Biogeography published by John Wiley \& Sons Ltd.},
	issn = {1466-8238},
	shorttitle = {{AusAMF}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/geb.70090},
	doi = {10.1111/geb.70090},
	abstract = {Motivation Arbuscular mycorrhizal (AM) fungi are central to plant nutrient acquisition, soil carbon dynamics, and ecosystem resilience. Yet, their biogeography remains incompletely characterised, particularly across underrepresented regions. Australia, with its characteristic ecological conditions, continental scale, and long-standing evolutionary trajectories, has been notably undersampled. This gap hinders our ability to make comprehensive inferences about AM fungal diversity, community composition, and ecological roles at global scales. The AusAMF database was created to address this deficiency by compiling high-throughput AM fungal community data across mainland Australia and Tasmania. The initial release comprises data from 610 georeferenced sites sampled between 2011 and 2023, covering all major climate zones and accompanied by standardised soil storage, DNA extraction, and sequencing procedures. Developed through a nationally coordinated effort, AusAMF offers a rare level of methodological consistency, enabling robust spatial and temporal comparisons while minimising post-sampling technical biases. Its design as a purpose-built, extensible platform ensures continued expansion using harmonised protocols—something not achieved through compiled datasets assembled retrospectively from disparate studies. Each sample is linked to associated environmental variables, allowing users to explore ecological drivers of AM fungal distributions, assess patterns of biodiversity, and support applications spanning from fundamental ecology to conservation planning. As such, AusAMF advances both regional and global efforts to characterise the diversity and ecological significance of these foundational plant symbionts. Main Types of Variables Contained Georeferenced occurrence and abundance of high-throughput amplicon sequences of arbuscular mycorrhizal fungi. Spatial Location and Grain Australia. Decimal degrees between 0.0001 and 0.1 resolution. Time Period and Grain 2011–2023. Month and year of sampling. Major Taxa and Level of Measurement Arbuscular mycorrhizal fungi identified to family, genus, and virtual taxon (VT). Geographic occurrence and amplicon sequence abundance. Software Format Interact with processed data via online application (https://www.ausamf.com). Dataset available as .csv files and raw sequencing data as .fastq files.},
	language = {en},
	number = {7},
	urldate = {2026-03-17},
	journal = {Global Ecology and Biogeography},
	author = {Frew, Adam and Powell, Jeff R. and Heuck, Meike K. and Albornoz, Felipe E. and Birnbaum, Christina and Dearnaley, John D. W. and Egidi, Eleonora and Finn, Luke and Kath, Jarrod and Koorem, Kadri and Oja, Jane and Öpik, Maarja and Vahter, Tanel and Vasar, Martti and Watts-Williams, Stephanie and Zheng, Yuxiong and Aguilar-Trigueros, Carlos A.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/geb.70090},
	keywords = {Australia, DNA metabarcoding, arbuscular mycorrhizal fungi, high-throughput sequencing, plant symbionts, soil fungi, symbiosis},
	pages = {e70090},
}

Motivation Arbuscular mycorrhizal (AM) fungi are central to plant nutrient acquisition, soil carbon dynamics, and ecosystem resilience. Yet, their biogeography remains incompletely characterised, particularly across underrepresented regions. Australia, with its characteristic ecological conditions, continental scale, and long-standing evolutionary trajectories, has been notably undersampled. This gap hinders our ability to make comprehensive inferences about AM fungal diversity, community composition, and ecological roles at global scales. The AusAMF database was created to address this deficiency by compiling high-throughput AM fungal community data across mainland Australia and Tasmania. The initial release comprises data from 610 georeferenced sites sampled between 2011 and 2023, covering all major climate zones and accompanied by standardised soil storage, DNA extraction, and sequencing procedures. Developed through a nationally coordinated effort, AusAMF offers a rare level of methodological consistency, enabling robust spatial and temporal comparisons while minimising post-sampling technical biases. Its design as a purpose-built, extensible platform ensures continued expansion using harmonised protocols—something not achieved through compiled datasets assembled retrospectively from disparate studies. Each sample is linked to associated environmental variables, allowing users to explore ecological drivers of AM fungal distributions, assess patterns of biodiversity, and support applications spanning from fundamental ecology to conservation planning. As such, AusAMF advances both regional and global efforts to characterise the diversity and ecological significance of these foundational plant symbionts. Main Types of Variables Contained Georeferenced occurrence and abundance of high-throughput amplicon sequences of arbuscular mycorrhizal fungi. Spatial Location and Grain Australia. Decimal degrees between 0.0001 and 0.1 resolution. Time Period and Grain 2011–2023. Month and year of sampling. Major Taxa and Level of Measurement Arbuscular mycorrhizal fungi identified to family, genus, and virtual taxon (VT). Geographic occurrence and amplicon sequence abundance. Software Format Interact with processed data via online application (https://www.ausamf.com). Dataset available as .csv files and raw sequencing data as .fastq files.

@article{zheng_stand_2025,
	title = {Stand ages and soil compartments jointly shape ecosystem multifunctionality via changes in bacterial and fungal diversity and community composition},
	volume = {514},
	issn = {1573-5036},
	url = {https://doi.org/10.1007/s11104-025-07566-5},
	doi = {10.1007/s11104-025-07566-5},
	abstract = {Soil microbes play critical roles in supporting multiple ecosystem functions in forests. Their community characteristics are strongly influenced by the soil compartments they occupy (e.g., rhizosphere and bulk soils) as well as stand ages during plantation restoration. However, little is known about whether the effects of microbial communities on soil multifunctionality differ between soil compartments and how these effects are influenced by stand stages.},
	language = {en},
	number = {2},
	urldate = {2026-03-17},
	journal = {Plant and Soil},
	author = {Zheng, Yuxiong and Frew, Adam and Egidi, Eleonora and Yang, Zhijie and Lin, Chengfang},
	month = sep,
	year = {2025},
	keywords = {Microbial diversity, Plantation forests, Rhizosphere soil, Soil multifunctionality, Stand ages},
	pages = {3079--3099},
}

Soil microbes play critical roles in supporting multiple ecosystem functions in forests. Their community characteristics are strongly influenced by the soil compartments they occupy (e.g., rhizosphere and bulk soils) as well as stand ages during plantation restoration. However, little is known about whether the effects of microbial communities on soil multifunctionality differ between soil compartments and how these effects are influenced by stand stages.

@article{jiao_contrasting_2025,
	title = {Contrasting effects of above and belowground litter inputs in shaping the soil microbiome worldwide},
	volume = {515},
	issn = {1573-5036},
	url = {https://doi.org/10.1007/s11104-025-07591-4},
	doi = {10.1007/s11104-025-07591-4},
	abstract = {Microbes are the primary decomposers of litter, yet how above and belowground litter inputs contribute to soil microbial structure and function remains unclear across global environmental gradients.},
	language = {en},
	number = {1},
	urldate = {2026-03-17},
	journal = {Plant and Soil},
	author = {Jiao, Hongzhe and Delgado-Baquerizo, Manuel and Frew, Adam and Li, Weiwei and Zhai, Kaiyan and Yu, Qingshui and Zhou, Guiyao},
	month = oct,
	year = {2025},
	keywords = {Litter input, Meta-analysis, Microbial biomass, SOM decomposition, Soil microbiome},
	pages = {363--375},
}

Microbes are the primary decomposers of litter, yet how above and belowground litter inputs contribute to soil microbial structure and function remains unclear across global environmental gradients.

@article{liu_glycoalkaloid-free_2025,
	title = {Glycoalkaloid-{Free} {Starch} {Potatoes} {Generated} by {CRISPR}/{Cas9}-{Mediated} {Mutations} of {Genes} in the {Glycoalkaloid} {Biosynthesis} {Pathway} {Enable} {More} {Sustainable} {Uses} of {By}-{Products} {From} {Starch} {Production}},
	copyright = {© 2025 Sweden's Starch Producers Association and The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley \& Sons Ltd.},
	issn = {1467-7652},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.70412},
	doi = {10.1111/pbi.70412},
	abstract = {Steroidal glycoalkaloids (SGAs) are toxic cholesterol-derived secondary metabolites present in several Solanaceae species. In potato, tuber SGA levels are for reasons of toxicity of concern in both table and starch cultivars. In the latter, SGAs bind to proteins and fibres in starch production side-streams and prevent their further uses as food and feed. To enable more sustainable uses of starch by-products, we have here reduced SGA biosynthesis in a starch potato cultivar using DNA-free CRISPR/Cas9. Six SGA genes were targeted, encoding enzymes acting either before cholesterol (SMO1-L, DWF1-L, DWF7-L), or after (16DOX, CYP88B1, TAMiso2). Editing efficiencies varied between 20\% and 49\%, and generated mutants were investigated under greenhouse and field conditions. Target mass-spectrometric analyses confirmed reduced SGA levels and alterations of sterol metabolism in mutated events. Plant height and tuber yield were reduced in several events, although this was not correlated to low SGA levels. Several knockout mutants had almost SGA-free leaves and tubers, the latter also under two SGA-inducing conditions. Similarly, both fibre and protein fractions isolated from side-streams in the starch production process from mutant tubers had very low SGA levels. By contrast, the corresponding wild-type SGA levels were almost 10-fold and, respectively, 40-fold higher than the recommended upper safe limit. The results demonstrate that glycoalkaloid-free mutants can be generated and grown with moderate yield reductions under both greenhouse and field conditions. This suggests a potential for sustainable production of high-value products, e.g., food-grade protein and fibre, from starch production side-streams of SGA knockout tubers.},
	language = {en},
	urldate = {2025-10-24},
	journal = {Plant Biotechnology Journal},
	author = {Liu, Ying and Merino, Irene and Gutensohn, Mareike and Johansson, Annika I. and Johansson, Kalle and Andersson, Mariette and Hofvander, Per and Sitbon, Folke},
	month = oct,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.70412},
	keywords = {CRISPR/Cas9, potato (Solanum tuberosum), potato protein, starch potatoes, steroidal glycoalkaloids, sustainable food production},
}

Steroidal glycoalkaloids (SGAs) are toxic cholesterol-derived secondary metabolites present in several Solanaceae species. In potato, tuber SGA levels are for reasons of toxicity of concern in both table and starch cultivars. In the latter, SGAs bind to proteins and fibres in starch production side-streams and prevent their further uses as food and feed. To enable more sustainable uses of starch by-products, we have here reduced SGA biosynthesis in a starch potato cultivar using DNA-free CRISPR/Cas9. Six SGA genes were targeted, encoding enzymes acting either before cholesterol (SMO1-L, DWF1-L, DWF7-L), or after (16DOX, CYP88B1, TAMiso2). Editing efficiencies varied between 20% and 49%, and generated mutants were investigated under greenhouse and field conditions. Target mass-spectrometric analyses confirmed reduced SGA levels and alterations of sterol metabolism in mutated events. Plant height and tuber yield were reduced in several events, although this was not correlated to low SGA levels. Several knockout mutants had almost SGA-free leaves and tubers, the latter also under two SGA-inducing conditions. Similarly, both fibre and protein fractions isolated from side-streams in the starch production process from mutant tubers had very low SGA levels. By contrast, the corresponding wild-type SGA levels were almost 10-fold and, respectively, 40-fold higher than the recommended upper safe limit. The results demonstrate that glycoalkaloid-free mutants can be generated and grown with moderate yield reductions under both greenhouse and field conditions. This suggests a potential for sustainable production of high-value products, e.g., food-grade protein and fibre, from starch production side-streams of SGA knockout tubers.

@article{ibanez_circadian_2025,
	title = {The circadian clock of {Populus} affects physiological, transcriptional and metabolomic responses to osmotic and ionic components of salt stress},
	volume = {2},
	copyright = {2025 The Author(s)},
	issn = {2948-281X},
	url = {https://www.nature.com/articles/s44323-025-00052-2},
	doi = {10.1038/s44323-025-00052-2},
	abstract = {The circadian oscillator is an innate timing mechanism present in most organisms, including plants. In this study, Populus tremula × P. tremuloides (Populus) trees with reduced expression of circadian clock components were exposed to gradually increases in the osmotic and ionic components of salt stress. Reduced levels of the morning components PttLATE ELONGATED HYPOCOTYL 1 and 2 (PttLHY1,2) or of the evening components PttPSEUDO-RESPONSE REGULATOR 7a and b (PttPRR7a,b) and PttGIGANTEA1,2 (PttGI1,2) affected growth adaptation under stress conditions. PttLHY1,2 regulated growth under NaCl treatment via the control of PttCyclin D3 expression. PttPRR7a,b and PttGI1,2 were instrumental in maintaining growth in roots by enabling effective adaptation of the metabolome. Major changes in the root metabolome under prolonged stress included alterations in carbohydrate, amino acids, and fatty acids. This study places the circadian clock at the centre of adaptation to adverse conditions in trees and will help the development of stress-resistant trees.},
	language = {en},
	number = {1},
	urldate = {2025-10-03},
	journal = {npj Biological Timing and Sleep},
	publisher = {Nature Publishing Group},
	author = {Ibáñez, Cristian and Vergara, Alexander and Castro, David and Bascunan-Godoy, Luisa and Sjölander, Johan and Jurca, Manuela and Pin, Pierre A. and Nilsson, Ove and Eriksson, Maria E.},
	month = oct,
	year = {2025},
	keywords = {Circadian rhythm signalling peptides and proteins, Plant sciences},
	pages = {34},
}

The circadian oscillator is an innate timing mechanism present in most organisms, including plants. In this study, Populus tremula × P. tremuloides (Populus) trees with reduced expression of circadian clock components were exposed to gradually increases in the osmotic and ionic components of salt stress. Reduced levels of the morning components PttLATE ELONGATED HYPOCOTYL 1 and 2 (PttLHY1,2) or of the evening components PttPSEUDO-RESPONSE REGULATOR 7a and b (PttPRR7a,b) and PttGIGANTEA1,2 (PttGI1,2) affected growth adaptation under stress conditions. PttLHY1,2 regulated growth under NaCl treatment via the control of PttCyclin D3 expression. PttPRR7a,b and PttGI1,2 were instrumental in maintaining growth in roots by enabling effective adaptation of the metabolome. Major changes in the root metabolome under prolonged stress included alterations in carbohydrate, amino acids, and fatty acids. This study places the circadian clock at the centre of adaptation to adverse conditions in trees and will help the development of stress-resistant trees.

@article{donev_glucuronoyl_2025,
	title = {Glucuronoyl {Esterase} of {Pathogenic} {Phanerochaete} carnosa {Induces} {Immune} {Responses} in {Aspen} {Independently} of {Its} {Enzymatic} {Activity}},
	volume = {n/a},
	copyright = {© 2025 The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley \& Sons Ltd.},
	issn = {1467-7652},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.70357},
	doi = {10.1111/pbi.70357},
	abstract = {Microbial enzymes expressed in plants add new functionalities but occasionally trigger undesirable immune responses. Phanerochaete carnosa glucuronoyl esterase (PcGCE) hydrolyses the bond between lignin and 4-O-methyl-α-D-glucuronic acid substituent of glucuronoxylan. PcGCE constitutively expressed in Arabidopsis or hybrid aspen (Populus tremula × tremuloides) improved saccharification but also induced premature leaf senescence. To understand what triggered this senescence, we characterised PcGCE-expressing hybrid aspen by microscopy and omics approaches, supplemented by grafting and recombinant protein application experiments. PcGCE induced massive immune responses followed by senescence in the leaves. Expressing an inactive (PcGCES217A) enzyme has led to similar phenotypes, excluding a possibility that damage-associated molecular patterns (DAMPs) released by glucuronoyl esterase triggered immune responses. Grafting experiments showed that PcGCE transcripts are not mobile but they induce systemic responses. Recombinant PcGCE protein applied to leaves did not induce such responses; thus, PcGCE is probably not perceived as a pathogen-associated molecular pattern (PAMP). We suggest that the observed high expression of PcGCE from the 35S promoter triggers the unfolded protein response. Indeed, restricting PcGCE expression to short-lived xylem cells by using the wood-specific promoter avoided all detrimental effects. Thus, wood-specific expression is a viable strategy for PcGCE deployment in planta, which might be applicable for other stress-inducing proteins.},
	language = {en},
	number = {n/a},
	urldate = {2025-09-19},
	journal = {Plant Biotechnology Journal},
	author = {Donev, Evgeniy N. and Derba-Maceluch, Marta and Liu, Xiao-Kun and Bwanika, Henri Colyn and Dobrowolska, Izabela and Thapa, Mohit and Leśniewska, Joanna and Šimura, Jan and Yi-Lin Tsai, Alex and Krajewski, Konrad S. and Boström, Dan and Kleczkowski, Leszek A. and Eriksson, Maria E. and Ljung, Karin and Master, Emma R. and Mellerowicz, Ewa J.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.70357},
	keywords = {PTI, Populus, biotic stress, glucuronoyl esterase, lignocellulose improvement, transgenic crops, unfolded protein response},
}

Microbial enzymes expressed in plants add new functionalities but occasionally trigger undesirable immune responses. Phanerochaete carnosa glucuronoyl esterase (PcGCE) hydrolyses the bond between lignin and 4-O-methyl-α-D-glucuronic acid substituent of glucuronoxylan. PcGCE constitutively expressed in Arabidopsis or hybrid aspen (Populus tremula × tremuloides) improved saccharification but also induced premature leaf senescence. To understand what triggered this senescence, we characterised PcGCE-expressing hybrid aspen by microscopy and omics approaches, supplemented by grafting and recombinant protein application experiments. PcGCE induced massive immune responses followed by senescence in the leaves. Expressing an inactive (PcGCES217A) enzyme has led to similar phenotypes, excluding a possibility that damage-associated molecular patterns (DAMPs) released by glucuronoyl esterase triggered immune responses. Grafting experiments showed that PcGCE transcripts are not mobile but they induce systemic responses. Recombinant PcGCE protein applied to leaves did not induce such responses; thus, PcGCE is probably not perceived as a pathogen-associated molecular pattern (PAMP). We suggest that the observed high expression of PcGCE from the 35S promoter triggers the unfolded protein response. Indeed, restricting PcGCE expression to short-lived xylem cells by using the wood-specific promoter avoided all detrimental effects. Thus, wood-specific expression is a viable strategy for PcGCE deployment in planta, which might be applicable for other stress-inducing proteins.

@article{low_zinc_2025,
	title = {{ZINC} {FINGER} {PROTEIN2} suppresses funiculus lignification to ensure seed loading efficiency in \textit{{Arabidopsis}}},
	volume = {60},
	issn = {1534-5807},
	url = {https://www.sciencedirect.com/science/article/pii/S1534580725000620},
	doi = {10.1016/j.devcel.2025.01.021},
	abstract = {The plant funiculus anchors the developing seed to the placenta within the inner dorsal pod strands of the silique wall and directly transports nutrients to the seeds. The lignified vasculature critically supports nutrient transport through the funiculus. However, molecular mechanisms underlying lignified secondary cell wall (SCW) biosynthesis in the funiculus remain elusive. Here, we show that the transcription factor ZINC FINGER PROTEIN2 (ZFP2) represses SCW formation in the cortex cells that surround the vasculature. This function is essential for efficient nutrient loading into the seeds. Notably, ZFP2 directly acts on the SCW transcription factor NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) to repress cortex cell lignification, providing a mechanism of how SCW biosynthesis is restricted to the vasculature of the funiculus to ensure proper seed loading in Arabidopsis.},
	number = {12},
	urldate = {2026-01-30},
	journal = {Developmental Cell},
	author = {Low, Pui Man and Kong, Que and Blaschek, Leonard and Ma, Zhiming and Lim, Peng Ken and Yang, Yuzhou and Quek, Trisha and Lim, Cuithbert J. R. and Singh, Sanjay K. and Crocoll, Christoph and Engquist, Ellen and Thorsen, Jakob S. and Pattanaik, Sitakanta and Tee, Wan Ting and Mutwil, Marek and Miao, Yansong and Yuan, Ling and Xu, Deyang and Persson, Staffan and Ma, Wei},
	month = jun,
	year = {2025},
	keywords = {ZINC FINGER PROTEIN2, funiculus, secondary cell wall biosynthesis, transcription factor, transcriptional repression},
	pages = {1719--1729.e6},
}

The plant funiculus anchors the developing seed to the placenta within the inner dorsal pod strands of the silique wall and directly transports nutrients to the seeds. The lignified vasculature critically supports nutrient transport through the funiculus. However, molecular mechanisms underlying lignified secondary cell wall (SCW) biosynthesis in the funiculus remain elusive. Here, we show that the transcription factor ZINC FINGER PROTEIN2 (ZFP2) represses SCW formation in the cortex cells that surround the vasculature. This function is essential for efficient nutrient loading into the seeds. Notably, ZFP2 directly acts on the SCW transcription factor NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) to repress cortex cell lignification, providing a mechanism of how SCW biosynthesis is restricted to the vasculature of the funiculus to ensure proper seed loading in Arabidopsis.

@article{zheng_pupylation-based_2025,
	title = {Pupylation-{Based} {Proximity} {Labeling} {Unravels} a {Comprehensive} {Protein} and {Phosphoprotein} {Interactome} of the {Arabidopsis} {TOR} {Complex}},
	volume = {12},
	copyright = {© 2025 The Author(s). Advanced Science published by Wiley-VCH GmbH},
	issn = {2198-3844},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/advs.202414496},
	doi = {10.1002/advs.202414496},
	abstract = {Target of rapamycin (TOR) is a signaling hub that integrates developmental, hormonal, and environmental signals to optimize carbon allocation and plant growth. In plant cells, TOR acts together with the proteins LST8-1 and RAPTOR1 to form a core TOR complex (TORC). While these proteins comprise a functional TORC, they engage with many other proteins to ensure precise signal outputs. Although TORC interactions have attracted significant attention in the recent past, large parts of the interactome are still unknown. In this resource study, PUP-IT is adapted, a fully endogenously expressed protein proximity labeling toolbox, to map TORC protein–protein interactions using the core set of TORC as baits. It is outlined how this interactome is differentially phosphorylated during changes in carbon availability, uncovering putative direct TOR kinase targets. An AlphaFold-Multimer approach is further used to validate many interactors, thus outlining a comprehensive TORC interactome that includes over a hundred new candidate interactors and provides an invaluable resource to the plant cell signaling community.},
	language = {en},
	number = {19},
	urldate = {2026-01-30},
	journal = {Advanced Science},
	author = {Zheng, Shuai and Blaschek, Leonard and Pottier, Delphine and Dijkhof, Luuk Robin Hoegen and Özmen, Beyza and Lim, Peng Ken and Tan, Qiao Wen and Mutwil, Marek and Hauser, Alexander Sebastian and Persson, Staffan},
	year = {2025},
	note = {\_eprint: https://advanced.onlinelibrary.wiley.com/doi/pdf/10.1002/advs.202414496},
	keywords = {AlphaFold, PUP-IT, proximity labeling, sugar signaling, target of rapamycin},
	pages = {2414496},
}

Target of rapamycin (TOR) is a signaling hub that integrates developmental, hormonal, and environmental signals to optimize carbon allocation and plant growth. In plant cells, TOR acts together with the proteins LST8-1 and RAPTOR1 to form a core TOR complex (TORC). While these proteins comprise a functional TORC, they engage with many other proteins to ensure precise signal outputs. Although TORC interactions have attracted significant attention in the recent past, large parts of the interactome are still unknown. In this resource study, PUP-IT is adapted, a fully endogenously expressed protein proximity labeling toolbox, to map TORC protein–protein interactions using the core set of TORC as baits. It is outlined how this interactome is differentially phosphorylated during changes in carbon availability, uncovering putative direct TOR kinase targets. An AlphaFold-Multimer approach is further used to validate many interactors, thus outlining a comprehensive TORC interactome that includes over a hundred new candidate interactors and provides an invaluable resource to the plant cell signaling community.

@article{ozmen_proximity_2025,
	title = {Proximity labeling techniques for protein–protein interaction mapping in plants},
	volume = {301},
	issn = {0021-9258},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925825023518},
	doi = {10.1016/j.jbc.2025.110501},
	abstract = {Protein–protein interactions (PPIs) are fundamental to understanding cellular processes, serving as the cornerstone of biological signaling, structural organization, and metabolic regulation. However, capturing PPIs in living organisms remains a significant challenge, particularly in complex and compartmentalized cellular environments. Research in this area has been greatly accelerated by the invention of proximity labeling (PL) techniques. By employing engineered enzymes capable of tagging proteins and other molecules in vivo, PL allows real-time mapping of biomolecular interactions within native environments. In plants, the implementation of PL presents unique challenges but has nonetheless emerged as a powerful tool. Here, we summarize the mechanisms, strengths, and weaknesses of different enzyme-based PL methods. We also highlight key considerations to optimize PL experiments in plants and propose targets for development to further improve their efficiency and flexibility.},
	number = {8},
	urldate = {2026-01-30},
	journal = {Journal of Biological Chemistry},
	author = {Özmen, Beyza and Blaschek, Leonard and Ogden, Michael and San Segundo, Marcos and Persson, Staffan and Zheng, Shuai},
	month = aug,
	year = {2025},
	keywords = {TOR complex, cellulose, plants, protein-protein interactions (PPIs), proximity labeling (PL)},
	pages = {110501},
}

Protein–protein interactions (PPIs) are fundamental to understanding cellular processes, serving as the cornerstone of biological signaling, structural organization, and metabolic regulation. However, capturing PPIs in living organisms remains a significant challenge, particularly in complex and compartmentalized cellular environments. Research in this area has been greatly accelerated by the invention of proximity labeling (PL) techniques. By employing engineered enzymes capable of tagging proteins and other molecules in vivo, PL allows real-time mapping of biomolecular interactions within native environments. In plants, the implementation of PL presents unique challenges but has nonetheless emerged as a powerful tool. Here, we summarize the mechanisms, strengths, and weaknesses of different enzyme-based PL methods. We also highlight key considerations to optimize PL experiments in plants and propose targets for development to further improve their efficiency and flexibility.

@article{castellano_genome_2025,
	title = {Genome {Assembly} of a {Living} {Fossil}, the {Atlantic} {Horseshoe} {Crab} {Limulus} polyphemus, {Reveals} {Lineage}-{Specific} {Whole}-{Genome} {Duplications}, {Transposable} {Element}-{Based} {Centromeres}, and a {ZW} {Sex} {Chromosome} {System}},
	volume = {42},
	issn = {1537-1719},
	url = {https://doi.org/10.1093/molbev/msaf021},
	doi = {10.1093/molbev/msaf021},
	abstract = {Horseshoe crabs, considered living fossils with a stable morphotype spanning ∼445 million years, are evolutionarily, ecologically, and biomedically important species experiencing rapid population decline. Of the four extant species of horseshoe crabs, the Atlantic horseshoe crab, Limulus polyphemus, has become an essential component of the modern medicine toolkit. Here, we present the first chromosome-level genome assembly, and the most contiguous and complete assembly to date, for L. polyphemus using nanopore long-read sequencing and chromatin conformation analysis. We find support for three horseshoe crab-specific whole-genome duplications, but none shared with Arachnopulmonata (spiders and scorpions). Moreover, we discovered tandem duplicates of endotoxin detection pathway components Factors C and G, identify candidate centromeres consisting of Gypsy retroelements, and classify the ZW sex chromosome system for this species and a sister taxon, Carcinoscorpius rotundicauda. Finally, we revealed this species has been experiencing a steep population decline over the last 5 million years, highlighting the need for international conservation interventions and fisheries-based management for this critical species.},
	number = {2},
	urldate = {2026-01-16},
	journal = {Molecular Biology and Evolution},
	author = {Castellano, Kate R and Neitzey, Michelle L and Starovoitov, Andrew and Barrett, Gabriel A and Reid, Noah M and Vuruputoor, Vidya S and Webster, Cynthia N and Storer, Jessica M and Pauloski, Nicole R and Ameral, Natalie J and McEvoy, Susan L and McManus, M Conor and Puritz, Jonathan B and Wegrzyn, Jill L and O’Neill, Rachel J},
	month = feb,
	year = {2025},
	pages = {msaf021},
}

Horseshoe crabs, considered living fossils with a stable morphotype spanning ∼445 million years, are evolutionarily, ecologically, and biomedically important species experiencing rapid population decline. Of the four extant species of horseshoe crabs, the Atlantic horseshoe crab, Limulus polyphemus, has become an essential component of the modern medicine toolkit. Here, we present the first chromosome-level genome assembly, and the most contiguous and complete assembly to date, for L. polyphemus using nanopore long-read sequencing and chromatin conformation analysis. We find support for three horseshoe crab-specific whole-genome duplications, but none shared with Arachnopulmonata (spiders and scorpions). Moreover, we discovered tandem duplicates of endotoxin detection pathway components Factors C and G, identify candidate centromeres consisting of Gypsy retroelements, and classify the ZW sex chromosome system for this species and a sister taxon, Carcinoscorpius rotundicauda. Finally, we revealed this species has been experiencing a steep population decline over the last 5 million years, highlighting the need for international conservation interventions and fisheries-based management for this critical species.

@article{birkeland_updated_2025,
	title = {An updated perspective: what genes make a tree a tree?},
	issn = {1360-1385},
	shorttitle = {An updated perspective},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138525002821},
	doi = {10.1016/j.tplants.2025.09.006},
	abstract = {We learn early on how to tell trees apart from other plants. However, it has proved hard to distinguish trees from other plants at the genetic level, and it is believed that there are no unique ‘tree genes’. With the rapid increase in available tree genomes, we can perform new comparative and evolutionary analyses of plant life histories and growth forms. Here we provide a fresh perspective on the genetic foundation for woodiness and perenniality in angiosperms by analyzing selection pressures and gene family evolution in the rosids using genomic data. We examine genes distinguishing trees from herbs and discuss future directions for uncovering the genetic factors that define a tree in this new era of tree genomics.},
	urldate = {2025-10-24},
	journal = {Trends in Plant Science},
	author = {Birkeland, Siri and Soldado, Eduardo R. and Ranade, Sonali S. and García-Gil, M. Rosario and Choudhary, Shruti and Kumar, Vikash and Tuominen, Hannele and Mellerowicz, Ewa J. and Street, Nathaniel R. and Hvidsten, Torgeir R.},
	month = oct,
	year = {2025},
	keywords = {comparative genomics, plant growth forms, plant life histories, rosids, tree genomics, woodiness},
}

We learn early on how to tell trees apart from other plants. However, it has proved hard to distinguish trees from other plants at the genetic level, and it is believed that there are no unique ‘tree genes’. With the rapid increase in available tree genomes, we can perform new comparative and evolutionary analyses of plant life histories and growth forms. Here we provide a fresh perspective on the genetic foundation for woodiness and perenniality in angiosperms by analyzing selection pressures and gene family evolution in the rosids using genomic data. We examine genes distinguishing trees from herbs and discuss future directions for uncovering the genetic factors that define a tree in this new era of tree genomics.

@article{ye_cambium_2025,
	title = {Cambium {LBDs} promote radial growth by regulating {PLL}-mediated pectin metabolism},
	copyright = {2025 The Author(s)},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-025-02151-1},
	doi = {10.1038/s41477-025-02151-1},
	abstract = {Plant growth originates from the interlinked action of cell division and cell growth. During radial growth of secondary tissues, bifacial cambial stem cells grow and divide to produce xylem and phloem precursors, which subsequently undergo expansion characteristic of their respective differentiation processes. In Arabidopsis roots, cytokinins and four downstream LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors are key players in promoting radial growth, though the underlying mechanisms remain unknown. Here our results indicate that these LBD genes primarily regulate cell growth rather than proliferation. Through a large-scale CRISPR–Cas9-aided reverse genetic screen, we identified a set of PECTATE LYASE-LIKE (PLL) genes that function downstream of cytokinin and the LBDs in the regulation of radial growth. We show that at least one of these PLLs, PLL18, possesses pectate lyase activity. In accordance with this activity, PLLs and LBDs promote radial growth by modifying the pectin composition and mechanical properties of the primary cell wall. Our findings thus connect the central role of cytokinins in radial growth with cell wall remodelling and pave a way for further research on hormone-mediated plant growth regulation and cell wall metabolism.},
	language = {en},
	urldate = {2025-11-21},
	journal = {Nature Plants},
	publisher = {Nature Publishing Group},
	author = {Ye, Lingling and Wang, Xin and Valle-Delgado, Juan José and Vainonen, Julia P. and Wopereis, Isaac and Kesari, Kavindra Kumar and Takahashi, Junko and Sierla, Maija and Mähönen, Ari Pekka},
	month = nov,
	year = {2025},
	keywords = {Cell wall, Cytokinin, Plant morphogenesis, Transgenic plants},
	pages = {1--16},
}

Plant growth originates from the interlinked action of cell division and cell growth. During radial growth of secondary tissues, bifacial cambial stem cells grow and divide to produce xylem and phloem precursors, which subsequently undergo expansion characteristic of their respective differentiation processes. In Arabidopsis roots, cytokinins and four downstream LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors are key players in promoting radial growth, though the underlying mechanisms remain unknown. Here our results indicate that these LBD genes primarily regulate cell growth rather than proliferation. Through a large-scale CRISPR–Cas9-aided reverse genetic screen, we identified a set of PECTATE LYASE-LIKE (PLL) genes that function downstream of cytokinin and the LBDs in the regulation of radial growth. We show that at least one of these PLLs, PLL18, possesses pectate lyase activity. In accordance with this activity, PLLs and LBDs promote radial growth by modifying the pectin composition and mechanical properties of the primary cell wall. Our findings thus connect the central role of cytokinins in radial growth with cell wall remodelling and pave a way for further research on hormone-mediated plant growth regulation and cell wall metabolism.

@article{sullivan_airborne_2025,
	title = {Airborne {eDNA} captures three decades of ecosystem biodiversity},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-67676-7},
	doi = {10.1038/s41467-025-67676-7},
	abstract = {Biodiversity loss threatens ecosystems and human well-being, making accurate, large-scale monitoring crucial. Environmental DNA (eDNA) has enabled species detection from substrates such as water, without the need for direct observation. Lately, airborne eDNA has been showing promise for tracking organisms from insects to mammals in terrestrial ecosystems. Conventional biodiversity assessments are often labor-intensive and limited in scope, leaving gaps in our understanding of ecosystem response to environmental change. Here, we demonstrate that airborne eDNA can detect organisms across the tree of life, quantify changes in abundance congruent with traditional monitoring, and reveal land-use induced regional decline of diversity in a northern boreal ecosystem over more than three decades. By analyzing 34 years of archived aerosol filters, we reconstruct weekly temporal relative abundance data for more than 2700 genera using non-targeted methods. This study provides unified, ecosystem-scale biodiversity surveillance spanning multiple decades, with data collected at weekly intervals on both the individual species and community level. Previously, large scale analyses of ecosystem changes, targeting all types of organisms, has been prohibitively expensive and difficult to attempt. Here, we present a way of holistically doing this type of analysis in a single framework.},
	language = {en},
	number = {1},
	urldate = {2026-01-09},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Sullivan, Alexis R. and Karlsson, Edvin and Svensson, Daniel and Brindefalk, Björn and Villegas, Jose Antonio and Mikko, Amanda and Bellieny, Daniel and Siddique, Abu Bakar and Johansson, Anna-Mia and Grahn, Håkan and Sundell, David and Norman, Anita and Esseen, Per-Anders and Sjödin, Andreas and Singh, Navinder J. and Brodin, Tomas and Forsman, Mats and Stenberg, Per},
	month = dec,
	year = {2025},
	keywords = {Biodiversity, Molecular ecology},
	pages = {11281},
}

Biodiversity loss threatens ecosystems and human well-being, making accurate, large-scale monitoring crucial. Environmental DNA (eDNA) has enabled species detection from substrates such as water, without the need for direct observation. Lately, airborne eDNA has been showing promise for tracking organisms from insects to mammals in terrestrial ecosystems. Conventional biodiversity assessments are often labor-intensive and limited in scope, leaving gaps in our understanding of ecosystem response to environmental change. Here, we demonstrate that airborne eDNA can detect organisms across the tree of life, quantify changes in abundance congruent with traditional monitoring, and reveal land-use induced regional decline of diversity in a northern boreal ecosystem over more than three decades. By analyzing 34 years of archived aerosol filters, we reconstruct weekly temporal relative abundance data for more than 2700 genera using non-targeted methods. This study provides unified, ecosystem-scale biodiversity surveillance spanning multiple decades, with data collected at weekly intervals on both the individual species and community level. Previously, large scale analyses of ecosystem changes, targeting all types of organisms, has been prohibitively expensive and difficult to attempt. Here, we present a way of holistically doing this type of analysis in a single framework.

@article{goretti_splicing_2025,
	title = {The splicing genes {SmEa} and {SmEb} regulate plant development during vegetative growth in poplar},
	volume = {25},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-025-07676-3},
	doi = {10.1186/s12870-025-07676-3},
	abstract = {Spliceosomes are large evolutionary conserved ribonucleoprotein complexes containing at their core heptameric rings of Sm (or LSm) proteins and U-rich snRNAs. The role of Sm proteins in animal development is well established, and recent research has begun to link mutations in these genes to growth defects in plants. One of the most studied Sm genes is SmE1/PCP, mutants of which display a temperature-dependent phenotype in Arabidopsis thaliana.},
	language = {en},
	number = {1},
	urldate = {2026-01-09},
	journal = {BMC Plant Biology},
	author = {Goretti, Daniela and Collani, Silvio and Marcon, Alice and Nilsson, Ove and Schmid, Markus},
	month = dec,
	year = {2025},
	keywords = {CRISPR/Cas9, Development, Poplar, Sm, Splicing},
	pages = {1723},
}

Spliceosomes are large evolutionary conserved ribonucleoprotein complexes containing at their core heptameric rings of Sm (or LSm) proteins and U-rich snRNAs. The role of Sm proteins in animal development is well established, and recent research has begun to link mutations in these genes to growth defects in plants. One of the most studied Sm genes is SmE1/PCP, mutants of which display a temperature-dependent phenotype in Arabidopsis thaliana.

@article{buzan_biodiversity_2025,
	title = {Biodiversity {Genomics} {Research} {Practices} {Require} {Harmonising} to {Meet} {Stakeholder} {Needs} in {Conservation}},
	volume = {34},
	copyright = {© 2025 The Author(s). Molecular Ecology published by John Wiley \& Sons Ltd.},
	issn = {1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.70001},
	doi = {10.1111/mec.70001},
	abstract = {Biodiversity resilience relies on genetic diversity, which sustains the evolutionary potential of organisms in dynamic ecosystems. Genomics is a powerful tool for accurately estimating genetic diversity across genomes of species and populations. However, integration of genomic data into conservation efforts faces challenges due to the heterogeneity of approaches employed. Establishing common sets of standards for genomic data production and analysis is essential to consistently interpret results and clearly communicate outcomes to stakeholders. While the European Reference Genome Atlas (ERGA) community has contributed significantly to the standardisation of reference genome methodologies in synergy with other initiatives, there is now an urgent need to extend these principles to downstream analyses. ERGA aims to build on its experience to help establish harmonised approaches in applied biodiversity genomics research, aligned with ongoing efforts to define standardised metrics for measuring and reporting genetic diversity. Establishing consensus on best practices for genome-wide data generation methods and applications will substantially increase accuracy, interpretability, and comparability, together with enhanced stakeholder capacities. By identifying key opportunities and challenges, as well as conducting preliminary stakeholder mapping and examining case studies, the goal is to build an inclusive framework that ensures the relevance and widespread adoption of these best practices: fostering trust and confidence in genomics research practices to meet stakeholder needs in biodiversity conservation. We call upon the broader research community to join efforts in establishing these approaches, recognising the importance of participation of end-users, to foster the integration of genomic data into the toolkit for measuring and reporting genetic diversity.},
	language = {en},
	number = {23},
	urldate = {2025-12-18},
	journal = {Molecular Ecology},
	author = {Buzan, Elena and de Guttry, Christian and Bortoluzzi, Chiara and Street, Nathaniel R. and Lucek, Kay and Rosling, Anna and Ometto, Lino and Mouton, Alice and Marins, Luísa S. and Ruiz-López, María José and Melo-Ferreira, José and Ottosson, Elisabet and Mazzoni, Camila J. and Waterhouse, Robert M.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.70001},
	keywords = {best practices, biodiversity genomics, genome-wide genetic diversity, stakeholder engagement, standardisation, whole genome resequencing data},
	pages = {e70001},
}

Biodiversity resilience relies on genetic diversity, which sustains the evolutionary potential of organisms in dynamic ecosystems. Genomics is a powerful tool for accurately estimating genetic diversity across genomes of species and populations. However, integration of genomic data into conservation efforts faces challenges due to the heterogeneity of approaches employed. Establishing common sets of standards for genomic data production and analysis is essential to consistently interpret results and clearly communicate outcomes to stakeholders. While the European Reference Genome Atlas (ERGA) community has contributed significantly to the standardisation of reference genome methodologies in synergy with other initiatives, there is now an urgent need to extend these principles to downstream analyses. ERGA aims to build on its experience to help establish harmonised approaches in applied biodiversity genomics research, aligned with ongoing efforts to define standardised metrics for measuring and reporting genetic diversity. Establishing consensus on best practices for genome-wide data generation methods and applications will substantially increase accuracy, interpretability, and comparability, together with enhanced stakeholder capacities. By identifying key opportunities and challenges, as well as conducting preliminary stakeholder mapping and examining case studies, the goal is to build an inclusive framework that ensures the relevance and widespread adoption of these best practices: fostering trust and confidence in genomics research practices to meet stakeholder needs in biodiversity conservation. We call upon the broader research community to join efforts in establishing these approaches, recognising the importance of participation of end-users, to foster the integration of genomic data into the toolkit for measuring and reporting genetic diversity.

@article{paulisic_transcriptional_2025,
	title = {Transcriptional dynamics and chromatin accessibility in the regulation of shade-responsive genes in {Arabidopsis}},
	volume = {26},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-025-03901-2},
	doi = {10.1186/s13059-025-03901-2},
	abstract = {Open chromatin regions host DNA regulatory motifs that are accessible to transcription factors and the transcriptional machinery. In Arabidopsis, responses to light are heavily regulated at the transcriptional level. Shade, for example, can limit photosynthesis and is rapidly perceived by phytochromes as a reduction of red to far-red light ratio (LRFR). Under shade, phytochromes become inactive, enabling PHYTOCHROME INTERACTING FACTORs (PIFs), particularly PIF7, to promote genome-wide reprogramming essential for LRFR responses. An initial strong and fast regulation of shade-responsive genes is followed by attenuation of this response under prolonged shade.},
	language = {en},
	number = {1},
	urldate = {2025-12-18},
	journal = {Genome Biology},
	author = {Paulišić, Sandi and Boccaccini, Alessandra and Dreos, René and Ambrosini, Giovanna and Guex, Nicolas and Benstein, Ruben Maximilian and Schmid, Markus and Fankhauser, Christian},
	month = dec,
	year = {2025},
	keywords = {ATAC-seq, Arabidopsis, Chromatin accessibility, PIF7, Shade, Transcription},
	pages = {422},
}

Open chromatin regions host DNA regulatory motifs that are accessible to transcription factors and the transcriptional machinery. In Arabidopsis, responses to light are heavily regulated at the transcriptional level. Shade, for example, can limit photosynthesis and is rapidly perceived by phytochromes as a reduction of red to far-red light ratio (LRFR). Under shade, phytochromes become inactive, enabling PHYTOCHROME INTERACTING FACTORs (PIFs), particularly PIF7, to promote genome-wide reprogramming essential for LRFR responses. An initial strong and fast regulation of shade-responsive genes is followed by attenuation of this response under prolonged shade.

@article{zhang_unraveling_2025,
	title = {Unraveling nitrogen uptake and metabolism: gene families, expression dynamics and functional insights in aspen ({Populus} tremula)},
	volume = {45},
	issn = {1758-4469},
	shorttitle = {Unraveling nitrogen uptake and metabolism},
	url = {https://doi.org/10.1093/treephys/tpaf099},
	doi = {10.1093/treephys/tpaf099},
	abstract = {The influence of nitrogen on wood formation is well established. To gain insight into the underlying molecular mechanism, we first identified genes in 14 gene families that are involved in nitrogen uptake and metabolism in European aspen (Populus tremula L.) genome annotation. Gene expression data from a de novo RNA sequencing (RNA-seq) analysis and data available from the AspWood database (plantgenie.org) provided putative candidate genes for the uptake of nitrate, ammonium and amino acids from the xylem sap as well as their further assimilation in the secondary xylem tissues of the stem. For a population-wide analysis of the nitrogen-related genes, we utilized RNA-seq data from the cambial region of the stems of 5-year-old aspen trees, representing 99 natural aspen accessions, and compared the expression of the nitrogen-related genes to stem diameter. Novel regulatory interactions were identified in expression quantitative loci and co-expression network analyses in these data. The expression of certain nitrate and amino acid transporters correlated negatively with stem diameter, suggesting that excessive nitrogen retrieval from the xylem sap suppresses radial growth of the stem. The expression of a glutamine synthetase correlated with the expression of these transporters, a link further supported by increased plant growth in transgenic glutamine synthetase overexpressing trees. This study provides insight into the genetic basis of nitrogen uptake and assimilation and its connection to wood formation, providing interesting targets for improving nitrogen-use efficiency and growth of aspen trees.},
	number = {13},
	urldate = {2025-12-05},
	journal = {Tree Physiology},
	author = {Zhang, Yupeng and Choudhary, Shruti and Renström, Anna and Luomaranta, Mikko and Chantreau, Maxime and Fleig, Verena and Gaboreanu, Ioana and Grones, Carolin and Nilsson, Ove and Robinson, Kathryn M and Tuominen, Hannele},
	month = nov,
	year = {2025},
	pages = {100--113},
}

The influence of nitrogen on wood formation is well established. To gain insight into the underlying molecular mechanism, we first identified genes in 14 gene families that are involved in nitrogen uptake and metabolism in European aspen (Populus tremula L.) genome annotation. Gene expression data from a de novo RNA sequencing (RNA-seq) analysis and data available from the AspWood database (plantgenie.org) provided putative candidate genes for the uptake of nitrate, ammonium and amino acids from the xylem sap as well as their further assimilation in the secondary xylem tissues of the stem. For a population-wide analysis of the nitrogen-related genes, we utilized RNA-seq data from the cambial region of the stems of 5-year-old aspen trees, representing 99 natural aspen accessions, and compared the expression of the nitrogen-related genes to stem diameter. Novel regulatory interactions were identified in expression quantitative loci and co-expression network analyses in these data. The expression of certain nitrate and amino acid transporters correlated negatively with stem diameter, suggesting that excessive nitrogen retrieval from the xylem sap suppresses radial growth of the stem. The expression of a glutamine synthetase correlated with the expression of these transporters, a link further supported by increased plant growth in transgenic glutamine synthetase overexpressing trees. This study provides insight into the genetic basis of nitrogen uptake and assimilation and its connection to wood formation, providing interesting targets for improving nitrogen-use efficiency and growth of aspen trees.

@article{derba-maceluch_glucuronoyl_2025,
	title = {Glucuronoyl {Esterase} {Expressed} in {Aspen} {Xylem} {Affects} γ-{Ester} {Linkages} {Between} {Lignin} and {Glucuronoxylan} {Reducing} {Recalcitrance} and {Accelerating} {Growth}},
	volume = {23},
	copyright = {© 2025 The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley \& Sons Ltd.},
	issn = {1467-7652},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.70301},
	doi = {10.1111/pbi.70301},
	abstract = {Wood is the most abundant renewable natural resource composed of different polysaccharides and lignin, but its utilisation is hampered by intermolecular linkages between these components forming lignin-carbohydrate complexes (LCCs) causing recalcitrance. The links between glucuronoxylan and the γ-C of lignin (γ-ester linkages) are thought to contribute to one-third of LCCs, but direct evidence for their natural occurrence and their role in recalcitrance has been scarce so far. To address these issues, Phanerochaete carnosa glucuronoyl esterase (PcGCE), hydrolysing γ-ester linkages, was expressed in cell walls of developing wood in hybrid aspen (Populus tremula L. × tremuloides Michx.). The enzyme reduced HSQC 2D NMR signals corresponding to the γ-esters and xylan in dioxane-extracted LCCs without altering glucuronoxylan content or structure. This increased acid solubility of lignin and decreased lignin content. Reduced wood recalcitrance was shown by increased sugar yields and glucose production rates (by approx. 20\%) in saccharification without pretreatment and increased xylan extractability by subcritical water (by approx. 70\%). Moreover, trees expressing PcGCE exhibited greater primary and secondary growth. Transcriptomics and metabolomics analyses in developing wood suggested that growth could have been induced by a higher transcription of SMR2 and RPOTmp, which was likely triggered by the secondary cell wall integrity signalling. The results provide evidence for the natural existence of LCC γ-esters and their significant contribution to lignocellulose recalcitrance. Furthermore, they show that reducing γ-ester linkages could increase plant productivity.},
	language = {en},
	number = {12},
	urldate = {2025-12-05},
	journal = {Plant Biotechnology Journal},
	author = {Derba-Maceluch, Marta and García Romañach, Laura and Hedenström, Mattias and Mitra, Madhusree and Donev, Evgeniy N. and Urbancsok, János and Yassin, Zakiya and Gandla, Madhavi L. and Sivan, Pramod and Šimura, Jan and Scheepers, Gerhard and Jönsson, Leif J. and Vilaplana, Francisco and Mellerowicz, Ewa J.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.70301},
	keywords = {ce15, glucuronoxylan, glucuronoyl esterase, hardwood genetic engineering, lignin-carbohydrate complexes, lignocellulose, secondary cell wall},
	pages = {5417--5434},
}

Wood is the most abundant renewable natural resource composed of different polysaccharides and lignin, but its utilisation is hampered by intermolecular linkages between these components forming lignin-carbohydrate complexes (LCCs) causing recalcitrance. The links between glucuronoxylan and the γ-C of lignin (γ-ester linkages) are thought to contribute to one-third of LCCs, but direct evidence for their natural occurrence and their role in recalcitrance has been scarce so far. To address these issues, Phanerochaete carnosa glucuronoyl esterase (PcGCE), hydrolysing γ-ester linkages, was expressed in cell walls of developing wood in hybrid aspen (Populus tremula L. × tremuloides Michx.). The enzyme reduced HSQC 2D NMR signals corresponding to the γ-esters and xylan in dioxane-extracted LCCs without altering glucuronoxylan content or structure. This increased acid solubility of lignin and decreased lignin content. Reduced wood recalcitrance was shown by increased sugar yields and glucose production rates (by approx. 20%) in saccharification without pretreatment and increased xylan extractability by subcritical water (by approx. 70%). Moreover, trees expressing PcGCE exhibited greater primary and secondary growth. Transcriptomics and metabolomics analyses in developing wood suggested that growth could have been induced by a higher transcription of SMR2 and RPOTmp, which was likely triggered by the secondary cell wall integrity signalling. The results provide evidence for the natural existence of LCC γ-esters and their significant contribution to lignocellulose recalcitrance. Furthermore, they show that reducing γ-ester linkages could increase plant productivity.

@article{biswal_ectopic_2025,
	title = {Ectopic expression of pectate lyase \textit{{Ptxt}}{PL1}-27 in aspen affects leaf cuticle development},
	volume = {28},
	issn = {2589-0042},
	url = {https://www.sciencedirect.com/science/article/pii/S2589004225022242},
	doi = {10.1016/j.isci.2025.113963},
	abstract = {Cuticle - a hydrophobic barrier of cutin and waxes covering the outer cell wall surface of plants - enables survival in terrestrial habitats. However, it is not understood how the hydrophobic cuticle precursors travel through the homogalacturonan-rich hydrophilic cell wall. To elucidate the role of homogalacturonan in cuticle development, we disrupted its integrity by overexpressing a pectate lyase, PtxtPL1-27, in aspen. PtxtPL1-27 had pleiotropic effects on shoot development, including the reduction of cuticle thickness and changes in cutin and wax composition, but the expression of cutin biosynthetic genes was little affected. Despite a reduction in homogalacturonan content in the leaves, labeling with the homogalacturonan-specific antibody JIM5 in the outer epidermal cell wall layer increased and displayed an altered pattern. Moreover, the ultrastructure of cell walls was changed concomitant with lipid accumulation. We propose that the disruption of homogalacturonan integrity affected the cutinsome-dependent transport and polymerization of cutin monomers in the cell wall.},
	number = {12},
	urldate = {2025-11-28},
	journal = {iScience},
	author = {Biswal, Ajaya K. and Banasiak, Alicja and Fernández-Moreno, Josefina-Patricia and Mitra, Madhusree and Harholt, Jesper and Derba-Maceluch, Marta and Majda, Mateusz and Kushwah, Sunita and Kumar, Vikash and Abreu, Ilka and Sivan, Pramod and Pattathil, Sivakumar and Immerzeel, Peter and Gorzsás, András and Moritz, Thomas and Hahn, Michael G. and Scheller, Henrik Vibe and Aharoni, Asaph and Mellerowicz, Ewa J.},
	month = dec,
	year = {2025},
	keywords = {Plant Biology, Plant anatomy, Plant development, Plant physiology},
	pages = {113963},
}

Cuticle - a hydrophobic barrier of cutin and waxes covering the outer cell wall surface of plants - enables survival in terrestrial habitats. However, it is not understood how the hydrophobic cuticle precursors travel through the homogalacturonan-rich hydrophilic cell wall. To elucidate the role of homogalacturonan in cuticle development, we disrupted its integrity by overexpressing a pectate lyase, PtxtPL1-27, in aspen. PtxtPL1-27 had pleiotropic effects on shoot development, including the reduction of cuticle thickness and changes in cutin and wax composition, but the expression of cutin biosynthetic genes was little affected. Despite a reduction in homogalacturonan content in the leaves, labeling with the homogalacturonan-specific antibody JIM5 in the outer epidermal cell wall layer increased and displayed an altered pattern. Moreover, the ultrastructure of cell walls was changed concomitant with lipid accumulation. We propose that the disruption of homogalacturonan integrity affected the cutinsome-dependent transport and polymerization of cutin monomers in the cell wall.

@article{jiao_integrating_2025,
	title = {Integrating parental breeding value, genetic gain, and gamete contribution for elite family selection in {Platycladus} orientalis},
	volume = {37},
	issn = {1993-0607},
	url = {https://doi.org/10.1007/s11676-025-01943-7},
	doi = {10.1007/s11676-025-01943-7},
	abstract = {Platycladus orientalis (L.) Franco seed orchards play an important role in sustainable forestry in China but balancing genetic gain and genetic diversity remains a significant challenge. Two key factors influence the success of seed orchards: parental breeding value and gamete contribution, as they determine both the genetic gain and diversity of the seed crops produced. This study aimed to optimize breeding strategies by analyzing parental breeding value, gamete contribution, and genetic gain across two growth periods (89 families in 2008 and 52 families in 2021). We evaluated height, diameter at breast height, and stem volume of progeny in a primary seed orchard, uncovering significant genetic variation among families. Interestingly, no correlation was found between growth traits and gamete contribution, indicating their independence. Using comprehensive scoring and PCA-biplot analysis, we consistently identified several elite families with superior growth performance in both years. We propose an optimal breeding strategy that combines 30\% selective harvesting and 50\% selective thinning to effectively balance genetic gain and genetic diversity, addressing a critical goal in tree improvement programs. The selected families and optimized strategy provide a scalable framework not only for P. orientalis but also for other conifer species globally, enhancing both productivity and genetic diversity in afforestation efforts.},
	language = {en},
	number = {1},
	urldate = {2025-11-28},
	journal = {Journal of Forestry Research},
	author = {Jiao, Si-Qian and Li, Meiyu and Li, Zhi-Chao and Bao, Yu-Tao and Zhang, Hui-Jin and Yang, Xiao-Lei and El-Kassaby, Yousry Aly and Cheng, Shi-Ping and Mao, Jian-Feng},
	month = nov,
	year = {2025},
	keywords = {Breeding strategy, Comprehensive evaluation, Genetic gain, Platycladus orientalis, Progeny test},
	pages = {5},
}

Platycladus orientalis (L.) Franco seed orchards play an important role in sustainable forestry in China but balancing genetic gain and genetic diversity remains a significant challenge. Two key factors influence the success of seed orchards: parental breeding value and gamete contribution, as they determine both the genetic gain and diversity of the seed crops produced. This study aimed to optimize breeding strategies by analyzing parental breeding value, gamete contribution, and genetic gain across two growth periods (89 families in 2008 and 52 families in 2021). We evaluated height, diameter at breast height, and stem volume of progeny in a primary seed orchard, uncovering significant genetic variation among families. Interestingly, no correlation was found between growth traits and gamete contribution, indicating their independence. Using comprehensive scoring and PCA-biplot analysis, we consistently identified several elite families with superior growth performance in both years. We propose an optimal breeding strategy that combines 30% selective harvesting and 50% selective thinning to effectively balance genetic gain and genetic diversity, addressing a critical goal in tree improvement programs. The selected families and optimized strategy provide a scalable framework not only for P. orientalis but also for other conifer species globally, enhancing both productivity and genetic diversity in afforestation efforts.

@article{wang_genetic_2025,
	title = {Genetic control of seasonal meristem arrest in trees},
	volume = {122},
	url = {https://www.pnas.org/doi/10.1073/pnas.2505641122},
	doi = {10.1073/pnas.2505641122},
	abstract = {Perennial plants, such as trees native to temperate and boreal regions, exhibit meristems that undergo annual cycles of activity and rest to synchronize their growth cycles with seasonal changes, ensuring survival under harsh winter conditions. The arrest of shoot meristem growth, known as growth cessation, is a critical initial step for trees to enter dormancy. This process is triggered by a combination of endogenous and exogenous signals, yet the molecular mechanisms and signaling pathways underlying growth cessation remain poorly understood. In this study, we demonstrate that Populus orthologs of APETALA2-like transcription factors (AP2Ls), the primary regulators of global proliferative arrest (GPA) in Arabidopsis, play a crucial role in the regulation of seasonal growth cessation in hybrid aspen trees. In particular, AP2Ls act as important activators of the expression of FLOWERING LOCUS T2 (FT2), a key gene for short-day-induced growth cessation. This contrasts with the established role of AP2Ls as repressors of FT in annual plants. Yet, the pathway itself is conserved with the pathway regulating GPA in annual plants, a completely different process during the plant life cycle. Our research highlights both the conserved roles and functional diversities of AP2Ls in a more general balancing of meristem proliferation and arrest in perennial plants, providing insights into the evolutionary adaptation of growth regulation mechanisms across plant species.},
	number = {48},
	urldate = {2025-11-28},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {Wang, Jun and Liao, Xiaoli and Wu, Zhihao and Sane, Shashank and Han, Shaopeng and Chen, Qihui and Shi, Xueping and Dai, Xiaokang and Klintenäs, Maria and Nilsson, Ove and Ding, Jihua},
	month = dec,
	year = {2025},
	pages = {e2505641122},
}

Perennial plants, such as trees native to temperate and boreal regions, exhibit meristems that undergo annual cycles of activity and rest to synchronize their growth cycles with seasonal changes, ensuring survival under harsh winter conditions. The arrest of shoot meristem growth, known as growth cessation, is a critical initial step for trees to enter dormancy. This process is triggered by a combination of endogenous and exogenous signals, yet the molecular mechanisms and signaling pathways underlying growth cessation remain poorly understood. In this study, we demonstrate that Populus orthologs of APETALA2-like transcription factors (AP2Ls), the primary regulators of global proliferative arrest (GPA) in Arabidopsis, play a crucial role in the regulation of seasonal growth cessation in hybrid aspen trees. In particular, AP2Ls act as important activators of the expression of FLOWERING LOCUS T2 (FT2), a key gene for short-day-induced growth cessation. This contrasts with the established role of AP2Ls as repressors of FT in annual plants. Yet, the pathway itself is conserved with the pathway regulating GPA in annual plants, a completely different process during the plant life cycle. Our research highlights both the conserved roles and functional diversities of AP2Ls in a more general balancing of meristem proliferation and arrest in perennial plants, providing insights into the evolutionary adaptation of growth regulation mechanisms across plant species.

@article{aro_multivariate_2025,
	title = {Multivariate models improve accuracy of genomic prediction for spring frost tolerance in {Norway} spruce},
	volume = {18},
	copyright = {© 2025 The Author(s). The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.},
	issn = {1940-3372},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/tpg2.70151},
	doi = {10.1002/tpg2.70151},
	abstract = {Warming spring temperatures increase the risk of frost damage to emerging Norway spruce (Picea abies) buds by advancing their spring phenology and increasing the frost event frequency. We present a field-based electrolyte leakage assay to assess basal frost tolerance in newly emerging buds. Using this assay, we estimated genetic parameters and tested the effectiveness of multivariate genomic selection (GS) models integrating frost tolerance, bud burst phenology, and height growth. Multivariate models significantly improved frost tolerance prediction accuracy, particularly when incorporating bud burst data, due to a strong genetic correlation between traits (r ≈ –0.63) and high heritability of bud burst (h2 ≈ 0.60). The observed genetic correlations suggest that early-flushing genotypes exhibit higher tolerance to spring frost. Our findings underscore the importance of basal frost tolerance as a complementary trait to traditional phenological frost-avoidance strategies. Additionally, we emphasize that early-stage bud burst assessments in controlled environments can accelerate genomic predictions, overcoming the limitations imposed by long growth cycles. Integrating multi-trait genomic prediction models optimized with bud burst as an assisting trait and optimized model parameters enhances prediction accuracy of spring frost tolerance and supports the development of climate-resilient breeding strategies in Norway spruce.},
	language = {en},
	number = {4},
	urldate = {2025-11-28},
	journal = {The Plant Genome},
	author = {Aro, Tuuli and Tan, Biyue and Chen, Zhi-Qiang and Hallingbäck, Henrik and Suontama, Mari and Westin, Johan and Wu, Harry and Hurry, Vaughan},
	year = {2025},
	note = {\_eprint: https://acsess.onlinelibrary.wiley.com/doi/pdf/10.1002/tpg2.70151},
	pages = {e70151},
}

Warming spring temperatures increase the risk of frost damage to emerging Norway spruce (Picea abies) buds by advancing their spring phenology and increasing the frost event frequency. We present a field-based electrolyte leakage assay to assess basal frost tolerance in newly emerging buds. Using this assay, we estimated genetic parameters and tested the effectiveness of multivariate genomic selection (GS) models integrating frost tolerance, bud burst phenology, and height growth. Multivariate models significantly improved frost tolerance prediction accuracy, particularly when incorporating bud burst data, due to a strong genetic correlation between traits (r ≈ –0.63) and high heritability of bud burst (h2 ≈ 0.60). The observed genetic correlations suggest that early-flushing genotypes exhibit higher tolerance to spring frost. Our findings underscore the importance of basal frost tolerance as a complementary trait to traditional phenological frost-avoidance strategies. Additionally, we emphasize that early-stage bud burst assessments in controlled environments can accelerate genomic predictions, overcoming the limitations imposed by long growth cycles. Integrating multi-trait genomic prediction models optimized with bud burst as an assisting trait and optimized model parameters enhances prediction accuracy of spring frost tolerance and supports the development of climate-resilient breeding strategies in Norway spruce.

@article{chanwala_tug--war_2025,
	title = {The tug-of-war between growth and cold tolerance in plants: how to create resilient crops with maintained biomass},
	volume = {0},
	issn = {1674-2052},
	shorttitle = {The tug-of-war between growth and cold tolerance in plants},
	url = {https://www.cell.com/molecular-plant/abstract/S1674-2052(25)00396-X},
	doi = {10.1016/j.molp.2025.11.009},
	language = {English},
	number = {0},
	urldate = {2025-11-28},
	journal = {Molecular Plant},
	publisher = {Elsevier},
	author = {Chanwala, Jeky and Kindgren, Peter},
	month = nov,
	year = {2025},
}

@article{le_bail_essential_2025,
	title = {Essential developmental processes in {Physcomitrium} patens require distinct levels of total activity provided by functionally redundant {PpROP} {GTPases}},
	volume = {248},
	copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.70603},
	doi = {10.1111/nph.70603},
	abstract = {RHO (RAS homologous) GTPases regulate important cellular and developmental processes in most eukaryotes. Plant-specific ROP (RHO of plants) GTPase families expanded and functionally diversified during the evolution of vascular plants, but contain few members in nonvascular extant relatives of early land plants. Here, a systematic investigation of essential PpROP functions in the development of the nonvascular moss Physcomitrium patens is presented. This investigation was based on: knocking out individually or all possible combinations of each of the four PpROP genes, which encode nearly identical proteins; complementing knockout lines with wild-type (WT) or mutated PpROPs, or with heterologous homologs; and inducing PpROP overexpression. PpROPs were found to have previously unknown functions in cell proliferation, caulonema differentiation, and gametophore formation. PpROP functions were observed to display variable dependence on guanosine diphosphate (GDP)/guanosine triphosphate (GTP) cycling and to rely on distinct downstream signaling. Different cellular and developmental processes were determined to require distinct levels of total PpROP activity, rather than individual PpROPs. These observations provide important insights into PpROP functions and signaling in P. patens, enhancing our understanding of the evolution of the regulation of developmental processes by ROP/RHO GTPases. The evolutionary origin of the remarkable functional integration and sequence conservation within the PpROP family is discussed.},
	language = {en},
	number = {6},
	urldate = {2025-11-21},
	journal = {New Phytologist},
	author = {Le Bail, Aude and Kost, Benedikt and Nüssel, Janina and Lolis, Tamara Isabeau and Koch, David and Voll, Hildegard and Schulmeister, Sylwia and Kaier, Alexander and Ljung, Karin and Ntefidou, Maria},
	year = {2025},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.70603},
	keywords = {GTP/GDP cycling, Physcomitrium patens, RHO/ROP GTPases, apical initial cells, caulonema differentiation, gametophore development, plant evolution, polarity},
	pages = {2865--2890},
}

RHO (RAS homologous) GTPases regulate important cellular and developmental processes in most eukaryotes. Plant-specific ROP (RHO of plants) GTPase families expanded and functionally diversified during the evolution of vascular plants, but contain few members in nonvascular extant relatives of early land plants. Here, a systematic investigation of essential PpROP functions in the development of the nonvascular moss Physcomitrium patens is presented. This investigation was based on: knocking out individually or all possible combinations of each of the four PpROP genes, which encode nearly identical proteins; complementing knockout lines with wild-type (WT) or mutated PpROPs, or with heterologous homologs; and inducing PpROP overexpression. PpROPs were found to have previously unknown functions in cell proliferation, caulonema differentiation, and gametophore formation. PpROP functions were observed to display variable dependence on guanosine diphosphate (GDP)/guanosine triphosphate (GTP) cycling and to rely on distinct downstream signaling. Different cellular and developmental processes were determined to require distinct levels of total PpROP activity, rather than individual PpROPs. These observations provide important insights into PpROP functions and signaling in P. patens, enhancing our understanding of the evolution of the regulation of developmental processes by ROP/RHO GTPases. The evolutionary origin of the remarkable functional integration and sequence conservation within the PpROP family is discussed.

@article{renzi_creatine_2025,
	title = {Creatine kinase {B} regulates glycolysis and \textit{de novo} lipogenesis pathways to control lipid accumulation during adipogenesis},
	volume = {44},
	issn = {2211-1247},
	url = {https://www.sciencedirect.com/science/article/pii/S2211124725012604},
	doi = {10.1016/j.celrep.2025.116489},
	abstract = {White adipocyte differentiation or adipogenesis requires coordination of metabolic sensing and transcriptional modifications to orchestrate lipid storage. Creatine and its kinases are implicated in adipose energy buffering, but the roles of cytosolic (CKB) and mitochondrial (CKMT2) creatine kinases in adipogenesis are unclear. We find that both CKB and CKMT2 are progressively upregulated during differentiation. Functional studies show that CKB restrains de novo lipogenesis (DNL) by limiting activation of carbohydrate-responsive element-binding protein (ChREBP), a key regulator of lipogenic genes. Mechanistically, CKB interacts with AKT and regulates its activation in response to insulin. Loss of CKB causes persistent AKT-mTORC1 signaling, increases glycolytic flux, and enhances ChREBP activation, thereby promoting glucose-derived lipid synthesis. Thus, CKB acts as a metabolic rheostat linking creatine-kinase activity to insulin signaling and nutrient-responsive transcription. We propose a CKB-AKT-ChREBP regulatory axis that contributes to metabolic remodeling and lipid homeostasis during adipocyte differentiation.},
	number = {11},
	urldate = {2025-11-14},
	journal = {Cell Reports},
	author = {Renzi, Gianluca and Higos, Romane and Vlassakev, Ivan and Bello, Abdoul Akim and Omar-Hmeadi, Muhmmad and Hansen, Mattias and Merabtene, Fatiha and Rouault, Christine and Hodek, Ondrej and Massier, Lucas and Antonny, Bruno and Marcelin, Geneviève and Rahbani, Janane F. and Lecoutre, Simon and Maqdasy, Salwan},
	month = nov,
	year = {2025},
	keywords = {AKT-mTORC, CKB, ChREBP, adipogenesis, creatine kinase, lipogenesis, white adipocyte},
	pages = {116489},
}

White adipocyte differentiation or adipogenesis requires coordination of metabolic sensing and transcriptional modifications to orchestrate lipid storage. Creatine and its kinases are implicated in adipose energy buffering, but the roles of cytosolic (CKB) and mitochondrial (CKMT2) creatine kinases in adipogenesis are unclear. We find that both CKB and CKMT2 are progressively upregulated during differentiation. Functional studies show that CKB restrains de novo lipogenesis (DNL) by limiting activation of carbohydrate-responsive element-binding protein (ChREBP), a key regulator of lipogenic genes. Mechanistically, CKB interacts with AKT and regulates its activation in response to insulin. Loss of CKB causes persistent AKT-mTORC1 signaling, increases glycolytic flux, and enhances ChREBP activation, thereby promoting glucose-derived lipid synthesis. Thus, CKB acts as a metabolic rheostat linking creatine-kinase activity to insulin signaling and nutrient-responsive transcription. We propose a CKB-AKT-ChREBP regulatory axis that contributes to metabolic remodeling and lipid homeostasis during adipocyte differentiation.

@article{fenech_cyp71a_2025,
	title = {The {CYP71A}, {NIT}, {AMI}, and {IAMH} gene families are dispensable for indole-3-acetaldoxime-mediated auxin biosynthesis in {Arabidopsis}},
	volume = {37},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koaf242},
	doi = {10.1093/plcell/koaf242},
	abstract = {The auxin indole-3-acetic acid (IAA) governs plant development and environmental responses. Although the indole-3-pyruvic acid (IPyA) pathway is the predominant route for IAA biosynthesis, other pathways have been proposed, such as the indole-3-acetaldoxime (IAOx) pathway. The IAOx pathway has garnered attention due to its supposed activation in auxin-overproducing mutants (e.g. sur1, sur2, ugt74b1) and the auxin-like responses triggered by exogenous application of its proposed intermediates IAOx, indole-3-acetonitrile (IAN), and indole-3-acetamide (IAM). However, despite the supporting evidence for individual steps of the IAOx pathway, its overall physiological relevance remains inconclusive. Here, using a comprehensive genetic approach combined with metabolic and phenotypic profiling, we demonstrate that mutating gene families proposed to function in the IAOx pathway in Arabidopsis (Arabidopsis thaliana) does not result in prominent auxin-deficient phenotypes, nor are these genes required for the high auxin production in the sur2 mutant. Our findings also challenge the previously postulated linear IAOx pathway. Exogenously provided IAOx, IAN, and IAM can be converted to IAA in vivo, but they do not act as precursors for each other. Finally, our findings question the physiological relevance of IAM and IAN as IAA precursors in plants and suggest the existence of a yet-uncharacterized route for IAA production in the sur2 mutant, likely involving IAOx as an intermediate. The identification of the metabolic steps and the corresponding genes in this pathway may uncover another IAA biosynthesis route in plants.},
	number = {11},
	urldate = {2025-11-14},
	journal = {The Plant Cell},
	author = {Fenech, Mario and Brumos, Javier and Pěnčík, Aleš and Edwards, Brianne and Belcapo, Sara and DeLacey, Jennifer and Patel, Arjun and Kater, Martin and Li, Xu and Ljung, Karin and Novak, Ondrej and Alonso, José M and Stepanova, Anna N},
	month = nov,
	year = {2025},
	pages = {koaf242},
}

The auxin indole-3-acetic acid (IAA) governs plant development and environmental responses. Although the indole-3-pyruvic acid (IPyA) pathway is the predominant route for IAA biosynthesis, other pathways have been proposed, such as the indole-3-acetaldoxime (IAOx) pathway. The IAOx pathway has garnered attention due to its supposed activation in auxin-overproducing mutants (e.g. sur1, sur2, ugt74b1) and the auxin-like responses triggered by exogenous application of its proposed intermediates IAOx, indole-3-acetonitrile (IAN), and indole-3-acetamide (IAM). However, despite the supporting evidence for individual steps of the IAOx pathway, its overall physiological relevance remains inconclusive. Here, using a comprehensive genetic approach combined with metabolic and phenotypic profiling, we demonstrate that mutating gene families proposed to function in the IAOx pathway in Arabidopsis (Arabidopsis thaliana) does not result in prominent auxin-deficient phenotypes, nor are these genes required for the high auxin production in the sur2 mutant. Our findings also challenge the previously postulated linear IAOx pathway. Exogenously provided IAOx, IAN, and IAM can be converted to IAA in vivo, but they do not act as precursors for each other. Finally, our findings question the physiological relevance of IAM and IAN as IAA precursors in plants and suggest the existence of a yet-uncharacterized route for IAA production in the sur2 mutant, likely involving IAOx as an intermediate. The identification of the metabolic steps and the corresponding genes in this pathway may uncover another IAA biosynthesis route in plants.

@article{albrectsen_nordic_2025,
	title = {Nordic {Countries} as an {Opportunity} for {Sustainable}, {Low} {Pest} {Seed} {Potato} {Production} in a {Climate} {Change} {Scenario}},
	issn = {1871-4528},
	url = {https://doi.org/10.1007/s11540-025-09935-0},
	doi = {10.1007/s11540-025-09935-0},
	abstract = {Based on discussions within the Northern Tubers of Potato network (N’TOP-net), this review highlights northern Scandinavia’s potential for sustainable, low pest seed potato production. While long transport distances currently limit large-scale supply for consumption or processing, low pest pressure and stricter EU plant protection regulations increase its value for seed production. Climate change is expected to extend the growing season, driving renewed interest in Northern Scandinavia’s role in European food security. Finland exemplifies this potential, and parts of northern and central Sweden—historically suppliers of disease-free seed potatoes, even exported to Brazil—offer expansion opportunities. Nordic potato production, key biotic stressors, and opportunities for regional cooperation are examined, with a focus on novel farming practices, breeding innovations, and disease surveillance to improve resilience and sustainability. Despite shared values in cultivar selection, certification, and potato preferences, Nordic production strategies remain uncoordinated for long-term sustainability. We advocate for transnational, interdisciplinary collaboration to enhance Europe’s food security through joint efforts in three key areas: (1) soil-conserving farming, (2) breeding for adaptation to longer day length and resistance traits, and (3) transnational pest and disease surveillance. A Nordic potato initiative can strengthen European cooperation on sustainable production amid climate change. However, as policies must balance the benefits of longer growing seasons with emerging risks such as pests, droughts, and flooding, coordinated research, regulatory adaptation, and climate resilience investments are essential for safeguarding seed potato quality, food security, and supply chain stability.},
	language = {en},
	urldate = {2025-11-07},
	journal = {Potato Research},
	author = {Albrectsen, Benedicte Riber and Mäkinen, Kristiina and Mahawar, Lovely and Mishra, Arti and Abuley, Isaac Kwesi and Veillon, Isalyne and Gopan, Apsara Indhu and Sajeevan, Radha Sivarajan and Resjö, Svante and Andreasson, Erik and Liljeroth, Erland and Marhavý, Peter and Rossmann, Simeon Lim and Hansen, Jens Grønbech},
	month = oct,
	year = {2025},
	keywords = {Climate change adaptation, Food security strategy, Potato disease management, Seed potato production, Sustainable farming},
}

Based on discussions within the Northern Tubers of Potato network (N’TOP-net), this review highlights northern Scandinavia’s potential for sustainable, low pest seed potato production. While long transport distances currently limit large-scale supply for consumption or processing, low pest pressure and stricter EU plant protection regulations increase its value for seed production. Climate change is expected to extend the growing season, driving renewed interest in Northern Scandinavia’s role in European food security. Finland exemplifies this potential, and parts of northern and central Sweden—historically suppliers of disease-free seed potatoes, even exported to Brazil—offer expansion opportunities. Nordic potato production, key biotic stressors, and opportunities for regional cooperation are examined, with a focus on novel farming practices, breeding innovations, and disease surveillance to improve resilience and sustainability. Despite shared values in cultivar selection, certification, and potato preferences, Nordic production strategies remain uncoordinated for long-term sustainability. We advocate for transnational, interdisciplinary collaboration to enhance Europe’s food security through joint efforts in three key areas: (1) soil-conserving farming, (2) breeding for adaptation to longer day length and resistance traits, and (3) transnational pest and disease surveillance. A Nordic potato initiative can strengthen European cooperation on sustainable production amid climate change. However, as policies must balance the benefits of longer growing seasons with emerging risks such as pests, droughts, and flooding, coordinated research, regulatory adaptation, and climate resilience investments are essential for safeguarding seed potato quality, food security, and supply chain stability.

@article{rosenkranz_cis-_2025,
	title = {Cis- and trans-action of the cold-induced {lncRNAs}, {SVALKA} and {SVALNA}, regulate {CBF1} and {CBF3} in {Arabidopsis}},
	volume = {26},
	issn = {1469-221X},
	url = {https://www.embopress.org/doi/full/10.1038/s44319-025-00568-5},
	doi = {10.1038/s44319-025-00568-5},
	abstract = {Long noncoding RNAs (lncRNAs) are emerging as key regulatory players of coding gene expression in eukaryotes. Here, we investigate the roles of the lncRNAs SVALKA (SVK) and SVALNA (SVN) in regulating CBF1 and CBF3 gene expression in Arabidopsis under cold stress conditions. We integrated omics approaches, together with genetics and molecular biology, to uncover the transcriptional dynamics and regulatory mechanisms of SVK and SVN. Our results demonstrate that SVK functions as a cis- and trans-acting lncRNA, regulating both CBF1 and CBF3 through RNAPII collision and chromatin remodeling, while SVN serves a cis role by negatively regulating CBF3 via a RNAPII collision mechanism. We identified isoforms of SVK, originating from distinct transcription start sites and undergo alternative splicing which might be important to adapt stability, crucial for the regulatory functions. Furthermore, we show that two positionally conserved lncRNAs, originating from the upstream antisense strand of neighboring genes, can have different molecular mechanisms to regulate their targets. This study elucidates the complex interplay of lncRNAs in gene regulation, highlighting their essential roles in modulating responses to environmental stresses. Our findings contribute to a deeper understanding of the mechanisms underlying lncRNA functionality and their significance in gene regulatory networks in eukaryotes.},
	number = {20},
	urldate = {2025-11-07},
	journal = {EMBO reports},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Rosenkranz, Isabell and Mermet, Sarah and Zacharaki, Vasiliki and Kindgren, Peter},
	month = oct,
	year = {2025},
	note = {Num Pages: 5087},
	keywords = {Arabidopsis, Cold Response, Epigenetic Regulation, Long Non-coding RNAs},
	pages = {5070--5087},
}

Long noncoding RNAs (lncRNAs) are emerging as key regulatory players of coding gene expression in eukaryotes. Here, we investigate the roles of the lncRNAs SVALKA (SVK) and SVALNA (SVN) in regulating CBF1 and CBF3 gene expression in Arabidopsis under cold stress conditions. We integrated omics approaches, together with genetics and molecular biology, to uncover the transcriptional dynamics and regulatory mechanisms of SVK and SVN. Our results demonstrate that SVK functions as a cis- and trans-acting lncRNA, regulating both CBF1 and CBF3 through RNAPII collision and chromatin remodeling, while SVN serves a cis role by negatively regulating CBF3 via a RNAPII collision mechanism. We identified isoforms of SVK, originating from distinct transcription start sites and undergo alternative splicing which might be important to adapt stability, crucial for the regulatory functions. Furthermore, we show that two positionally conserved lncRNAs, originating from the upstream antisense strand of neighboring genes, can have different molecular mechanisms to regulate their targets. This study elucidates the complex interplay of lncRNAs in gene regulation, highlighting their essential roles in modulating responses to environmental stresses. Our findings contribute to a deeper understanding of the mechanisms underlying lncRNA functionality and their significance in gene regulatory networks in eukaryotes.

@article{liu_genome_2025,
	title = {Genome and transcriptome analysis provide insights into the genetics and breeding of {Salix} suchowensis growth traits},
	volume = {56},
	issn = {1573-5095},
	url = {https://doi.org/10.1007/s11056-025-10132-7},
	doi = {10.1007/s11056-025-10132-7},
	abstract = {Shrub willow species (Salix sp.) are ideal for cultivation as bioenergy source and can serve as effective models for genetic research due to their rapid growth rates. Understanding the genetic basis of growth traits in willows can enhance the development of high-quality cultivars. In this study, we performed genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) mapping, and transcriptome-wide association analyses to investigate the genetic basis of plant height (Height) and ground diameter (GD) in a full-sib population of Salix suchowensis derived from eight parental lines, which were phenotyped across three sites in southwest China. We identified 15 quantitative trait loci (QTLs) associated with Height and 10 QTLs associated with GD. Furthermore, we identified 938 eQTLs influencing the expression of 685 genes, including a trans-eQTL hub, as well as eight co-expression modules correlated with Height and GD. Transcriptome-wide association studies (TWAS) revealed five genes linked to Height and three genes associated with GD. By jointly modeling genetic variations and environmental factors, we developed a multi-site predictive model that outperformed the genomic best linear unbiased prediction. This study provides valuable insights into the genetic regulatory mechanisms underlying key growth traits in S. suchowensis and establishes a genomic prediction model to facilitate the rapid genetic improvement of the species.},
	language = {en},
	number = {6},
	urldate = {2025-11-07},
	journal = {New Forests},
	author = {Liu, Wei and Gu, Shaobo and Zhu, Mingjia and Han, Yu and Dai, Xiaogang and Wu, Huaitong and Yin, Tongming and Guo, Linjie and Feng, Landi and Zan, Yanjun and Liu, Jianquan},
	month = oct,
	year = {2025},
	keywords = {Breeding prediction, Ground diameter, Plant height, QTL, QTL-by-environment interactions, Salix suchowensis},
	pages = {63},
}

Shrub willow species (Salix sp.) are ideal for cultivation as bioenergy source and can serve as effective models for genetic research due to their rapid growth rates. Understanding the genetic basis of growth traits in willows can enhance the development of high-quality cultivars. In this study, we performed genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) mapping, and transcriptome-wide association analyses to investigate the genetic basis of plant height (Height) and ground diameter (GD) in a full-sib population of Salix suchowensis derived from eight parental lines, which were phenotyped across three sites in southwest China. We identified 15 quantitative trait loci (QTLs) associated with Height and 10 QTLs associated with GD. Furthermore, we identified 938 eQTLs influencing the expression of 685 genes, including a trans-eQTL hub, as well as eight co-expression modules correlated with Height and GD. Transcriptome-wide association studies (TWAS) revealed five genes linked to Height and three genes associated with GD. By jointly modeling genetic variations and environmental factors, we developed a multi-site predictive model that outperformed the genomic best linear unbiased prediction. This study provides valuable insights into the genetic regulatory mechanisms underlying key growth traits in S. suchowensis and establishes a genomic prediction model to facilitate the rapid genetic improvement of the species.

@article{zacharaki_convergent_2025,
	title = {Convergent antisense transcription primes hosting genes for stress responsiveness in plants},
	volume = {18},
	issn = {1674-2052},
	url = {https://www.sciencedirect.com/science/article/pii/S167420522500351X},
	doi = {10.1016/j.molp.2025.10.001},
	abstract = {Plants need to constantly surveil their surroundings to adapt to environmental fluctuations, which they achieve primarily through transcriptional reprogramming. Thus, plants are excellent models for identifying novel transcriptional regulatory mechanisms. In this study, we characterize the regulation mediated by long non-coding transcription that initiates on the complementary strand in the 5ʹ end of coding genes (convergent antisense transcription, CASt). In Arabidopsis, CASt is associated with stress-responsive genes that are highly expressed. Our analysis shows that CASt depends on a specific gene architecture that is evolutionarily conserved in higher plants. CASt is present in genes with an extended first intron and over-represented in genes encoding functional transporters in Arabidopsis, such as the AMINO ACID PERMEASE (AAP) transporter family. Experimental evidence points to a role for CASt in priming their host genes for stress responsiveness in evolutionary divergent plant species. Furthermore, we were able to predict stress responsiveness in rice AAP genes based on the presence of a long first intron and CASt. Collectively, we show an evolutionary strategy and regulatory mechanism specific to plants for enhancing stress responsiveness through modification of gene architecture and antisense transcription.},
	number = {11},
	urldate = {2025-11-07},
	journal = {Molecular Plant},
	author = {Zacharaki, Vasiliki and Quevedo, Marti and Nardeli, Sarah Muniz and Meena, Shiv Kumar and Monte, Elena and Kindgren, Peter},
	month = nov,
	year = {2025},
	keywords = {Antisense transcription, Arabidopsis, Cold acclimation, Transporters, antisense transcription, cold acclimation, transporters},
	pages = {1920--1931},
}

Plants need to constantly surveil their surroundings to adapt to environmental fluctuations, which they achieve primarily through transcriptional reprogramming. Thus, plants are excellent models for identifying novel transcriptional regulatory mechanisms. In this study, we characterize the regulation mediated by long non-coding transcription that initiates on the complementary strand in the 5ʹ end of coding genes (convergent antisense transcription, CASt). In Arabidopsis, CASt is associated with stress-responsive genes that are highly expressed. Our analysis shows that CASt depends on a specific gene architecture that is evolutionarily conserved in higher plants. CASt is present in genes with an extended first intron and over-represented in genes encoding functional transporters in Arabidopsis, such as the AMINO ACID PERMEASE (AAP) transporter family. Experimental evidence points to a role for CASt in priming their host genes for stress responsiveness in evolutionary divergent plant species. Furthermore, we were able to predict stress responsiveness in rice AAP genes based on the presence of a long first intron and CASt. Collectively, we show an evolutionary strategy and regulatory mechanism specific to plants for enhancing stress responsiveness through modification of gene architecture and antisense transcription.

@article{larsson_boreal_2025,
	title = {Boreal tree species selection enhances forest carbon stocks through above- rather than below-ground changes},
	volume = {596},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112725005687},
	doi = {10.1016/j.foreco.2025.123060},
	abstract = {Forest management has the potential to impact the net forest carbon (C) balance, and a better understanding of how tree species influence soil C provides a potential tool to promote higher C uptake and storage in forests. In this study, we utilized two common garden experiments located in northern and central Sweden to compare soil organic C stocks associated with six different boreal tree species (Betula pendula, Larix sp., Picea abies, Picea glauca, Pinus contorta and Pinus sylvestris), approximately 30 years after planting. We measured both above- and below-ground C inputs and C outputs via decomposition and analyzed how these factors influenced soil C stocks. Our results showed that the vertical distribution of SOC differed between the species, and furthermore, many of the SOC input and output processes measured were species-dependent. Despite this, we found no differences in total belowground soil C stock between the species. The aboveground biomass C stocks, in contrast, were highly species-specific, with the rank order of species differing between the two sites. As such, our study indicates that tree species choice may serve as a tool to promote ecosystem C stocks, and in turn enhance the climate change mitigation potential of forests.},
	urldate = {2025-10-24},
	journal = {Forest Ecology and Management},
	author = {Larsson, Marcus and Gundale, Michael J. and Spitzer, Clydecia M. and Nordin, Annika},
	month = nov,
	year = {2025},
	keywords = {Boreal forest, Boreal tree species, Forest growth, Litter input, Root production, Soil organic carbon},
	pages = {123060},
}

Forest management has the potential to impact the net forest carbon (C) balance, and a better understanding of how tree species influence soil C provides a potential tool to promote higher C uptake and storage in forests. In this study, we utilized two common garden experiments located in northern and central Sweden to compare soil organic C stocks associated with six different boreal tree species (Betula pendula, Larix sp., Picea abies, Picea glauca, Pinus contorta and Pinus sylvestris), approximately 30 years after planting. We measured both above- and below-ground C inputs and C outputs via decomposition and analyzed how these factors influenced soil C stocks. Our results showed that the vertical distribution of SOC differed between the species, and furthermore, many of the SOC input and output processes measured were species-dependent. Despite this, we found no differences in total belowground soil C stock between the species. The aboveground biomass C stocks, in contrast, were highly species-specific, with the rank order of species differing between the two sites. As such, our study indicates that tree species choice may serve as a tool to promote ecosystem C stocks, and in turn enhance the climate change mitigation potential of forests.

@article{tronnet_extracellular_2025,
	title = {Extracellular {ATP} is an environmental cue in bacteria},
	volume = {44},
	issn = {2211-1247},
	url = {https://www.sciencedirect.com/science/article/pii/S2211124725011271},
	doi = {10.1016/j.celrep.2025.116356},
	abstract = {In animals and plants, extracellular ATP (eATP) functions as a signal and regulates the immune response. During inflammation, intestinal bacteria are exposed to elevated eATP originating from the mucosa. However, whether bacteria respond to eATP is unclear. Here, we show that non-pathogenic Escherichia coli responds to eATP by modifying its transcriptional and metabolic landscapes. A genome-scale promoter library showed that the response is dependent on time, concentration, and medium and ATP specific. Second messengers and genes related to metabolism, biofilm formation, and envelope stress were regulated downstream of eATP. Metabolomics confirmed that eATP triggers enrichment of compounds with bioactive properties in the host or bacteria. Combined genome-scale modeling revealed modifications to global metabolic and biomass building blocks. Consequently, eATP altered the sensitivity to antibiotics and antimicrobial peptides. Finally, in pathogens, eATP controlled virulence factor expression. Our results indicate that eATP is an environmental cue in prokaryotes, which broadly regulates physiology, antimicrobial resistance, and virulence.},
	number = {10},
	urldate = {2025-10-17},
	journal = {Cell Reports},
	author = {Tronnet, Sophie and Pandey, Vikash and Lloret-Berrocal, Miriam and Pérez-del-Pozo, Mario and Hernández-Ortego, Carlos and Söderholm, Niklas and Billker, Oliver and Nordström, Anders and Puhar, Andrea},
	month = oct,
	year = {2025},
	keywords = {Enterobacteriaceae, antimicrobial resistance, extracellular ATP, gene expression, inflammation, intestinal bacteria, metabolites, physiology, purinergic signaling, virulence},
	pages = {116356},
}

In animals and plants, extracellular ATP (eATP) functions as a signal and regulates the immune response. During inflammation, intestinal bacteria are exposed to elevated eATP originating from the mucosa. However, whether bacteria respond to eATP is unclear. Here, we show that non-pathogenic Escherichia coli responds to eATP by modifying its transcriptional and metabolic landscapes. A genome-scale promoter library showed that the response is dependent on time, concentration, and medium and ATP specific. Second messengers and genes related to metabolism, biofilm formation, and envelope stress were regulated downstream of eATP. Metabolomics confirmed that eATP triggers enrichment of compounds with bioactive properties in the host or bacteria. Combined genome-scale modeling revealed modifications to global metabolic and biomass building blocks. Consequently, eATP altered the sensitivity to antibiotics and antimicrobial peptides. Finally, in pathogens, eATP controlled virulence factor expression. Our results indicate that eATP is an environmental cue in prokaryotes, which broadly regulates physiology, antimicrobial resistance, and virulence.

@article{rydman_metabolomics_2025,
	title = {A {Metabolomics} and {Transcriptomics} {Resource} for {Identifying} {Candidate} {Genes} in the {Biosynthesis} of {Specialised} {Metabolites} in {Populus} tremula},
	volume = {177},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70567},
	doi = {10.1111/ppl.70567},
	abstract = {This study aims to identify candidate genes involved in the biosynthesis of salicinoid phenolic glycosides (SPGs), a group of specialised metabolites characteristic of the Salicaceae family. While the integration of multi-omics data represents a powerful approach to link genes encoding enzymes and their regulatory factors to metabolite biosynthesis, suitable multi-omics data resources are scarce. We present a comprehensive dataset comprising untargeted liquid chromatography–mass spectrometry (LC–MS) and mRNA-sequencing data from various organs of European aspen (Populus tremula L.) and from genotypes that produce contrasting sets of SPGs. We present a reproducible pipeline for the analysis of the LC–MS data, including predicted annotation of potential novel SPGs. We demonstrate the utility of the resource by identifying candidate genes involved in the biosynthesis of SPGs with a cinnamoyl moiety. By integrating gene and metabolite differential analyses with a gene co-expression network, we identified two HXXXD-type acyltransferase genes and one UDP-glucosyltransferase gene as candidates for future downstream characterisation. The combined gene expression and metabolomics resource is integrated into PlantGenIE.org to facilitate easy access and data mining. All raw data are available in public databases, and all data and results files are available at an associated Figshare repository.},
	language = {en},
	number = {5},
	urldate = {2025-10-13},
	journal = {Physiologia Plantarum},
	author = {Rydman, Sara M. and Lihavainen, Jenna and Robinson, Kathryn M. and Jansson, Stefan and Albrectsen, Benedicte R. and Street, Nathaniel R.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70567},
	keywords = {Populus tremula, RNA-Seq, aspen, biosynthesis, chemotype, liquid chromatography–mass spectrometry (LC–MS), metabolomics, phenolic glycosides, salicinoid, specialised metabolite},
	pages = {e70567},
}

This study aims to identify candidate genes involved in the biosynthesis of salicinoid phenolic glycosides (SPGs), a group of specialised metabolites characteristic of the Salicaceae family. While the integration of multi-omics data represents a powerful approach to link genes encoding enzymes and their regulatory factors to metabolite biosynthesis, suitable multi-omics data resources are scarce. We present a comprehensive dataset comprising untargeted liquid chromatography–mass spectrometry (LC–MS) and mRNA-sequencing data from various organs of European aspen (Populus tremula L.) and from genotypes that produce contrasting sets of SPGs. We present a reproducible pipeline for the analysis of the LC–MS data, including predicted annotation of potential novel SPGs. We demonstrate the utility of the resource by identifying candidate genes involved in the biosynthesis of SPGs with a cinnamoyl moiety. By integrating gene and metabolite differential analyses with a gene co-expression network, we identified two HXXXD-type acyltransferase genes and one UDP-glucosyltransferase gene as candidates for future downstream characterisation. The combined gene expression and metabolomics resource is integrated into PlantGenIE.org to facilitate easy access and data mining. All raw data are available in public databases, and all data and results files are available at an associated Figshare repository.

@article{corredor_apoptotic_2025,
	title = {Apoptotic bodies in phytoplankton suggest evolutionary conservation of cell death mechanisms},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-63956-4},
	doi = {10.1038/s41467-025-63956-4},
	abstract = {Programmed Cell Death (PCD) in eukaryotes is a regulated process occurring during development, cell differentiation and aging. Apoptosis is a particularly well studied morphotype of PCD, only observed in animal cells (metazoan). Its most definitive hallmark is the formation and release of membrane-enclosed extracellular vesicles called Apoptotic Bodies (ABs). Although apoptotic-like features have been described in plants, yeast, protozoa and phytoplankton, the production of ABs has been thought to be limited to multicellular animals. Here we report the production and release of extracellular ABs in a non-metazoan unicellular eukaryote, the cryptophyte alga Guillardia theta. Morphologies of G. theta cells during aging and pharmacologically-induced cell death confirm the presence of ABs and apoptosis in phytoplankton. G. theta ABs have similar composition to metazoan ABs, carrying DNA, proteins, lipids, carbohydrates, fragments of organelles and cytosol portions. Our results demonstrate that G. theta, a microalga that arose from secondary endosymbiosis, experiences apoptotic cell death in physiological conditions, similar to animal cells. Since secondary endosymbiosis occurred prior to the origin of multicellularity, our discovery questions the evolutionary origin of PCD.},
	language = {en},
	number = {1},
	urldate = {2025-10-03},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Corredor, Luisa and Vergou, Georgia Antonia and Skalický, Vladimír and Antoniadi, Ioanna and Wheaton, Benjamin J. and Ljung, Karin and Gorzsás, András and Funk, Christiane},
	month = sep,
	year = {2025},
	keywords = {Apoptosis, Cellular microbiology, Plant cell death},
	pages = {8427},
}

Programmed Cell Death (PCD) in eukaryotes is a regulated process occurring during development, cell differentiation and aging. Apoptosis is a particularly well studied morphotype of PCD, only observed in animal cells (metazoan). Its most definitive hallmark is the formation and release of membrane-enclosed extracellular vesicles called Apoptotic Bodies (ABs). Although apoptotic-like features have been described in plants, yeast, protozoa and phytoplankton, the production of ABs has been thought to be limited to multicellular animals. Here we report the production and release of extracellular ABs in a non-metazoan unicellular eukaryote, the cryptophyte alga Guillardia theta. Morphologies of G. theta cells during aging and pharmacologically-induced cell death confirm the presence of ABs and apoptosis in phytoplankton. G. theta ABs have similar composition to metazoan ABs, carrying DNA, proteins, lipids, carbohydrates, fragments of organelles and cytosol portions. Our results demonstrate that G. theta, a microalga that arose from secondary endosymbiosis, experiences apoptotic cell death in physiological conditions, similar to animal cells. Since secondary endosymbiosis occurred prior to the origin of multicellularity, our discovery questions the evolutionary origin of PCD.

@article{guo_near-gapless_2025,
	title = {Near-gapless telomere-to-telomere reference nuclear genome and variable mitochondrial genome of \textit{{Amborella} trichopoda}},
	volume = {52},
	issn = {1673-8527},
	url = {https://www.sciencedirect.com/science/article/pii/S1673852725001250},
	doi = {10.1016/j.jgg.2025.04.016},
	number = {9},
	urldate = {2025-09-26},
	journal = {Journal of Genetics and Genomics},
	author = {Guo, Zhonglong and Guo, Jing-Fang and Wei, Zhi-Yan and Zhang, Ren-Gang and McMahan, Scott and Nie, Shuai and Yan, Xue-Mei and Zhou, Shan-Shan and Yun, Quan-Zheng and Wu, Jia-Yi and Ge, Jing and Yang, Yong and Xue, Jia-Yu and Mao, Jian-Feng},
	month = sep,
	year = {2025},
	pages = {1151--1154},
}

@article{lei_comprehensive_2025,
	title = {Comprehensive analysis of 1,771 transcriptomes from 7 tissues enhance genetic and biological interpretations of maize complex traits},
	volume = {15},
	issn = {2160-1836},
	url = {https://doi.org/10.1093/g3journal/jkaf140},
	doi = {10.1093/g3journal/jkaf140},
	abstract = {By reanalyzing 1,771 RNA-seq datasets from 7 tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation, evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex traits. Through an integrative analysis of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and several candidate genes for a number of agronomic traits, including leaf during the day for the anthesis-silking interval, leaf during the day for kernel Zeinoxanthin level, and root for ear height, highlighting the potential contribution of tissue-specific gene expression to variation in agronomic traits. Using transcriptome-wide association and colocalization analysis, we associated tissue-specific expression variation of 74 genes to agronomic traits variation. Our findings provide novel insights into the genetic and biological mechanisms underlying maize complex traits, and the multi-tissue regulatory atlas serves as a primary source for biological interpretation, functional validation, and genomic improvement of maize.},
	number = {9},
	urldate = {2025-09-19},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Lei, Mengyu and Si, Huan and Zhu, Mingjia and Han, Yu and Liu, Wei and Dai, Yifei and Ji, Yan and Liu, Zhengwen and Hao, Fan and Hao, Ran and Zhao, Jiarui and Ye, Guoyou and Zan, Yanjun},
	month = sep,
	year = {2025},
	pages = {jkaf140},
}

By reanalyzing 1,771 RNA-seq datasets from 7 tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation, evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex traits. Through an integrative analysis of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and several candidate genes for a number of agronomic traits, including leaf during the day for the anthesis-silking interval, leaf during the day for kernel Zeinoxanthin level, and root for ear height, highlighting the potential contribution of tissue-specific gene expression to variation in agronomic traits. Using transcriptome-wide association and colocalization analysis, we associated tissue-specific expression variation of 74 genes to agronomic traits variation. Our findings provide novel insights into the genetic and biological mechanisms underlying maize complex traits, and the multi-tissue regulatory atlas serves as a primary source for biological interpretation, functional validation, and genomic improvement of maize.

@article{marcon_transcriptional_2025,
	title = {A transcriptional roadmap of the yearly growth cycle in {Populus} trees},
	volume = {37},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koaf208},
	doi = {10.1093/plcell/koaf208},
	abstract = {Populus species have adapted to many different boreal environments, characterized by fluctuating seasons. The environmental shifts throughout the year trigger molecular responses in trees, regulating crucial developmental processes. To study these molecular responses, we performed RNA sequencing on 207 samples from European aspen (Populus tremula) trees grown outdoors during different stages of their annual growth cycle, together with samples from hybrid aspen (Populus tremula × tremuloides hybrid T89) trees grown in controlled conditions mimicking seasonal changes in day length and temperature. This created a complete transcriptional roadmap of the yearly growth cycle of Populus trees. Co-expression network analyses produced 46 modules, 36 of which show a seasonal expression profile where many aspects were mimicked by indoor samples. However, several modules differed between outdoor and indoor conditions, indicating that important aspects of growth regulation are missed in experiments conducted under controlled conditions. The module networks identify gene hubs involved in season-specific molecular processes of Populus trees during the year. To make the dataset easily accessible, we developed POPUL-R (https://lauragarciaromanach.shinyapps.io/popul\_r\_mini/), a Shiny app enabling users to visualize gene expression data and create interactive networks. POPUL-R will be a valuable tool for the scientific community to explore the role of specific genes in the annual growth cycle of trees.},
	number = {9},
	urldate = {2025-09-12},
	journal = {The Plant Cell},
	author = {Marcon, Alice and Romañach, Laura García and André, Domenique and Ding, Jihua and Zhang, Bo and Hvidsten, Torgeir R and Nilsson, Ove},
	month = sep,
	year = {2025},
	pages = {koaf208},
}

Populus species have adapted to many different boreal environments, characterized by fluctuating seasons. The environmental shifts throughout the year trigger molecular responses in trees, regulating crucial developmental processes. To study these molecular responses, we performed RNA sequencing on 207 samples from European aspen (Populus tremula) trees grown outdoors during different stages of their annual growth cycle, together with samples from hybrid aspen (Populus tremula × tremuloides hybrid T89) trees grown in controlled conditions mimicking seasonal changes in day length and temperature. This created a complete transcriptional roadmap of the yearly growth cycle of Populus trees. Co-expression network analyses produced 46 modules, 36 of which show a seasonal expression profile where many aspects were mimicked by indoor samples. However, several modules differed between outdoor and indoor conditions, indicating that important aspects of growth regulation are missed in experiments conducted under controlled conditions. The module networks identify gene hubs involved in season-specific molecular processes of Populus trees during the year. To make the dataset easily accessible, we developed POPUL-R (https://lauragarciaromanach.shinyapps.io/popul_r_mini/), a Shiny app enabling users to visualize gene expression data and create interactive networks. POPUL-R will be a valuable tool for the scientific community to explore the role of specific genes in the annual growth cycle of trees.

@article{boussardon_comparative_2025,
	title = {Comparative {Study} of the {Mitochondrial} {Proteome} {From} {Mesophyll}, {Vascular}, and {Guard} {Cells} in {Response} to {Carbon} {Starvation}},
	volume = {177},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70465},
	doi = {10.1111/ppl.70465},
	abstract = {A leaf is an organ composed of different tissues that fulfill specific functions. We hypothesized that since cells in vascular or mesophyll tissues as well as in stoma are developmentally tuned to operate their functions, mitochondria from these cells could exhibit significant metabolic differences. Using the IMTACT method, mitochondria were isolated from these three specific cell types, and the subsequent proteomes were analyzed. At steady state, mitochondria from vascular and guard cells had a significantly higher abundance of proteins associated with the mtETC, the TCA cycle, and the metabolic use of amino acids (glutamate, proline, isoleucine, leucine, and valine) as alternative substrates. Intriguingly, the mitochondria from guard cells also had a much lower abundance of proteins involved in the translation machinery, thus raising questions about the efficiency of the mitochondrial protein turnover in these cells. In a second step, we carried out the same comparative analysis, but with plants that were subjected to carbon starvation by placing them in prolonged darkness for three or 6 days. For all cell types studied, an increased abundance of proteins involved in branched-chain amino acid metabolism was detected. However, while guard cell mitochondria underwent a drastic reduction in proteins involved in respiration, translation, and RNA editing, suggesting a sharp downregulation of mitochondrial functions, mitochondrial proteomes from mesophyll and vascular cells did not show many differences, except for an increased arginine/proline/glutamate metabolism. Together, the results reported here support a differential regulation of the mitochondrial metabolism among the cell types constituting a leaf, a difference that is exacerbated upon stress.},
	language = {en},
	number = {5},
	urldate = {2025-09-05},
	journal = {Physiologia Plantarum},
	author = {Boussardon, Clément and Hussain, Shah and Keech, Olivier},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70465},
	keywords = {cell-specific, glutamate, mitochondria, proteome, translation},
	pages = {e70465},
}

A leaf is an organ composed of different tissues that fulfill specific functions. We hypothesized that since cells in vascular or mesophyll tissues as well as in stoma are developmentally tuned to operate their functions, mitochondria from these cells could exhibit significant metabolic differences. Using the IMTACT method, mitochondria were isolated from these three specific cell types, and the subsequent proteomes were analyzed. At steady state, mitochondria from vascular and guard cells had a significantly higher abundance of proteins associated with the mtETC, the TCA cycle, and the metabolic use of amino acids (glutamate, proline, isoleucine, leucine, and valine) as alternative substrates. Intriguingly, the mitochondria from guard cells also had a much lower abundance of proteins involved in the translation machinery, thus raising questions about the efficiency of the mitochondrial protein turnover in these cells. In a second step, we carried out the same comparative analysis, but with plants that were subjected to carbon starvation by placing them in prolonged darkness for three or 6 days. For all cell types studied, an increased abundance of proteins involved in branched-chain amino acid metabolism was detected. However, while guard cell mitochondria underwent a drastic reduction in proteins involved in respiration, translation, and RNA editing, suggesting a sharp downregulation of mitochondrial functions, mitochondrial proteomes from mesophyll and vascular cells did not show many differences, except for an increased arginine/proline/glutamate metabolism. Together, the results reported here support a differential regulation of the mitochondrial metabolism among the cell types constituting a leaf, a difference that is exacerbated upon stress.

@article{meyer_expanded_2025,
	title = {The {Expanded} {LYR} {Motif}-{Containing} {Protein} {Family} in {Archaeplastida}},
	volume = {177},
	copyright = {© 2025 Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70482},
	doi = {10.1111/ppl.70482},
	abstract = {The LYR motif (LYRM)-containing proteins are small eukaryote-specific proteins that have been defined based on the presence of a Lys-Tyr-Arg amino acid motif and a conserved triplet of α-helices. Twelve LYRM proteins were described in humans. They are involved in core mitochondrial processes as subunits or assembly/stabilising factors of mitochondrial complexes. Their function depends on their ability to interact with the acylated form of acyl-carrier proteins (mtACPs), which places these proteins as direct contributors to two intertwined functional processes, energy metabolism and mitochondrial biogenesis. To gain insight into LYRM proteins in Archaeplastida, we first analyzed the Arabidopsis thaliana genome and then a set of organisms representing the different groups of the Archaeplastida clade. This analysis revealed the existence of 17 classes encompassing 10 of the 12 LYRM classes found in humans. Eleven classes exist in Arabidopsis, and six additional classes are present in some organisms but not in Arabidopsis, thus expanding previous observations. Subsequent data mining based on literature, gene expression, and in silico analyses allowed us to speculate about the possible molecular function of some currently uncharacterised LYRMs in plants. Altogether, this study revealed the diversification of the LYRM protein family in Archaeplastida and more globally among eukaryotes, in which the LYRM-mtACP associations represent central molecular systems to regulate mitochondrial biogenesis upon fluctuating growth conditions.},
	language = {en},
	number = {5},
	urldate = {2025-09-05},
	journal = {Physiologia Plantarum},
	author = {Meyer, Etienne H. and Lopez-Lopez, Alicia and Keech, Olivier and Rouhier, Nicolas},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70482},
	keywords = {Archaeplastida, LYR-motif containing proteins, classification, mitochondria},
	pages = {e70482},
}

The LYR motif (LYRM)-containing proteins are small eukaryote-specific proteins that have been defined based on the presence of a Lys-Tyr-Arg amino acid motif and a conserved triplet of α-helices. Twelve LYRM proteins were described in humans. They are involved in core mitochondrial processes as subunits or assembly/stabilising factors of mitochondrial complexes. Their function depends on their ability to interact with the acylated form of acyl-carrier proteins (mtACPs), which places these proteins as direct contributors to two intertwined functional processes, energy metabolism and mitochondrial biogenesis. To gain insight into LYRM proteins in Archaeplastida, we first analyzed the Arabidopsis thaliana genome and then a set of organisms representing the different groups of the Archaeplastida clade. This analysis revealed the existence of 17 classes encompassing 10 of the 12 LYRM classes found in humans. Eleven classes exist in Arabidopsis, and six additional classes are present in some organisms but not in Arabidopsis, thus expanding previous observations. Subsequent data mining based on literature, gene expression, and in silico analyses allowed us to speculate about the possible molecular function of some currently uncharacterised LYRMs in plants. Altogether, this study revealed the diversification of the LYRM protein family in Archaeplastida and more globally among eukaryotes, in which the LYRM-mtACP associations represent central molecular systems to regulate mitochondrial biogenesis upon fluctuating growth conditions.

@article{zhang_phytochrome_2025,
	title = {Phytochrome {B} and phytochrome-interacting-factor4 modulate tree seasonal growth in cold environments},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-63391-5},
	doi = {10.1038/s41467-025-63391-5},
	abstract = {Plants that live at high latitudes and altitudes must adapt to growth in cold environments. Trees survive freezing winter conditions by ceasing growth and forming protective winter buds at the end of the growing season. To optimize growth and adaptation, the timing of growth cessation and bud set is critical. Like the well-studied Populus species (poplars, aspens, cottonwoods), many trees respond to the shortening photoperiods of fall to induce growth cessation. Temperature also has a role in this process, but the mechanism is unknown. Here, we show that the PHYTOCHROME B (PHYB)-PHYTOCHROME INTERACTING FACTOR4 (PIF4) module controls the interplay between photoperiod cues and temperature to prevent premature growth cessation and bud set at cooler temperatures. PHYB is essential for the ability of aspen trees to maintain growth under lower temperatures in permissive long days. This is mediated through PIF4, which promotes growth cessation, specifically in response to low temperatures rather than to changes in photoperiod. PIF4 can directly bind to the promoter region of the vegetative growth marker gene FLOWERING LOCUS T2 (FT2). In contrast to annual plants, it does so to suppress its transcription. Furthermore, lower temperatures can suppress PIF4 function at the transcriptional and protein levels to prevent premature growth cessation. These data show how poplar trees balance the antagonistic roles of PHYB and PIF4 to optimise the timing of growth cessation and bud set in cold environments, and this has been achieved with contrasting mechanisms compared to the annual plant model.},
	language = {en},
	number = {1},
	urldate = {2025-09-05},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Zhang, Bo and Lee, Keh Chien and Romañach, Laura García and Ding, Jihua and Marcon, Alice and Nilsson, Ove},
	month = aug,
	year = {2025},
	keywords = {Abiotic, Light responses, Plant molecular biology, Plant morphogenesis},
	pages = {8114},
}

Plants that live at high latitudes and altitudes must adapt to growth in cold environments. Trees survive freezing winter conditions by ceasing growth and forming protective winter buds at the end of the growing season. To optimize growth and adaptation, the timing of growth cessation and bud set is critical. Like the well-studied Populus species (poplars, aspens, cottonwoods), many trees respond to the shortening photoperiods of fall to induce growth cessation. Temperature also has a role in this process, but the mechanism is unknown. Here, we show that the PHYTOCHROME B (PHYB)-PHYTOCHROME INTERACTING FACTOR4 (PIF4) module controls the interplay between photoperiod cues and temperature to prevent premature growth cessation and bud set at cooler temperatures. PHYB is essential for the ability of aspen trees to maintain growth under lower temperatures in permissive long days. This is mediated through PIF4, which promotes growth cessation, specifically in response to low temperatures rather than to changes in photoperiod. PIF4 can directly bind to the promoter region of the vegetative growth marker gene FLOWERING LOCUS T2 (FT2). In contrast to annual plants, it does so to suppress its transcription. Furthermore, lower temperatures can suppress PIF4 function at the transcriptional and protein levels to prevent premature growth cessation. These data show how poplar trees balance the antagonistic roles of PHYB and PIF4 to optimise the timing of growth cessation and bud set in cold environments, and this has been achieved with contrasting mechanisms compared to the annual plant model.

@article{campos_pacheco_bioinspired_2025,
	title = {Bioinspired mycobacterial lipid coating of porous particles for enhanced antimicrobial efficacy},
	volume = {213},
	issn = {0928-0987},
	url = {https://www.sciencedirect.com/science/article/pii/S0928098725002246},
	doi = {10.1016/j.ejps.2025.107225},
	abstract = {The study aimed to investigate the unique lipid composition of Mycobacterium bovis BCG and its potential to enhance antimicrobial efficacy of lipid-coated mesoporous silica particles (MSPs). The bacterial lipids (BL) were extracted with petroleum ether and analyzed via LC-MS, revealing a complex mixture of phospholipids, including cardiolipin, phosphatidylcholine, phosphatidylethanolamine, and triacylglycerols. Lipid coating (using bacterial lipids and lung surfactant DPPC as the main component) was performed on MSPs via vesicle fusion approach and confirmed with ATR-FTIR spectroscopy. MSPs were loaded with clofazimine (CLZ), as a drug model for tuberculosis. The obtained BL-DPPC-coated CLZ-MSPs were more effective in inhibiting mycobacterial growth and killing intracellular mycobacteria compared to uncoated and DPPC-coated CLZ-MSPs. The bacterial lipids showed a good safety profile on M1-like and M2-like human primary macrophages without inducing a strong immune response or formation of foam cells. These findings suggest that the obtained bacterial lipid coatings can improve antimicrobial efficacy in treating both extracellular and intracellular mycobacteria infections directly in the lungs.},
	urldate = {2025-08-29},
	journal = {European Journal of Pharmaceutical Sciences},
	author = {Campos Pacheco, Jesús E. and Davids, Camilla and Yalovenko, Tetiana and Näsström, Elin and Ahnlund, Maria and Godaly, Gabriela and Valetti, Sabrina},
	month = oct,
	year = {2025},
	keywords = {Bacterial lipids, Cardiolipin, Clofazimine (CLZ), Lipid coating, Mesoporous silica particles (MSPs), Mycobacterial infections, Mycobacterium bovis BCG},
	pages = {107225},
}

The study aimed to investigate the unique lipid composition of Mycobacterium bovis BCG and its potential to enhance antimicrobial efficacy of lipid-coated mesoporous silica particles (MSPs). The bacterial lipids (BL) were extracted with petroleum ether and analyzed via LC-MS, revealing a complex mixture of phospholipids, including cardiolipin, phosphatidylcholine, phosphatidylethanolamine, and triacylglycerols. Lipid coating (using bacterial lipids and lung surfactant DPPC as the main component) was performed on MSPs via vesicle fusion approach and confirmed with ATR-FTIR spectroscopy. MSPs were loaded with clofazimine (CLZ), as a drug model for tuberculosis. The obtained BL-DPPC-coated CLZ-MSPs were more effective in inhibiting mycobacterial growth and killing intracellular mycobacteria compared to uncoated and DPPC-coated CLZ-MSPs. The bacterial lipids showed a good safety profile on M1-like and M2-like human primary macrophages without inducing a strong immune response or formation of foam cells. These findings suggest that the obtained bacterial lipid coatings can improve antimicrobial efficacy in treating both extracellular and intracellular mycobacteria infections directly in the lungs.

@article{hu_spatial_2025,
	title = {The spatial shifts and vulnerability assessment of ecological niches under climate change scenarios at the genus level: {A} case study of \textit{{Betula}}, {China}},
	volume = {14},
	issn = {2197-5620},
	shorttitle = {The spatial shifts and vulnerability assessment of ecological niches under climate change scenarios at the genus level},
	url = {https://www.sciencedirect.com/science/article/pii/S2197562025000697},
	doi = {10.1016/j.fecs.2025.100360},
	abstract = {As global warming persistently alters and rapidly reshapes landscapes and habitats, conventional species distribution models relying solely on maintaining static conditions within the current climate are likely to falter, particularly at the genus level. Hence, we hypothesize that climate change will differentially affect ecological niches of the same genus species with various latitudinal positioning and local topography, and the high-latitude species may experience greater niche contraction than low-latitude species, and that mountainous regions with high elevational variability may serve as critical climate refugia. Herein, we simulate niche alterations and integrate an ensemble model (EM) strategy, taking into account species dispersal limitations factors (topography, soil, and ultraviolet), to construct a comprehensive habitat suitability (CHS) model for assessing the future vulnerability of the Betula genus, most of which are timber species in China. Our findings reveal that the niche spatial (geographic distribution) of most species (62\%) within the Betula genus will undergo a gradual decline under climate change, supporting our hypothesis of latitudinal differentiation in climate vulnerability. Intriguingly, the projected high-latitude niche reduction within the genus cannot be counterbalanced by the anticipated niche expansion of closely related species in low-latitude regions, even considering the evident latitudinal gradient distribution of species. Nonetheless, the niche spatial of six Betula species in southwestern China remains stable or expands under warming scenarios, strongly supporting our secondary hypothesis about topographic buffering effects, which probably means the unique topography (i.e., the largest elevation difference) of this region may serve as a sanctuary for preserving Betula genetic diversity. Our results underscore the uncertain nature of pre-existing niche systems at the genus level under climate change, emphasizing the need for diligent resource management and conservation planning for vulnerable timber species.},
	urldate = {2025-08-29},
	journal = {Forest Ecosystems},
	author = {Hu, Xian-Ge and Chen, Jiahui and Yang, Ying and Shi, Man and Liu, Peng and Lin, Yiheng and Mao, Jian-Feng and El-Kassaby, Yousry A. and Lin, Erpei and Huang, Huahong},
	month = dec,
	year = {2025},
	keywords = {Climate change, Ensemble model (EM), Niches spatial, genus},
	pages = {100360},
}

As global warming persistently alters and rapidly reshapes landscapes and habitats, conventional species distribution models relying solely on maintaining static conditions within the current climate are likely to falter, particularly at the genus level. Hence, we hypothesize that climate change will differentially affect ecological niches of the same genus species with various latitudinal positioning and local topography, and the high-latitude species may experience greater niche contraction than low-latitude species, and that mountainous regions with high elevational variability may serve as critical climate refugia. Herein, we simulate niche alterations and integrate an ensemble model (EM) strategy, taking into account species dispersal limitations factors (topography, soil, and ultraviolet), to construct a comprehensive habitat suitability (CHS) model for assessing the future vulnerability of the Betula genus, most of which are timber species in China. Our findings reveal that the niche spatial (geographic distribution) of most species (62%) within the Betula genus will undergo a gradual decline under climate change, supporting our hypothesis of latitudinal differentiation in climate vulnerability. Intriguingly, the projected high-latitude niche reduction within the genus cannot be counterbalanced by the anticipated niche expansion of closely related species in low-latitude regions, even considering the evident latitudinal gradient distribution of species. Nonetheless, the niche spatial of six Betula species in southwestern China remains stable or expands under warming scenarios, strongly supporting our secondary hypothesis about topographic buffering effects, which probably means the unique topography (i.e., the largest elevation difference) of this region may serve as a sanctuary for preserving Betula genetic diversity. Our results underscore the uncertain nature of pre-existing niche systems at the genus level under climate change, emphasizing the need for diligent resource management and conservation planning for vulnerable timber species.

@article{zervakis_genomic_2025,
	title = {Genomic studies in {Linum} shed light on the evolution of the distyly supergene and the molecular basis of convergent floral evolution},
	volume = {247},
	copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.70392},
	doi = {10.1111/nph.70392},
	abstract = {Distyly, an example of convergent evolution, is governed by a supergene, the S-locus, in several species. Recent studies highlight similar genomic architectures of independently evolved S-loci, but its mode of origin and whether similar regulatory pathways underlie the convergent evolution of distyly remains unclear. We examined the evolution of supergenes and mechanisms underlying distyly in Linum species that diverged c. 33 million years ago (Ma). Using haplotype-resolved genomes and population genomics, we identified and characterized the S-loci of Linum perenne (distylous) and Linum grandiflorum (style length dimorphic), and compared them to that of Linum tenue (distylous). We then tested for a conserved hormonal mechanism regulating style length polymorphism in Linum. The S-locus supergene was consistently hemizygous in short-styled individuals across all three species, although it showed variation in size, gene content, repeat elements and extent of recombination suppression. Two S-linked candidate genes, TSS1 (style length) and WDR-44 (anther height/pollen self-incompatibility), were conserved. Consistent with a brassinosteroid-dependent role of TSS1, epibrassinolide treatment revealed a conserved, morph-specific effect on style length. S-locus structural polymorphism, candidate distyly genes and mechanisms regulating style length remain conserved {\textgreater} 30 Ma in Linum. In combination with findings from other systems, our results suggest that the brassinosteroid pathway frequently contributes to style length polymorphism.},
	language = {en},
	number = {6},
	urldate = {2025-08-29},
	journal = {New Phytologist},
	author = {Zervakis, Panagiotis-Ioannis and Postel, Zoé and Losvik, Aleksandra and Fracassetti, Marco and Solér, Lucile and Proux-Wéra, Estelle and Bunikis, Ignas and Churcher, Allison and Slotte, Tanja},
	year = {2025},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.70392},
	keywords = {balancing selection, brassinosteroid pathway, floral evolution, functional constraint, hemizygosity, heterostyly, mating system, structural variation},
	pages = {2964--2981},
}

Distyly, an example of convergent evolution, is governed by a supergene, the S-locus, in several species. Recent studies highlight similar genomic architectures of independently evolved S-loci, but its mode of origin and whether similar regulatory pathways underlie the convergent evolution of distyly remains unclear. We examined the evolution of supergenes and mechanisms underlying distyly in Linum species that diverged c. 33 million years ago (Ma). Using haplotype-resolved genomes and population genomics, we identified and characterized the S-loci of Linum perenne (distylous) and Linum grandiflorum (style length dimorphic), and compared them to that of Linum tenue (distylous). We then tested for a conserved hormonal mechanism regulating style length polymorphism in Linum. The S-locus supergene was consistently hemizygous in short-styled individuals across all three species, although it showed variation in size, gene content, repeat elements and extent of recombination suppression. Two S-linked candidate genes, TSS1 (style length) and WDR-44 (anther height/pollen self-incompatibility), were conserved. Consistent with a brassinosteroid-dependent role of TSS1, epibrassinolide treatment revealed a conserved, morph-specific effect on style length. S-locus structural polymorphism, candidate distyly genes and mechanisms regulating style length remain conserved \textgreater 30 Ma in Linum. In combination with findings from other systems, our results suggest that the brassinosteroid pathway frequently contributes to style length polymorphism.

@article{sharma_microbial_2025,
	title = {Microbial contributions to plant growth and stress tolerance: {Mechanisms} for sustainable plant production},
	volume = {17},
	issn = {2667-064X},
	shorttitle = {Microbial contributions to plant growth and stress tolerance},
	url = {https://www.sciencedirect.com/science/article/pii/S2667064X25002349},
	doi = {10.1016/j.stress.2025.100966},
	abstract = {Plant growth-promoting rhizobacteria (PGPRs) play a crucial role in enhancing plant development through a variety of direct and indirect mechanisms. These include the production of phytohormones, nitrogen fixation, phosphate solubilization, siderophore-mediated iron acquisition, and biocontrol of plant pathogens. Predominantly inhabiting the rhizosphere, PGPRs interact with plant roots via complex molecular and ecological processes involving signalling molecules, metabolite exchanges, and modulation of plant immune responses. Such interactions enhance nutrient uptake and stress tolerance but also contribute to long-term plant health and productivity across diverse environmental conditions. This review focuses on the genera Pseudomonas and Bacillus, which are extensively studied for their strong colonization abilities, metabolic versability, and demonstrated potential in improving crop resilience. Advances in microbial genomics, metagenomics, and high-throughput phenotyping have greatly enhanced our ability to identify, characterize, and apply beneficial microbes across a range of crop systems. However, key challenges remain, including limited understanding of native soil microbiotas, the functional outcome of microbiome-soil-plant interactions, and the development of agricultural practices that efficiently integrate microbial solutions. With potato (Solanum tuberosum) as a model crop, this review synthesizes current knowledge on PGRP-mediated growth promotion - primarily by Pseudomonas and Bacillus acting alone or in microbial consortia, identifies critical research gaps, and outlines future directions for the application of PGPRs in sustainable crop production.},
	urldate = {2025-08-22},
	journal = {Plant Stress},
	author = {Sharma, Neha and Mahawar, Lovely and Mishra, Arti and Albrectsen, Benedicte Riber},
	month = sep,
	year = {2025},
	keywords = {Baseline soil microflora, PGPR, Plant Growth Promotion, Plant Stress Mitigation, Plant growth promotion, Plant stress mitigation, Rethinking agricultural Practices, Rethinking agricultural practices},
	pages = {100966},
}

Plant growth-promoting rhizobacteria (PGPRs) play a crucial role in enhancing plant development through a variety of direct and indirect mechanisms. These include the production of phytohormones, nitrogen fixation, phosphate solubilization, siderophore-mediated iron acquisition, and biocontrol of plant pathogens. Predominantly inhabiting the rhizosphere, PGPRs interact with plant roots via complex molecular and ecological processes involving signalling molecules, metabolite exchanges, and modulation of plant immune responses. Such interactions enhance nutrient uptake and stress tolerance but also contribute to long-term plant health and productivity across diverse environmental conditions. This review focuses on the genera Pseudomonas and Bacillus, which are extensively studied for their strong colonization abilities, metabolic versability, and demonstrated potential in improving crop resilience. Advances in microbial genomics, metagenomics, and high-throughput phenotyping have greatly enhanced our ability to identify, characterize, and apply beneficial microbes across a range of crop systems. However, key challenges remain, including limited understanding of native soil microbiotas, the functional outcome of microbiome-soil-plant interactions, and the development of agricultural practices that efficiently integrate microbial solutions. With potato (Solanum tuberosum) as a model crop, this review synthesizes current knowledge on PGRP-mediated growth promotion - primarily by Pseudomonas and Bacillus acting alone or in microbial consortia, identifies critical research gaps, and outlines future directions for the application of PGPRs in sustainable crop production.

@article{renstrom_high-resolution_2025,
	title = {High-resolution imaging of the physical and chemical properties of {Populus} wood using {SilviScan}™ and near-infrared spectroscopy},
	volume = {-1},
	issn = {0928-1541, 2294-1932},
	url = {https://brill.com/view/journals/iawa/aop/article-10.1163-22941932-bja10179/article-10.1163-22941932-bja10179.xml},
	doi = {10.1163/22941932-bja10179},
	abstract = {Summary Spatial information on wood structure and chemistry is crucial for understanding wood functionality. We present a high-throughput and high-resolution near-infrared (NIR) method for combined imaging of the physical and chemical properties of stem sections from Populus trees. Pyrolysis-GC/MS data was used for sensitive and spatially resolved calibration of wood chemistry while SilviScan™ analyses provided reference data for wood physical properties with 25 μm resolution for wood density and 0.2–2.0 mm for microfibril angle (MFA). NIR prediction models were trained and calibrated on material from both field- and greenhouse-grown trees. Thus, the method was developed for NIR imaging of stem samples as small as 4 mm in diameter with an image resolution of 0.03 mm for small-diameter samples and 0.5 mm for samples with multiple annual rings. The NIR model performance, tested against data not used in the training set, reached the coefficient of determination ( R pred 2 ) values for wood density and MFA of 0.60 and 0.72, respectively. The NIR models for wood chemistry showed R pred 2 values of 0.78 and 0.77 for carbohydrates and lignin, respectively. Models for the G-, S- and H-type lignin had R pred 2 values between 0.58 and 0.86. In addition, we developed a prediction model for the determination of tension wood distribution. According to this model, tension wood was frequently observed in young greenhouse samples, which might explain the higher variation found in the chemical and physical properties of wood in greenhouse-grown compared to field-grown trees. The study also demonstrated that NIR-model estimations in image format can capture spatial variations that are not detectable in bulk analyses of wood properties. Examples of the method applied to greenhouse-grown trees highlight the efforts to develop NIR models with good prediction accuracies based on high-resolution data.},
	language = {eng},
	number = {aop},
	urldate = {2025-08-18},
	journal = {IAWA Journal},
	publisher = {Brill},
	author = {Renström, Anna and Scheepers, Gerhard and Yassin, Zakiya and Grahn, Thomas and Sivan, Pramod and Niittylä, Totte and Mellerowicz, Ewa J. and Tuominen, Hannele},
	month = feb,
	year = {2025},
	keywords = {NIR prediction models, NIR-imaging, Py-GC/MS, SilviScan, wood chemistry, wood properties},
	pages = {1--16},
}

Summary Spatial information on wood structure and chemistry is crucial for understanding wood functionality. We present a high-throughput and high-resolution near-infrared (NIR) method for combined imaging of the physical and chemical properties of stem sections from Populus trees. Pyrolysis-GC/MS data was used for sensitive and spatially resolved calibration of wood chemistry while SilviScan™ analyses provided reference data for wood physical properties with 25 μm resolution for wood density and 0.2–2.0 mm for microfibril angle (MFA). NIR prediction models were trained and calibrated on material from both field- and greenhouse-grown trees. Thus, the method was developed for NIR imaging of stem samples as small as 4 mm in diameter with an image resolution of 0.03 mm for small-diameter samples and 0.5 mm for samples with multiple annual rings. The NIR model performance, tested against data not used in the training set, reached the coefficient of determination ( R pred 2 ) values for wood density and MFA of 0.60 and 0.72, respectively. The NIR models for wood chemistry showed R pred 2 values of 0.78 and 0.77 for carbohydrates and lignin, respectively. Models for the G-, S- and H-type lignin had R pred 2 values between 0.58 and 0.86. In addition, we developed a prediction model for the determination of tension wood distribution. According to this model, tension wood was frequently observed in young greenhouse samples, which might explain the higher variation found in the chemical and physical properties of wood in greenhouse-grown compared to field-grown trees. The study also demonstrated that NIR-model estimations in image format can capture spatial variations that are not detectable in bulk analyses of wood properties. Examples of the method applied to greenhouse-grown trees highlight the efforts to develop NIR models with good prediction accuracies based on high-resolution data.

@article{cervela-cardona_metabolism_2025,
	title = {Metabolism in {Sync}: {The} {Circadian} {Clock}, a {Central} {Hub} for {Light}-{Driven} {Chloroplastic} and {Mitochondrial} {Entrainment}},
	volume = {14},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	shorttitle = {Metabolism in {Sync}},
	url = {https://www.mdpi.com/2223-7747/14/16/2464},
	doi = {10.3390/plants14162464},
	abstract = {Plants align their physiology with daily environmental cycles through the circadian clock, which integrates light and metabolic signals to optimize growth and stress responses. While light entrainment has been extensively studied, emerging evidence highlights the central role of metabolism—particularly from chloroplasts and mitochondria—in tuning circadian rhythms. In this review, we explore the bidirectional relationship between organelle metabolism and the circadian clock, focusing on how metabolic signals such as sugars, ROS, and organic acids function as entrainment cues. We discuss how the clock regulates organelle function at multiple levels, including transcriptional, translational, and post-translational mechanisms, and how organelle-derived signals feedback to modulate core clock components through retrograde pathways. Special attention is given to the integration of chloroplast and mitochondrial signals, emphasizing their synergistic roles in maintaining cellular homeostasis. Drawing on the “three-body problem” analogy, we illustrate the dynamic and reciprocal interactions among light, clock, and metabolism. This perspective underscores the need to reframe the circadian system, not merely as light-driven but also as a central integrator of energy status and environmental cues. Understanding this integrated network is essential to improve plant performance and resilience under fluctuating environmental conditions.},
	language = {en},
	number = {16},
	urldate = {2025-08-15},
	journal = {Plants},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Cervela-Cardona, Luis and Francisco, Marta and Strand, Åsa},
	month = jan,
	year = {2025},
	keywords = {chloroplast–mitochondria crosstalk, circadian clock, light signaling, metabolic entrainment, plant energy metabolism, retrograde signaling},
	pages = {2464},
}

Plants align their physiology with daily environmental cycles through the circadian clock, which integrates light and metabolic signals to optimize growth and stress responses. While light entrainment has been extensively studied, emerging evidence highlights the central role of metabolism—particularly from chloroplasts and mitochondria—in tuning circadian rhythms. In this review, we explore the bidirectional relationship between organelle metabolism and the circadian clock, focusing on how metabolic signals such as sugars, ROS, and organic acids function as entrainment cues. We discuss how the clock regulates organelle function at multiple levels, including transcriptional, translational, and post-translational mechanisms, and how organelle-derived signals feedback to modulate core clock components through retrograde pathways. Special attention is given to the integration of chloroplast and mitochondrial signals, emphasizing their synergistic roles in maintaining cellular homeostasis. Drawing on the “three-body problem” analogy, we illustrate the dynamic and reciprocal interactions among light, clock, and metabolism. This perspective underscores the need to reframe the circadian system, not merely as light-driven but also as a central integrator of energy status and environmental cues. Understanding this integrated network is essential to improve plant performance and resilience under fluctuating environmental conditions.

@article{bizjak-johansson_arginine-ironhexametaphosphate_2025,
	title = {Arginine-iron–hexametaphosphate complex as a novel nitrogen plant nutrition reducing nitrate leaching in {Scots} pine ({Pinus} sylvestris) seedling production},
	volume = {15},
	copyright = {2025 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-025-15665-7},
	doi = {10.1038/s41598-025-15665-7},
	abstract = {The industrial production of conifer seedlings in nurseries uses large amounts of fertilizers to ensure their proper growth and accurate nutrient status. However, inorganic nitrogen fertilization leads to nitrate leaching, which has negative environmental consequences. An alternative solution could be the use of controlled-release fertilizers that supply nutrients over longer periods and hence have a lower environmental impact. This study analysed the performance of a novel arginine–iron–hexametaphosphate complex on Scots pine (Pinus sylvestris) seedlings. The complex was characterized using a wide range of analytical tools, indicating that it is a precipitated complex rather than a crystalline compound. Plant growth on arginine–iron–hexametaphosphate was comparable to a commercial inorganic nitrogen controlled-release fertilizer but with significantly lower nitrate leaching. A nitrogen budget of seedlings and growth substrate showed that seedlings had acquired nitrogen in excess of the amount of nitrogen present at the start of the experiment, and this excess nitrogen was smaller in seedlings grown on the inorganic fertilizer. Measurements of acetylene reduction in seedlings indicated low but measurable rates of nitrogen fixation, potentially contributing to the excess nitrogen. Together, the results showed that the arginine–iron–hexametaphosphate complex is a good alternative to commonly used fertilizers and can contribute to sustainable seedling production.},
	language = {en},
	number = {1},
	urldate = {2025-08-15},
	journal = {Scientific Reports},
	publisher = {Nature Publishing Group},
	author = {Bizjak-Johansson, Tinkara and Bozaghian Bäckman, Marjan and Nilsson, Lina and Holmlund, Mattias and Skoglund, Nils and Näsholm, Torgny and Gratz, Regina},
	month = aug,
	year = {2025},
	keywords = {Plant development, Plant physiology},
	pages = {29619},
}

The industrial production of conifer seedlings in nurseries uses large amounts of fertilizers to ensure their proper growth and accurate nutrient status. However, inorganic nitrogen fertilization leads to nitrate leaching, which has negative environmental consequences. An alternative solution could be the use of controlled-release fertilizers that supply nutrients over longer periods and hence have a lower environmental impact. This study analysed the performance of a novel arginine–iron–hexametaphosphate complex on Scots pine (Pinus sylvestris) seedlings. The complex was characterized using a wide range of analytical tools, indicating that it is a precipitated complex rather than a crystalline compound. Plant growth on arginine–iron–hexametaphosphate was comparable to a commercial inorganic nitrogen controlled-release fertilizer but with significantly lower nitrate leaching. A nitrogen budget of seedlings and growth substrate showed that seedlings had acquired nitrogen in excess of the amount of nitrogen present at the start of the experiment, and this excess nitrogen was smaller in seedlings grown on the inorganic fertilizer. Measurements of acetylene reduction in seedlings indicated low but measurable rates of nitrogen fixation, potentially contributing to the excess nitrogen. Together, the results showed that the arginine–iron–hexametaphosphate complex is a good alternative to commonly used fertilizers and can contribute to sustainable seedling production.

@article{wang_ribosome_2025,
	title = {Ribosome biogenesis in plants requires the nuclear envelope and mitochondria localized {OPENER} complex},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-62652-7},
	doi = {10.1038/s41467-025-62652-7},
	abstract = {Eukaryotic ribosome biogenesis proceeds from nucleolus to cytosol assisted by various assembly factors. The process is evolutionarily conserved across eukaryotes but differences between the kingdoms are emerging. Here, we describe how the OPENER (OPNR) protein complex is required for 60S ribosome assembly in the model plant Arabidopsis thaliana. The complex is observed on both nuclear envelope and mitochondria, and contains OPNR, OPENER ASSOCIATED PROTEIN 1 (OAP1), OAP2, Cell Division Cycle 48 D (CDC48D) and Calmodulin-interacting protein 111 (CIP111). Depletion of the OPNR complex components results in reproductive lethality and cytoplasmic retention of assembly factors on 60S ribosomes. Subsequent biochemical analyses and structural modelling suggest that OPNR, OAP1 and OAP2 form a claw-like trimer which grabs the ribosome assembly factor RIBOSOMAL PROTEIN L24C (RPL24C) on the pre-60S ribosome. Our results reveal previously unrecognised subcellular complexity of ribosome biogenesis in plants, and point to mitochondria association as a feature to ensure sufficient translational capacity.},
	language = {en},
	number = {1},
	urldate = {2025-08-12},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Wang, Wei and Mahboubi, Amir and Zhu, Shaochun and Hanson, Johannes and Mateus, André and Niittylä, Totte},
	month = aug,
	year = {2025},
	keywords = {Plant cell biology, Plant molecular biology, Ribosome},
	pages = {7301},
}

Eukaryotic ribosome biogenesis proceeds from nucleolus to cytosol assisted by various assembly factors. The process is evolutionarily conserved across eukaryotes but differences between the kingdoms are emerging. Here, we describe how the OPENER (OPNR) protein complex is required for 60S ribosome assembly in the model plant Arabidopsis thaliana. The complex is observed on both nuclear envelope and mitochondria, and contains OPNR, OPENER ASSOCIATED PROTEIN 1 (OAP1), OAP2, Cell Division Cycle 48 D (CDC48D) and Calmodulin-interacting protein 111 (CIP111). Depletion of the OPNR complex components results in reproductive lethality and cytoplasmic retention of assembly factors on 60S ribosomes. Subsequent biochemical analyses and structural modelling suggest that OPNR, OAP1 and OAP2 form a claw-like trimer which grabs the ribosome assembly factor RIBOSOMAL PROTEIN L24C (RPL24C) on the pre-60S ribosome. Our results reveal previously unrecognised subcellular complexity of ribosome biogenesis in plants, and point to mitochondria association as a feature to ensure sufficient translational capacity.

@article{li_ecophysiological_2025,
	title = {Ecophysiological transition mediated by hybridization in a hybrid pine species complex},
	volume = {47},
	issn = {2468-2659},
	url = {https://www.sciencedirect.com/science/article/pii/S2468265925000952},
	doi = {10.1016/j.pld.2025.05.009},
	abstract = {Hybridization is a driving force in ecological transitions and speciation, yet direct evidence linking it to adaptive differentiation in natural systems remains limited. This study evaluates the role of hybridization in the speciation of Pinus densata, a keystone forest species on the southeastern Tibetan Plateau. By creating artificial interspecific F1s and a long-term common garden experiment on the plateau, we provide in situ assessments on 44 growth and physiological traits across four seasons, along with RNA sequencing. We found significant phenotypic divergence between P. densata and its putative parental species P. tabuliformis and P. yunnanensis, with P. densata demonstrating superior growth and dynamic balance between photosynthesis and photoprotection. The F1s closely resembled P. densata in most traits. Gene expression revealed 19\%–10\% of 34,000 examined genes as differentially expressed in P. densata and F1s relative to mid-parent expression values. Both additive (4\%) and non-additive gene actions (5\%–6\% in F1s, 10\%–12\% in P. densata) were common, while transgressive expression occurred more frequently in the stabilized natural hybrids, illustrating transcriptomic reprogramming brought by hybridization and further divergence by natural selection. We provide compelling evidence for hybridization-derived phenotypic divergence at both physiological and gene expression levels that could have contributed to the adaptation of P. densata to high plateau habitat where both parental species have low fitness. The altered physiology and gene expression in hybrids serve both as a substrate for novel ecological adaptation and as a mechanism for the initiation of reproductive isolation.},
	number = {4},
	urldate = {2025-08-01},
	journal = {Plant Diversity},
	author = {Li, Zhi-Chao and Xu, Chao-Qun and Zhao, Wei and Nie, Shuai and Bao, Yu-Tao and Liu, Hui and Xing, Zhen and Mao, Jian-Feng and Wang, Xiao-Ru},
	month = jul,
	year = {2025},
	keywords = {Ecological divergence, Gene action, Homoploid hybrid speciation, Physiological traits, RNA-Seq, Tibetan plateau},
	pages = {604--619},
}

Hybridization is a driving force in ecological transitions and speciation, yet direct evidence linking it to adaptive differentiation in natural systems remains limited. This study evaluates the role of hybridization in the speciation of Pinus densata, a keystone forest species on the southeastern Tibetan Plateau. By creating artificial interspecific F1s and a long-term common garden experiment on the plateau, we provide in situ assessments on 44 growth and physiological traits across four seasons, along with RNA sequencing. We found significant phenotypic divergence between P. densata and its putative parental species P. tabuliformis and P. yunnanensis, with P. densata demonstrating superior growth and dynamic balance between photosynthesis and photoprotection. The F1s closely resembled P. densata in most traits. Gene expression revealed 19%–10% of 34,000 examined genes as differentially expressed in P. densata and F1s relative to mid-parent expression values. Both additive (4%) and non-additive gene actions (5%–6% in F1s, 10%–12% in P. densata) were common, while transgressive expression occurred more frequently in the stabilized natural hybrids, illustrating transcriptomic reprogramming brought by hybridization and further divergence by natural selection. We provide compelling evidence for hybridization-derived phenotypic divergence at both physiological and gene expression levels that could have contributed to the adaptation of P. densata to high plateau habitat where both parental species have low fitness. The altered physiology and gene expression in hybrids serve both as a substrate for novel ecological adaptation and as a mechanism for the initiation of reproductive isolation.

@article{berggren_effects_2025,
	title = {Effects of propagation method and methyl jasmonate treatment on stem bark wound healing in {Norway} spruce seedlings},
	issn = {1612-4677},
	url = {https://doi.org/10.1007/s10342-025-01795-0},
	doi = {10.1007/s10342-025-01795-0},
	abstract = {Healing of stem bark wounds is important for minimizing pathogen infection risk, restoring nutrient transport and structural support in trees. Here, we explore how propagation through somatic embryogenesis (SE) and methyl jasmonate (MeJA) treatment affect wound healing ability in Norway spruce (Picea abies) plants. We inflicted a mechanical wound on the lower stem of MeJA- and non-treated plants produced via SE (emblings) or from seeds (seedlings). Visible signs of healing around the wound edges (onset of healing) were recorded 2 weeks post-wounding; wound size (exposed xylem) was measured every other week (June–September) in year 1, and May and September in year 2. Plant height and diameter were also measured. MeJA positively affected healing onset, with 48\% more MeJA- than non-treated plants exhibiting early healing. This resulted in a sharp decrease in wound size for MeJA-treated plants 2–4 weeks post-wounding. However, these benefits only occurred early on, as MeJA reduced the overall healing rate (tissue growth/day) by 9\%. For SE, fewer emblings (70\%) showed early healing signs compared to seedlings (91\%). Yet, non-treated emblings showed the highest healing rate during year 1; in year 2, these effects persisted with all emblings having a 61\% faster healing rate and 68\% more had completely closed their wounds relative to seedlings. Wounding did not affect growth, MeJA negatively affected diameter but not height, and overall emblings grew less than seedlings. We conclude that MeJA may stimulate stem wound healing initiation in Norway spruce, but slow down healing rate and vice versa for SE plants.},
	language = {en},
	urldate = {2025-07-25},
	journal = {European Journal of Forest Research},
	author = {Berggren, Kristina and Tudoran, Amelia and Chen, Yayuan and Tikkinen, Mikko and Bylund, Helena and Björkman, Christer and Egertsdotter, Ulrika and Puentes, Adriana},
	month = jun,
	year = {2025},
	keywords = {Arboriculture, Emblings, Jasmonic acid, Mechanical wounding, Picea abies, Plant regeneration, Plant tolerance, Regeneration, Seedlings, Shoot apical meristem, Somatic embryogenesis, Wound healing rate, Wounding},
}

Healing of stem bark wounds is important for minimizing pathogen infection risk, restoring nutrient transport and structural support in trees. Here, we explore how propagation through somatic embryogenesis (SE) and methyl jasmonate (MeJA) treatment affect wound healing ability in Norway spruce (Picea abies) plants. We inflicted a mechanical wound on the lower stem of MeJA- and non-treated plants produced via SE (emblings) or from seeds (seedlings). Visible signs of healing around the wound edges (onset of healing) were recorded 2 weeks post-wounding; wound size (exposed xylem) was measured every other week (June–September) in year 1, and May and September in year 2. Plant height and diameter were also measured. MeJA positively affected healing onset, with 48% more MeJA- than non-treated plants exhibiting early healing. This resulted in a sharp decrease in wound size for MeJA-treated plants 2–4 weeks post-wounding. However, these benefits only occurred early on, as MeJA reduced the overall healing rate (tissue growth/day) by 9%. For SE, fewer emblings (70%) showed early healing signs compared to seedlings (91%). Yet, non-treated emblings showed the highest healing rate during year 1; in year 2, these effects persisted with all emblings having a 61% faster healing rate and 68% more had completely closed their wounds relative to seedlings. Wounding did not affect growth, MeJA negatively affected diameter but not height, and overall emblings grew less than seedlings. We conclude that MeJA may stimulate stem wound healing initiation in Norway spruce, but slow down healing rate and vice versa for SE plants.

@article{bogdziewiez_q-warg_2025,
	title = {The {Q}-{Warg} {Pipeline}: {A} {Robust} and {Versatile} {Workflow} for {Quantitative} {Analysis} of {Protoplast} {Culture} {Conditions}},
	volume = {9},
	copyright = {© 2025 The Author(s). Plant Direct published by American Society of Plant Biologists and the Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {2475-4455},
	shorttitle = {The {Q}-{Warg} {Pipeline}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pld3.70090},
	doi = {10.1002/pld3.70090},
	abstract = {Single cells offer a simplified model for investigating complex mechanisms such as cell–cell adhesion. Protoplasts, plant cells without cell walls (CWs), have been instrumental in plant research, industrial applications, and breeding. However, because of the absence of a CW, protoplasts are not considered “true” plant cells, making them less relevant for biophysical studies. Current protocols for CW recovery in protoplasts vary widely among laboratories and starting materials, requiring lab-specific optimizations that often depend on expert knowledge and qualitative assessments. To address this, we have developed a user-friendly streamlined workflow, the Q-Warg pipeline, which enables quantitative comparison of various conditions for CW recovery post-protoplasting. This pipeline employs fluorescence imaging and tailored processing to measure parameters such as morphometry, cell viability, and CW staining intensity. Using this approach, we optimized culture conditions to obtain single plant cells (SPCs) with recovered CWs. Additionally, we demonstrated the robustness and versatility of the workflow by quantifying different fluorescent signals in protoplast suspensions. Overall, the Q-Warg pipeline provides a widely accessible and user-friendly solution for robust and unbiased characterization of protoplasts culture. The quantitative data generated by the pipeline will be useful in the future to decipher the mechanisms regulating protoplast viability and regeneration.},
	language = {en},
	number = {7},
	urldate = {2025-07-25},
	journal = {Plant Direct},
	author = {Bogdziewiez, Léa and Froeling, Rik and Schöppl, Patricia and Juquel, Jeanne and Antoniadi, Ioanna and Skalický, Vladimìr and Mathey, Ambroise and Fattaccioli, Jacques and Sprakel, Joris and Verger, Stéphane},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/pld3.70090},
	keywords = {Arabidopsis thaliana, cell wall, fluorescence, protoplasts, quantification, recovery, regeneration, viability},
	pages = {e70090},
}

Single cells offer a simplified model for investigating complex mechanisms such as cell–cell adhesion. Protoplasts, plant cells without cell walls (CWs), have been instrumental in plant research, industrial applications, and breeding. However, because of the absence of a CW, protoplasts are not considered “true” plant cells, making them less relevant for biophysical studies. Current protocols for CW recovery in protoplasts vary widely among laboratories and starting materials, requiring lab-specific optimizations that often depend on expert knowledge and qualitative assessments. To address this, we have developed a user-friendly streamlined workflow, the Q-Warg pipeline, which enables quantitative comparison of various conditions for CW recovery post-protoplasting. This pipeline employs fluorescence imaging and tailored processing to measure parameters such as morphometry, cell viability, and CW staining intensity. Using this approach, we optimized culture conditions to obtain single plant cells (SPCs) with recovered CWs. Additionally, we demonstrated the robustness and versatility of the workflow by quantifying different fluorescent signals in protoplast suspensions. Overall, the Q-Warg pipeline provides a widely accessible and user-friendly solution for robust and unbiased characterization of protoplasts culture. The quantitative data generated by the pipeline will be useful in the future to decipher the mechanisms regulating protoplast viability and regeneration.

@article{schneider_reverse_2025,
	title = {Reverse microdialysis of sucrose stimulates soil fungal and bacterial growth at the microscale},
	volume = {25},
	issn = {1471-2180},
	url = {https://doi.org/10.1186/s12866-025-04082-5},
	doi = {10.1186/s12866-025-04082-5},
	abstract = {The rhizosphere is a critical microenvironment that plays key roles in plant nutrient availability, largely due to root interactions with rhizospheric microbes. However, we lack suitable methods that can elucidate mechanisms determining rhizospheric community structure and function within the context of a dynamic, undisturbed soil. Microdialysis has been used for low intrusive soil nutrient sampling at the scale of a fine root, with small probes that also enable release of defined compounds. We evaluated whether microdialysis could simulate exudation, by the release of sucrose, and stimulate changes in a soil microbial community, allowing us to determine the microbes that responded most to carbon release.},
	number = {1},
	urldate = {2025-07-25},
	journal = {BMC Microbiology},
	author = {Schneider, Andreas N. and Buckley, Scott and Lorenzo, Zulema Carracedo and Gratz, Regina and Nilsson, Lina and Swaine, Mark and Street, Nathaniel R. and Taylor, Andy F. S. and Jämtgård, Sandra},
	month = jul,
	year = {2025},
	keywords = {Amplicon sequencing, Bacteria, Fungi, Microdialysis, Root exudation},
	pages = {436},
}

The rhizosphere is a critical microenvironment that plays key roles in plant nutrient availability, largely due to root interactions with rhizospheric microbes. However, we lack suitable methods that can elucidate mechanisms determining rhizospheric community structure and function within the context of a dynamic, undisturbed soil. Microdialysis has been used for low intrusive soil nutrient sampling at the scale of a fine root, with small probes that also enable release of defined compounds. We evaluated whether microdialysis could simulate exudation, by the release of sucrose, and stimulate changes in a soil microbial community, allowing us to determine the microbes that responded most to carbon release.

@article{quevedo_retrograde_2025,
	title = {Retrograde signals control dynamic changes to the chromatin state at photosynthesis-associated loci},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-61831-w},
	doi = {10.1038/s41467-025-61831-w},
	abstract = {Retrograde signalling networks originating in the organelles dictate nuclear gene expression and are essential for control and regulation of cellular energy metabolism. We investigate whether such plastid retrograde signals control nuclear gene expression by altering the chromatin state during the establishment of photosynthetic function in response to light. An Arabidopsis thaliana cell culture provides the required temporal resolution to map four histone modifications during the greening process. We uncover sequential and distinct epigenetic reprogramming events where an epigenetic switch from a histone methylation to an acetylation at photosynthesis-associated loci is dependent on a plastid retrograde signal. The transcription factors VIVIPAROUS1/ABI3-LIKE (VAL1), RELATIVE OF EARLY FLOWERING 6 (REF6) and GOLDEN2-LIKE FACTOR1/2 (GLKs) are linked to the H3K27ac deposition at photosynthesis associated loci that precedes full activation of the photosynthesis genes. Our work demonstrates that retrograde signals play a role in the epigenetic reprogramming essential to the establishment of photosynthesis in plant cells.},
	language = {en},
	number = {1},
	urldate = {2025-07-25},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Quevedo, Marti and Kubalová, Ivona and Brun, Alexis and Cervela-Cardona, Luis and Monte, Elena and Strand, Åsa},
	month = jul,
	year = {2025},
	keywords = {Epigenetics, Organelles, Plant signalling},
	pages = {6527},
}

Retrograde signalling networks originating in the organelles dictate nuclear gene expression and are essential for control and regulation of cellular energy metabolism. We investigate whether such plastid retrograde signals control nuclear gene expression by altering the chromatin state during the establishment of photosynthetic function in response to light. An Arabidopsis thaliana cell culture provides the required temporal resolution to map four histone modifications during the greening process. We uncover sequential and distinct epigenetic reprogramming events where an epigenetic switch from a histone methylation to an acetylation at photosynthesis-associated loci is dependent on a plastid retrograde signal. The transcription factors VIVIPAROUS1/ABI3-LIKE (VAL1), RELATIVE OF EARLY FLOWERING 6 (REF6) and GOLDEN2-LIKE FACTOR1/2 (GLKs) are linked to the H3K27ac deposition at photosynthesis associated loci that precedes full activation of the photosynthesis genes. Our work demonstrates that retrograde signals play a role in the epigenetic reprogramming essential to the establishment of photosynthesis in plant cells.

@article{mikko_sequencing_2025,
	title = {Sequencing airborne {DNA} to monitor crop pathogens and pests},
	volume = {28},
	issn = {2589-0042},
	url = {https://www.cell.com/iscience/abstract/S2589-0042(25)01173-3},
	doi = {10.1016/j.isci.2025.112912},
	language = {English},
	number = {7},
	urldate = {2025-07-25},
	journal = {iScience},
	publisher = {Elsevier},
	author = {Mikko, Amanda and Villegas, Jose Antonio and Svensson, Daniel and Karlsson, Edvin and Esseen, Per-Anders and Albrectsen, Benedicte Riber and Lundin, Ola and Forsman, Mats and Berlin, Anna and Stenberg, Per},
	month = jul,
	year = {2025},
	keywords = {Agricultural science, Airborne eDNA, Environmental biotechnology, Environmental monitoring, Genomics, Omics, metagenomics, non-targeted surveillance, pathogen surveillance, plant pathogens, plant pests},
}

@article{sivan_carbohydrate-binding_2025,
	title = {Carbohydrate-binding domain {CBM63} of microbial expansin-like {BsEXLX1} facilitates the adsorption of expansin-related proteins to hemicelluloses in plant secondary cell walls},
	volume = {18},
	issn = {2731-3654},
	url = {https://doi.org/10.1186/s13068-025-02674-x},
	doi = {10.1186/s13068-025-02674-x},
	abstract = {Overcoming lignocellulose recalcitrance to enzymatic or chemical processing is a prerequisite for biorefinery applications. Expansins and loosenins are non-lytic proteins that could assist reducing this recalcitrance by disrupting the intermolecular contacts between plant cell wall components. Here, immunolocalization with fluorescence and transmission electron microscopy (TEM) were used to study the ability of a Bacillus subtilis expansin-like protein (BsEXLX1), a Phanerochaete carnosa loosenin protein (PcaLOOL12) and a fusion protein of PcaLOOL12 with the carbohydrate-binding module 63 (CBM63) of BsEXLX1 (i.e., PcaLOOL12-CBM63) to bind secondary cell walls (SCW) of aspen fibres, including fresh aspen wood, milled wood fibres (MWF) and MWF subjected to subcritical water extraction.},
	number = {1},
	urldate = {2025-07-25},
	journal = {Biotechnology for Biofuels and Bioproducts},
	author = {Sivan, Pramod and Dahiya, Deepika and Jabalera, Ylenia and Koitto, Taru and Perez-Jimenez, Raul and Mellerowicz, Ewa J. and Master, Emma and Vilaplana, Francisco},
	month = jul,
	year = {2025},
	keywords = {Expansin, Hemicelluloses, Loosenin, Secondary cell wall},
	pages = {70},
}

Overcoming lignocellulose recalcitrance to enzymatic or chemical processing is a prerequisite for biorefinery applications. Expansins and loosenins are non-lytic proteins that could assist reducing this recalcitrance by disrupting the intermolecular contacts between plant cell wall components. Here, immunolocalization with fluorescence and transmission electron microscopy (TEM) were used to study the ability of a Bacillus subtilis expansin-like protein (BsEXLX1), a Phanerochaete carnosa loosenin protein (PcaLOOL12) and a fusion protein of PcaLOOL12 with the carbohydrate-binding module 63 (CBM63) of BsEXLX1 (i.e., PcaLOOL12-CBM63) to bind secondary cell walls (SCW) of aspen fibres, including fresh aspen wood, milled wood fibres (MWF) and MWF subjected to subcritical water extraction.

@article{ma_rack1a_2025,
	title = {{RACK1A} positively regulates opening of the apical hook in {Arabidopsis} thaliana via suppression of its auxin response gradient},
	volume = {122},
	url = {https://www.pnas.org/doi/10.1073/pnas.2407224122},
	doi = {10.1073/pnas.2407224122},
	abstract = {Apical hook development is an ideal model for studying differential growth in plants and is controlled by complex phytohormonal crosstalk, with auxin being the major player. Here, we identified a bioactive small molecule that decelerates apical hook opening in Arabidopsis thaliana. Our genetic studies suggest that this molecule enhances or maintains the auxin maximum found in the inner hook side and requires certain auxin signaling components to modulate apical hook opening. Using biochemical approaches, we then revealed the WD40 repeat scaffold protein RECEPTOR FOR ACTIVATED C KINASE 1A (RACK1A) as a direct target of this compound. We present data in support of RACK1A playing a positive role in apical hook opening by activating specific auxin signaling mechanisms and negatively regulating the differential auxin response gradient across the hook, thereby adjusting differential cell growth, an essential process for organ structure and function in plants.},
	number = {30},
	urldate = {2025-07-25},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {Ma, Qian and Liu, Sijia and Doyle, Siamsa M. and Raggi, Sara and Pařízková, Barbora and Barange, Deepak Kumar and Ratnakaram, Hemamshu and Wilkinson, Edward G. and Crespo Garcia, Isidro and Bygdell, Joakim and Wingsle, Gunnar and Boer, Dirk Roeland and Strader, Lucia C. and Almqvist, Fredrik and Novák, Ondřej and Robert, Stéphanie},
	month = jul,
	year = {2025},
	pages = {e2407224122},
}

Apical hook development is an ideal model for studying differential growth in plants and is controlled by complex phytohormonal crosstalk, with auxin being the major player. Here, we identified a bioactive small molecule that decelerates apical hook opening in Arabidopsis thaliana. Our genetic studies suggest that this molecule enhances or maintains the auxin maximum found in the inner hook side and requires certain auxin signaling components to modulate apical hook opening. Using biochemical approaches, we then revealed the WD40 repeat scaffold protein RECEPTOR FOR ACTIVATED C KINASE 1A (RACK1A) as a direct target of this compound. We present data in support of RACK1A playing a positive role in apical hook opening by activating specific auxin signaling mechanisms and negatively regulating the differential auxin response gradient across the hook, thereby adjusting differential cell growth, an essential process for organ structure and function in plants.

@article{hayatgheibi_cross-generational_2025,
	title = {Cross-generational genomic prediction of {Norway} spruce ({Picea} abies) wood properties: an evaluation using independent validation},
	volume = {26},
	issn = {1471-2164},
	shorttitle = {Cross-generational genomic prediction of {Norway} spruce ({Picea} abies) wood properties},
	url = {https://doi.org/10.1186/s12864-025-11861-x},
	doi = {10.1186/s12864-025-11861-x},
	abstract = {The evaluation of genomic selection (GS) efficiency in forestry has primarily relied on cross-validation schemes that split the same population within a single generation for both training and validation. While useful, this approach may not be reliable for multigenerational breeding. To our knowledge, this is the first study to assess genomic prediction in Norway spruce using a large dataset spanning two generations in two environments. We trained pedigree-based (ABLUP) and marker-based (GBLUP) prediction models under three approaches: forward prediction, backward prediction, and across-environment prediction. The models were evaluated for ring-width, solid-wood and tracheid characteristics, using {\textasciitilde} 6,000 phenotyped and {\textasciitilde} 2,500 genotyped individual. Predictive ability (PA) and prediction accuracy (ACC) were estimated using an independent validation method, ensuring no individuals were shared between training and validation datasets. To assess the trade-off between comprehensive radial history and practical direct methods, we compared GBLUP models trained with cumulative area-weighted density (AWE-GBLUP) and single annual-ring density (SAD-GBLUP) from mother plus-trees. These models were validated using early and mature-stage progeny density measurements across two trials.},
	number = {1},
	urldate = {2025-07-25},
	journal = {BMC Genomics},
	author = {Hayatgheibi, Haleh and Hallingbäck, Henrik R. and Gezan, Salvador A. and Lundqvist, Sven-Olof and Grahn, Thomas and Scheepers, Gerhard and Ranade, Sonali Sachin and Kärkkäinen, Katri and García Gil, M. Rosario},
	month = jul,
	year = {2025},
	keywords = {Cambial age, Cross-generation, GBLUP, Genomic selection, Norway Spruce, Wood properties},
	pages = {680},
}

The evaluation of genomic selection (GS) efficiency in forestry has primarily relied on cross-validation schemes that split the same population within a single generation for both training and validation. While useful, this approach may not be reliable for multigenerational breeding. To our knowledge, this is the first study to assess genomic prediction in Norway spruce using a large dataset spanning two generations in two environments. We trained pedigree-based (ABLUP) and marker-based (GBLUP) prediction models under three approaches: forward prediction, backward prediction, and across-environment prediction. The models were evaluated for ring-width, solid-wood and tracheid characteristics, using ~ 6,000 phenotyped and ~ 2,500 genotyped individual. Predictive ability (PA) and prediction accuracy (ACC) were estimated using an independent validation method, ensuring no individuals were shared between training and validation datasets. To assess the trade-off between comprehensive radial history and practical direct methods, we compared GBLUP models trained with cumulative area-weighted density (AWE-GBLUP) and single annual-ring density (SAD-GBLUP) from mother plus-trees. These models were validated using early and mature-stage progeny density measurements across two trials.

@article{zeng_mutations_2025,
	title = {Mutations in the floral regulator gene {HUA2} restore flowering to the {Arabidopsis} trehalose 6-phosphate synthase1 (tps1) mutant},
	volume = {198},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiaf225},
	doi = {10.1093/plphys/kiaf225},
	abstract = {Plant growth and development are regulated by many factors, including carbohydrate availability and signaling. Trehalose 6-phosphate (T6P), which is synthesized by TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1), is positively associated with and functions as a signal that informs the cell about the carbohydrate status. Mutations in TPS1 negatively affect the growth and development of Arabidopsis (Arabidopsis thaliana), and complete loss-of-function alleles are embryo-lethal, which can be overcome using inducible expression of TPS1 (GVG::TPS1) during embryogenesis. Using ethyl methane sulfonate mutagenesis in combination with genome re-sequencing, we have identified several alleles in the floral regulator gene HUA2 that restore flowering in tps1-2 GVG::TPS1. Genetic analyses using an HUA2 T-DNA insertion allele, hua2-4, confirmed this finding. RNA-seq analyses demonstrated that hua2-4 has widespread effects on the tps1-2 GVG::TPS1 transcriptome, including key genes and pathways involved in regulating flowering. Higher order mutants combining tps1-2 GVG::TPS1 and hua2-4 with alleles in the key flowering time regulators FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), and FLOWERING LOCUS C (FLC) were constructed to analyze the role of HUA2 during floral transition in tps1-2 in more detail. Our findings demonstrate that loss of HUA2 can restore flowering in tps1-2 GVG::TPS1, in part through activation of FT, with contributions from the upstream regulators SOC1 and FLC. Interestingly, we found that mutation of FLC is sufficient to induce flowering in tps1-2 GVG::TPS1. Furthermore, we observed that mutations in HUA2 modulate carbohydrate signaling and that this regulation might contribute to flowering in hua2-4 tps1-2 GVG::TPS1.},
	number = {2},
	urldate = {2025-06-27},
	journal = {Plant Physiology},
	author = {Zeng, Liping and Zacharaki, Vasiliki and van Es, Sam W and Wang, Yanwei and Schmid, Markus},
	month = jun,
	year = {2025},
	pages = {kiaf225},
}

Plant growth and development are regulated by many factors, including carbohydrate availability and signaling. Trehalose 6-phosphate (T6P), which is synthesized by TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1), is positively associated with and functions as a signal that informs the cell about the carbohydrate status. Mutations in TPS1 negatively affect the growth and development of Arabidopsis (Arabidopsis thaliana), and complete loss-of-function alleles are embryo-lethal, which can be overcome using inducible expression of TPS1 (GVG::TPS1) during embryogenesis. Using ethyl methane sulfonate mutagenesis in combination with genome re-sequencing, we have identified several alleles in the floral regulator gene HUA2 that restore flowering in tps1-2 GVG::TPS1. Genetic analyses using an HUA2 T-DNA insertion allele, hua2-4, confirmed this finding. RNA-seq analyses demonstrated that hua2-4 has widespread effects on the tps1-2 GVG::TPS1 transcriptome, including key genes and pathways involved in regulating flowering. Higher order mutants combining tps1-2 GVG::TPS1 and hua2-4 with alleles in the key flowering time regulators FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), and FLOWERING LOCUS C (FLC) were constructed to analyze the role of HUA2 during floral transition in tps1-2 in more detail. Our findings demonstrate that loss of HUA2 can restore flowering in tps1-2 GVG::TPS1, in part through activation of FT, with contributions from the upstream regulators SOC1 and FLC. Interestingly, we found that mutation of FLC is sufficient to induce flowering in tps1-2 GVG::TPS1. Furthermore, we observed that mutations in HUA2 modulate carbohydrate signaling and that this regulation might contribute to flowering in hua2-4 tps1-2 GVG::TPS1.

@article{gil-munoz_implications_2025,
	title = {Implications of {Breeding} for {Growth} on {Drought} {Tolerance} in {Scots} {Pine} ({Pinus} sylvestris {L}.)—{Insights} {From} {Metabolomics} and {High}-{Throughput} {Plant} {Architecture} {Analysis}},
	volume = {18},
	copyright = {© 2025 The Author(s). Evolutionary Applications published by John Wiley \& Sons Ltd.},
	issn = {1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.70122},
	doi = {10.1111/eva.70122},
	abstract = {Drought has been identified as one of the important environmental factors in the context of climate change due to its interaction with other biotic and abiotic stresses. However, only a few studies have reported the effect of breeding on forest adaptability to climate change. Using a common garden experiment with seedlings from families of Scots pine (Pinus sylvestris L.) from northern Sweden, we have found differences in drought tolerance between seedlings from breeding stands and those from natural forests. We performed a genetic analysis including high-throughput image-based phenotyping of seedling canopy and root traits and conducted metabolomic and hormone analyses with the aerial parts of the seedlings. Our results indicate that root architecture traits associated with drought tolerance exhibit moderate to high heritability. Analyses of seedling architecture reveal that families from breeding stands have higher drought resistance but lower genetic variation than the ones from natural forests, especially in the case of canopy traits. Metabolomic and hormone analyses of the aerial parts of the seedlings also support that the breeding stands may have a higher capacity to withstand or deal with drought conditions as compared to the natural forests. For example, increase in abscisic acid along with increase in tryptophan and auxin conjugates in the breeding stands compared to the natural forests under drought conditions may contribute to alleviation of drought response in the breeding stands. The methodology employed to evaluate drought tolerance and plant architecture in this study might be useful for future research and forest management focused on climate change adaptability.},
	language = {en},
	number = {6},
	urldate = {2025-06-27},
	journal = {Evolutionary Applications},
	author = {Gil-Muñoz, Francisco and Ranade, Sonali Sachin and Hayatgheibi, Haleh and Niemi, Juha and Östlund, Lars and García-Gil, María Rosario},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.70122},
	keywords = {abscisic acid, drought, metabolomics, root architecture, scots pine},
	pages = {e70122},
}

Drought has been identified as one of the important environmental factors in the context of climate change due to its interaction with other biotic and abiotic stresses. However, only a few studies have reported the effect of breeding on forest adaptability to climate change. Using a common garden experiment with seedlings from families of Scots pine (Pinus sylvestris L.) from northern Sweden, we have found differences in drought tolerance between seedlings from breeding stands and those from natural forests. We performed a genetic analysis including high-throughput image-based phenotyping of seedling canopy and root traits and conducted metabolomic and hormone analyses with the aerial parts of the seedlings. Our results indicate that root architecture traits associated with drought tolerance exhibit moderate to high heritability. Analyses of seedling architecture reveal that families from breeding stands have higher drought resistance but lower genetic variation than the ones from natural forests, especially in the case of canopy traits. Metabolomic and hormone analyses of the aerial parts of the seedlings also support that the breeding stands may have a higher capacity to withstand or deal with drought conditions as compared to the natural forests. For example, increase in abscisic acid along with increase in tryptophan and auxin conjugates in the breeding stands compared to the natural forests under drought conditions may contribute to alleviation of drought response in the breeding stands. The methodology employed to evaluate drought tolerance and plant architecture in this study might be useful for future research and forest management focused on climate change adaptability.

@article{zhong_maize_2025,
	title = {A maize near-isogenic line population designed for gene discovery and characterization of allelic effects},
	volume = {122},
	copyright = {© 2025 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.70228},
	doi = {10.1111/tpj.70228},
	abstract = {In this study, we characterized a panel of 1264 maize near-isogenic lines (NILs), developed from crosses between 18 diverse inbred lines and the recurrent parent B73, referred to as nested NILs (nNILs). In this study, 888 of the nNILs were genotyped using genotyping-by-sequencing (GBS). Subsequently, 24 of these nNILs, and all the parental lines, were re-genotyped using a high-density single nucleotide polymorphism (SNP) chip. A novel pipeline for calling introgressions, which does not rely on knowing the donor parent of each nNIL, was developed based on a hidden Markov model (HMM) algorithm. By comparing the introgressions detected using GBS data with those identified using chip data, we optimized the HMM parameters for analyzing the entire nNIL population. A total of 2969 introgressions were identified across the 888 nNILs. Individual introgression blocks ranged from 21 bp to 204 Mbp, with an average size of 17 Mbp. By comparing SNP genotypes within introgressed segments to the known genotypes of the donor lines, we determined that in about one third of the lines, the identity of the donors did not match expectation based on their pedigrees. We characterized the entire nNIL population for three foliar diseases. Using these data, we mapped a number of quantitative trait loci (QTL) for disease resistance in the nNIL population and observed extensive variation in effects among the alleles from different donor parents at most QTL identified. This population will be of significant utility for dissecting complex agronomic traits and allelic series in maize.},
	language = {en},
	number = {5},
	urldate = {2025-07-07},
	journal = {The Plant Journal},
	author = {Zhong, Tao and Mullens, Alex and Morales, Laura and Swarts, Kelly L. and Stafstrom, William C. and He, Yijian and Sermons, Shannon M and Yang, Qin and Lopez-Zuniga, Luis O. and Rucker, Elizabeth and Thomason, Wade E. and Nelson, Rebecca J. and Jamann, Tiffany and Balint-Kurti, Peter J. and Holland, James B.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.70228},
	keywords = {allelic series, disease resistance, maize, near isogenic line},
	pages = {e70228},
}

In this study, we characterized a panel of 1264 maize near-isogenic lines (NILs), developed from crosses between 18 diverse inbred lines and the recurrent parent B73, referred to as nested NILs (nNILs). In this study, 888 of the nNILs were genotyped using genotyping-by-sequencing (GBS). Subsequently, 24 of these nNILs, and all the parental lines, were re-genotyped using a high-density single nucleotide polymorphism (SNP) chip. A novel pipeline for calling introgressions, which does not rely on knowing the donor parent of each nNIL, was developed based on a hidden Markov model (HMM) algorithm. By comparing the introgressions detected using GBS data with those identified using chip data, we optimized the HMM parameters for analyzing the entire nNIL population. A total of 2969 introgressions were identified across the 888 nNILs. Individual introgression blocks ranged from 21 bp to 204 Mbp, with an average size of 17 Mbp. By comparing SNP genotypes within introgressed segments to the known genotypes of the donor lines, we determined that in about one third of the lines, the identity of the donors did not match expectation based on their pedigrees. We characterized the entire nNIL population for three foliar diseases. Using these data, we mapped a number of quantitative trait loci (QTL) for disease resistance in the nNIL population and observed extensive variation in effects among the alleles from different donor parents at most QTL identified. This population will be of significant utility for dissecting complex agronomic traits and allelic series in maize.

@article{chubanava_nad_2025,
	title = {{NAD} depletion in skeletal muscle does not compromise muscle function or accelerate aging},
	issn = {1550-4131},
	url = {https://www.sciencedirect.com/science/article/pii/S1550413125002128},
	doi = {10.1016/j.cmet.2025.04.002},
	abstract = {Nicotinamide adenine dinucleotide (NAD) is a ubiquitous electron carrier essential for energy metabolism and post-translational modification of numerous regulatory proteins. Dysregulations of NAD metabolism are widely regarded as detrimental to health, with NAD depletion commonly implicated in aging. However, the extent to which cellular NAD concentration can decline without adverse consequences remains unclear. To investigate this, we generated a mouse model in which nicotinamide phosphoribosyltransferase (NAMPT)-mediated NAD+ biosynthesis was disrupted in adult skeletal muscle. The intervention resulted in an 85\% reduction in muscle NAD+ abundance while maintaining tissue integrity and functionality, as demonstrated by preserved muscle morphology, contractility, and exercise tolerance. This absence of functional impairments was further supported by intact mitochondrial respiratory capacity and unaltered muscle transcriptomic and proteomic profiles. Furthermore, lifelong NAD depletion did not accelerate muscle aging or impair whole-body metabolism. Collectively, these findings suggest that NAD depletion does not contribute to age-related decline in skeletal muscle function.},
	urldate = {2025-05-09},
	journal = {Cell Metabolism},
	author = {Chubanava, Sabina and Karavaeva, Iuliia and Ehrlich, Amy M. and Justicia, Roger M. and Basse, Astrid L. and Kulik, Ivan and Dalbram, Emilie and Ahwazi, Danial and Heaselgrave, Samuel R. and Trošt, Kajetan and Stocks, Ben and Hodek, Ondřej and Rodrigues, Raissa N. and Havelund, Jesper F. and Schlabs, Farina L. and Larsen, Steen and Yonamine, Caio Y. and Henriquez-Olguín, Carlos and Giustarini, Daniela and Rossi, Ranieri and Gerhart-Hines, Zachary and Moritz, Thomas and Zierath, Juleen R. and Sakamoto, Kei and Jensen, Thomas E. and Færgeman, Nils J. and Lavery, Gareth G. and Deshmukh, Atul S. and Treebak, Jonas T.},
	month = apr,
	year = {2025},
	keywords = {NAD biosynthesis, NAD metabolism, NAMPT, aging, epigenetic clock, exercise, mitochondrial supercomplexes, nicotinamide, reactive oxygen species, skeletal muscle},
}

Nicotinamide adenine dinucleotide (NAD) is a ubiquitous electron carrier essential for energy metabolism and post-translational modification of numerous regulatory proteins. Dysregulations of NAD metabolism are widely regarded as detrimental to health, with NAD depletion commonly implicated in aging. However, the extent to which cellular NAD concentration can decline without adverse consequences remains unclear. To investigate this, we generated a mouse model in which nicotinamide phosphoribosyltransferase (NAMPT)-mediated NAD+ biosynthesis was disrupted in adult skeletal muscle. The intervention resulted in an 85% reduction in muscle NAD+ abundance while maintaining tissue integrity and functionality, as demonstrated by preserved muscle morphology, contractility, and exercise tolerance. This absence of functional impairments was further supported by intact mitochondrial respiratory capacity and unaltered muscle transcriptomic and proteomic profiles. Furthermore, lifelong NAD depletion did not accelerate muscle aging or impair whole-body metabolism. Collectively, these findings suggest that NAD depletion does not contribute to age-related decline in skeletal muscle function.

@article{tian_plantlncboost_2025,
	title = {{PlantLncBoost}: key features for plant {lncRNA} identification and significant improvement in accuracy and generalization},
	copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.},
	issn = {1469-8137},
	shorttitle = {{PlantLncBoost}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.70211},
	doi = {10.1111/nph.70211},
	abstract = {Long noncoding RNAs (lncRNAs) are critical regulators of numerous biological processes in plants. Nevertheless, their identification is challenging due to the low sequence conservation across various species. Existing computational methods for lncRNA identification often face difficulties in generalizing across diverse plant species, highlighting the need for more robust and versatile identification models. Here, we present PlantLncBoost, a novel computational tool designed to improve the generalization in plant lncRNA identification. By integrating advanced gradient boosting algorithms with comprehensive feature selection, our approach achieves both high accuracy and generalizability. We conducted an extensive analysis of 1662 features and identified three key features – ORF coverage, complex Fourier average, and atomic Fourier amplitude – that effectively distinguish lncRNAs from mRNAs. We assessed the performance of PlantLncBoost using comprehensive datasets from 20 plant species. The model exhibited exceptional performance, with an accuracy of 96.63\%, a sensitivity of 98.42\%, and a specificity of 94.93\%, significantly outperforming existing tools. Further analysis revealed that the features we selected effectively capture the differences between lncRNAs and mRNAs across a variety of plant species. PlantLncBoost represents a significant advancement in plant lncRNA identification. It is freely accessible on GitHub (https://github.com/xuechantian/PlantLncBoost) and has been integrated into a comprehensive analysis pipeline, Plant-LncRNA-pipeline v.2 (https://github.com/xuechantian/Plant-LncRNA-pipeline-v2).},
	language = {en},
	urldate = {2025-05-30},
	journal = {New Phytologist},
	author = {Tian, Xue-Chan and Nie, Shuai and Domingues, Douglas and Rossi Paschoal, Alexandre and Jiang, Li-Bo and Mao, Jian-Feng},
	month = may,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.70211},
	keywords = {Fourier transform, ORF coverage, feature selection, gradient boosting algorithms, long noncoding RNAs (lncRNAs), model selection},
}

Long noncoding RNAs (lncRNAs) are critical regulators of numerous biological processes in plants. Nevertheless, their identification is challenging due to the low sequence conservation across various species. Existing computational methods for lncRNA identification often face difficulties in generalizing across diverse plant species, highlighting the need for more robust and versatile identification models. Here, we present PlantLncBoost, a novel computational tool designed to improve the generalization in plant lncRNA identification. By integrating advanced gradient boosting algorithms with comprehensive feature selection, our approach achieves both high accuracy and generalizability. We conducted an extensive analysis of 1662 features and identified three key features – ORF coverage, complex Fourier average, and atomic Fourier amplitude – that effectively distinguish lncRNAs from mRNAs. We assessed the performance of PlantLncBoost using comprehensive datasets from 20 plant species. The model exhibited exceptional performance, with an accuracy of 96.63%, a sensitivity of 98.42%, and a specificity of 94.93%, significantly outperforming existing tools. Further analysis revealed that the features we selected effectively capture the differences between lncRNAs and mRNAs across a variety of plant species. PlantLncBoost represents a significant advancement in plant lncRNA identification. It is freely accessible on GitHub (https://github.com/xuechantian/PlantLncBoost) and has been integrated into a comprehensive analysis pipeline, Plant-LncRNA-pipeline v.2 (https://github.com/xuechantian/Plant-LncRNA-pipeline-v2).

@article{safronov_independent_2025,
	title = {Independent evolution of betulin biosynthesis in {Inonotus} obliquus},
	volume = {15},
	copyright = {2025 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-025-05414-1},
	doi = {10.1038/s41598-025-05414-1},
	abstract = {Chaga mushroom (Inonotus obliquus) is a fungal species in the family Hymenochaetaceae (Basidiomycota) and the causative agent of white rot decay in Betula species. We assembled a high-quality 50.7 Mbp genome from PacBio sequencing and identified a lineage-specific whole genome duplication event approximately 1.3 million years ago, which has contributed to a major increase in biochemical diversity in the species through preferential retention of cytochrome P450 superfamily members. Secondary metabolism has further evolved through small-scale segmental duplications, such as tandem duplications within fungal biosynthetic gene clusters. Metabolomic fingerprinting confirmed increased complexity in terpene biosynthesis chemistry compared to related species that lacked the duplication event. This metabolic diversity may have arisen from co-evolution with the primary host species, which evolved high betulin content in its bark 4–8 million years ago.},
	language = {en},
	number = {1},
	urldate = {2025-07-04},
	journal = {Scientific Reports},
	publisher = {Nature Publishing Group},
	author = {Safronov, Omid and Bal, Güleycan Lutfullahoglu and Sipari, Nina and Wilkens, Maya and Safdari, Pezhman and Smolander, Olli-Pekka and Laine, Pia K. and Lihavainen, Jenna and Silvan, Niko and Rajaraman, Sitaram and Paulin, Lars G. and Teeri, Teemu H. and Auvinen, Petri and Sarjala, Tytti and Overmyer, Kirk and Richter, Uwe and Salojärvi, Jarkko},
	month = jul,
	year = {2025},
	keywords = {Coevolution, Genomics, Molecular evolution},
	pages = {21319},
}

Chaga mushroom (Inonotus obliquus) is a fungal species in the family Hymenochaetaceae (Basidiomycota) and the causative agent of white rot decay in Betula species. We assembled a high-quality 50.7 Mbp genome from PacBio sequencing and identified a lineage-specific whole genome duplication event approximately 1.3 million years ago, which has contributed to a major increase in biochemical diversity in the species through preferential retention of cytochrome P450 superfamily members. Secondary metabolism has further evolved through small-scale segmental duplications, such as tandem duplications within fungal biosynthetic gene clusters. Metabolomic fingerprinting confirmed increased complexity in terpene biosynthesis chemistry compared to related species that lacked the duplication event. This metabolic diversity may have arisen from co-evolution with the primary host species, which evolved high betulin content in its bark 4–8 million years ago.

@article{liu_genomic_2025,
	title = {Genomic insights into the evolution of {Chinese} sweetgum and its autumn leaf coloration},
	volume = {198},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiaf218},
	doi = {10.1093/plphys/kiaf218},
	abstract = {Chinese sweetgum (Liquidambar formosana) is valued as a source of resin and timber and is an important ornamental tree due to its showy fall foliage. Here, we report the chromosome-level assembly of the Chinese sweetgum genome. Phylogenomic analyses showed the basal phylogenetic position of Chinese sweetgum in core eudicots. Comparative genomic analyses revealed that the well-known gamma event in the common ancestors of core eudicots is evident in the Chinese sweetgum genome, and ancestral triplicated blocks resulting from that event are more intact in Chinese sweetgum than in grapevine (Vitis vinifera). Because of its conserved genome structure, very slow rate of evolution, and basal phylogenetic position, the Chinese sweetgum genome is a good reference for comparative genome studies. Further, we reconstructed the entire metabolic pathway for anthocyanins and potential regulatory networks of autumn leaf coloration of this species via metabolomics and transcriptomics. The transcription factors LfMYB69, basic helix–loop–helix (LfbHLH4), and WD40-repeat (LfWDR1) may collectively regulate the transcription of anthocyanin biosynthetic genes. The regulation of chalcone synthase genes (LfCHS1-3) and dihydroflavonol 4-reductase genes (LfDFR1-2) by the LfMYB69–LfbHLH4–LfWDR1 complex was confirmed by luciferase assays. Epigenomic analyses revealed that 5 structural genes, including LfCHS1, and 2 regulatory LfMYBs are epigenetically regulated. This study expands our understanding of autumn leaf coloration and provides valuable genomic resources for comparative biology, breeding, and biotechnology.},
	number = {2},
	urldate = {2025-06-13},
	journal = {Plant Physiology},
	author = {Liu, Ping-Li and Jing, Zhao-Yang and Zhang, Ren-Gang and Chen, Ye and Zhu, Zhixin and Zhang, Xi and Jiang, Chen-Kun and Li, Ruili and Xie, Jian-Bo and Niu, Shihui and Zhang, Jinfeng and Kong, Lisheng and Zhao, Jian and Ma, Yongpeng and Zeisler-Diehl, Viktoria V and Schreiber, Lukas and Karahara, Ichirou and Mao, Jian-Feng and Jiao, Yuannian and Ge, Song and Lin, Jinxing},
	month = jun,
	year = {2025},
	pages = {kiaf218},
}

Chinese sweetgum (Liquidambar formosana) is valued as a source of resin and timber and is an important ornamental tree due to its showy fall foliage. Here, we report the chromosome-level assembly of the Chinese sweetgum genome. Phylogenomic analyses showed the basal phylogenetic position of Chinese sweetgum in core eudicots. Comparative genomic analyses revealed that the well-known gamma event in the common ancestors of core eudicots is evident in the Chinese sweetgum genome, and ancestral triplicated blocks resulting from that event are more intact in Chinese sweetgum than in grapevine (Vitis vinifera). Because of its conserved genome structure, very slow rate of evolution, and basal phylogenetic position, the Chinese sweetgum genome is a good reference for comparative genome studies. Further, we reconstructed the entire metabolic pathway for anthocyanins and potential regulatory networks of autumn leaf coloration of this species via metabolomics and transcriptomics. The transcription factors LfMYB69, basic helix–loop–helix (LfbHLH4), and WD40-repeat (LfWDR1) may collectively regulate the transcription of anthocyanin biosynthetic genes. The regulation of chalcone synthase genes (LfCHS1-3) and dihydroflavonol 4-reductase genes (LfDFR1-2) by the LfMYB69–LfbHLH4–LfWDR1 complex was confirmed by luciferase assays. Epigenomic analyses revealed that 5 structural genes, including LfCHS1, and 2 regulatory LfMYBs are epigenetically regulated. This study expands our understanding of autumn leaf coloration and provides valuable genomic resources for comparative biology, breeding, and biotechnology.

@incollection{gupta_nanomaterial-based_2025,
	address = {Cham},
	title = {Nanomaterial-{Based} {Sensors} and {Monitoring} {Devices} for {Water} {Quality} {Assessment}},
	isbn = {978-3-031-82794-5},
	url = {https://doi.org/10.1007/978-3-031-82794-5_13},
	doi = {10.1007/978-3-031-82794-5_13},
	abstract = {Industrialization, urbanization, and modern globalization increased the amount of pollutants in aquatic bodies, lowering the water purity. Surface and pollution of groundwater occur due to emerging pollutants, which result in drinking water scarcity. Plants and aquatic life, as well as human health, are significantly impacted by water contaminants, to ensure that natural aquifers provide clean, safe water and to comprehend how water contaminants change over time and space. Therefore, water quality monitoring has grown in significance during the past few years. Traditional methods of measuring water quality parameters are being replaced by new ideas and approaches. In the current era of sensors, biosensors, optical sensors, and microelectronic mechanical systems (MEMS) are significant sensing methods for detecting various water quality parameters. In addition, these sensors have a fast response time, excellent selectivity, sensitivity, affordability, and ease of use. This chapter focuses on the use of nanomaterial-based optical, electronic, and electrochemical sensors for the quick identification of water contaminants, such as microorganisms, anions, heavy metals, etc. There is a need for major development in the identification of pollutants in water due to the limits of present sensing technology. The benefits of sensing technologies based on nanomaterials are emphasized. The latest developments in nanomaterial-based sensors for quick detection of water contaminants have been discussed.},
	language = {en},
	urldate = {2025-07-04},
	booktitle = {Nano-solutions for {Sustainable} {Water} and {Wastewater} {Management}: {From} {Monitoring} to {Treatment}},
	publisher = {Springer Nature Switzerland},
	author = {Gupta, Urvashi and Jindal, Tanu and Tyagi, Jagriti and Salam, Menaka Devi and Saxena, Ananya and Upadhyay, Divya and Mishra, Arti and Shukla, Smriti},
	editor = {Garg, Manoj Chandra and Rajput, Vishnu D. and Minkina, Tatiana and Himanshu, Sushil Kumar},
	year = {2025},
	pages = {299--323},
}

Industrialization, urbanization, and modern globalization increased the amount of pollutants in aquatic bodies, lowering the water purity. Surface and pollution of groundwater occur due to emerging pollutants, which result in drinking water scarcity. Plants and aquatic life, as well as human health, are significantly impacted by water contaminants, to ensure that natural aquifers provide clean, safe water and to comprehend how water contaminants change over time and space. Therefore, water quality monitoring has grown in significance during the past few years. Traditional methods of measuring water quality parameters are being replaced by new ideas and approaches. In the current era of sensors, biosensors, optical sensors, and microelectronic mechanical systems (MEMS) are significant sensing methods for detecting various water quality parameters. In addition, these sensors have a fast response time, excellent selectivity, sensitivity, affordability, and ease of use. This chapter focuses on the use of nanomaterial-based optical, electronic, and electrochemical sensors for the quick identification of water contaminants, such as microorganisms, anions, heavy metals, etc. There is a need for major development in the identification of pollutants in water due to the limits of present sensing technology. The benefits of sensing technologies based on nanomaterials are emphasized. The latest developments in nanomaterial-based sensors for quick detection of water contaminants have been discussed.

@article{ma_ca2_2025,
	title = {Ca2+ waves and ethylene/{JA} crosstalk orchestrate wound responses in {Arabidopsis} roots},
	volume = {26},
	issn = {1469-221X},
	url = {https://www.embopress.org/doi/full/10.1038/s44319-025-00471-z},
	doi = {10.1038/s44319-025-00471-z},
	abstract = {Wounding triggers complex and multi-faceted responses in plants. Among these, calcium (Ca2+) waves serve as an immediate and localized response to strong stimuli, such as nematode infection or laser ablation. Here, we investigate the propagation patterns of Ca2+ waves induced by laser ablation and observe that glutamate-receptor-like channels (GLR3.3/GLR3.6), the stretch-activated anion channel MSL10, and the mechanosensitive Ca2+-permeable channels MCA1/MCA2 influence this process. These channels contribute to ethylene-associated signaling pathways, potentially through the WRKY33-ACS6 regulatory network. Furthermore, our findings show that ACC/ethylene signaling modulates Ca2+ wave propagation following laser ablation. Ethylene perception and synthesis at the site of damage regulate the local jasmonate response, which displays tissue-specific patterns upon laser ablation. Overall, our data provide new insights into the molecular and cellular processes underlying plant responses to localized damage, highlighting the roles of specific ion channels and hormone signaling pathways in shaping these responses in Arabidopsis roots.},
	number = {12},
	urldate = {2025-06-27},
	journal = {EMBO reports},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Ma, Xuemin and Hasan, M Shamim and Anjam, Muhammad Shahzad and Mahmud, Sakil and Bhattacharyya, Sabarna and Vothknecht, Ute C and Mendy, Badou and Grundler, Florian M W and Marhavý, Peter},
	month = jun,
	year = {2025},
	note = {Num Pages: 3203},
	keywords = {Ca2+ Wave, Ethylene, Jasmonate, Laser Ablation},
	pages = {3187--3203},
}

Wounding triggers complex and multi-faceted responses in plants. Among these, calcium (Ca2+) waves serve as an immediate and localized response to strong stimuli, such as nematode infection or laser ablation. Here, we investigate the propagation patterns of Ca2+ waves induced by laser ablation and observe that glutamate-receptor-like channels (GLR3.3/GLR3.6), the stretch-activated anion channel MSL10, and the mechanosensitive Ca2+-permeable channels MCA1/MCA2 influence this process. These channels contribute to ethylene-associated signaling pathways, potentially through the WRKY33-ACS6 regulatory network. Furthermore, our findings show that ACC/ethylene signaling modulates Ca2+ wave propagation following laser ablation. Ethylene perception and synthesis at the site of damage regulate the local jasmonate response, which displays tissue-specific patterns upon laser ablation. Overall, our data provide new insights into the molecular and cellular processes underlying plant responses to localized damage, highlighting the roles of specific ion channels and hormone signaling pathways in shaping these responses in Arabidopsis roots.

@article{kumar_shape_2025,
	title = {“{Shape} of {Cell}”—{An} {Auxin} and {Cell} {Wall} {Duet}},
	volume = {177},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70294},
	doi = {10.1111/ppl.70294},
	abstract = {Understanding the mechanisms underlying cell shape acquisition is of fundamental importance in plant science, as this process ultimately defines the structure and function of plant organs. Plants produce cells of diverse shapes and sizes, including pavement cells and stomata of leaves, elongated epidermal cells of the hypocotyl, and cells with outgrowths such as root hairs, and so forth. Plant cells experience mechanical forces of variable magnitude during their development and interaction with neighboring cells and the surrounding environment. From the time of cytokinesis, they are encaged in a complex cell wall matrix, which offers mechanical support and enables directional growth and a differential rate of expansion towards adjacent cells via its mechanochemical heterogeneity. The phytohormone auxin is well characterized for its role in cell expansion and cell elasticity. The interaction between dynamic auxin redistribution and the mechanical properties of the cell wall within tissues drives the development of specific cell shapes. Here, we focus on the regulatory feedback loop involving auxin activity, its influence on cell wall chemistry and mechanical properties, and the coordination of cell shape formation. Integrating insights from molecular and cell biology, biophysics, and computational modeling, we explore the mechanistic link between auxin signaling and cell wall dynamics in shaping plant cells.},
	language = {en},
	number = {3},
	urldate = {2025-06-13},
	journal = {Physiologia Plantarum},
	author = {Kumar, Vinod and Yadav, Sandeep and Heymans, Adrien and Robert, Stéphanie},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70294},
	keywords = {auxin, cell shape, cell wall, cytoskeleton, mechanical stress},
	pages = {e70294},
}

Understanding the mechanisms underlying cell shape acquisition is of fundamental importance in plant science, as this process ultimately defines the structure and function of plant organs. Plants produce cells of diverse shapes and sizes, including pavement cells and stomata of leaves, elongated epidermal cells of the hypocotyl, and cells with outgrowths such as root hairs, and so forth. Plant cells experience mechanical forces of variable magnitude during their development and interaction with neighboring cells and the surrounding environment. From the time of cytokinesis, they are encaged in a complex cell wall matrix, which offers mechanical support and enables directional growth and a differential rate of expansion towards adjacent cells via its mechanochemical heterogeneity. The phytohormone auxin is well characterized for its role in cell expansion and cell elasticity. The interaction between dynamic auxin redistribution and the mechanical properties of the cell wall within tissues drives the development of specific cell shapes. Here, we focus on the regulatory feedback loop involving auxin activity, its influence on cell wall chemistry and mechanical properties, and the coordination of cell shape formation. Integrating insights from molecular and cell biology, biophysics, and computational modeling, we explore the mechanistic link between auxin signaling and cell wall dynamics in shaping plant cells.

@article{faleiro_assessment_2025,
	title = {Assessment of the impact of biodegradable lignin nanoparticles encapsulating {IAA} on tomato development: from seed to fruit},
	volume = {25},
	issn = {1471-2229},
	shorttitle = {Assessment of the impact of biodegradable lignin nanoparticles encapsulating {IAA} on tomato development},
	url = {https://doi.org/10.1186/s12870-025-06539-1},
	doi = {10.1186/s12870-025-06539-1},
	abstract = {Polymeric nanoparticles have emerged as promising nanocarriers for plant growth regulators (PGRs) in agriculture, enhancing plant growth and boosting fruit and cereal yields. Among these, lignin nanoparticles (LNPs) stand out due to their biodegradability and low production cost. However, few studies have evaluated the biological effects of LNPs encapsulating PGRs — particularly their dose-dependent impacts across the entire plant life cycle. Therefore, our study aims to evaluate the efficiency of lignin nanoparticles (LNPs) encapsulating indole-3-acetic acid (IAA) compared with free application of the hormone. We employed a multidisciplinary approach to comprehensively assess the impacts of different LNPs-IAA concentrations. Germination tests and morphometric analyses were conducted, along with anatomical analyses of seeds, seedlings, and vegetative organs using light microscopy. Confocal microscopy analyses to examine LNP uptake and translocation. Additionally, leaf gas exchange parameters and photosynthetic pigment levels were measured. The lignin nanoparticles were also characterized in terms of length, polydispersity index, zeta potential and encapsulation efficiency. All variables were subjected to normality tests, variance analysis, and post-hoc tests. Structural analysis revealed that LNP application did not alter overall plant anatomy architecture, except for inducing differences in xylem area among vegetative organs. Additionally, LNPs were rapidly absorbed by seeds in less than 5 h and were transported exclusively via the apoplastic pathway. The composition of lignin nanoparticles influenced germination rates and time. Application with lower concentrations showed minimal statistical significance, whereas higher concentrations exhibited phytotoxic effects. Thus, our study highlights the critical importance of optimizing nanocarrier concentrations for plant growth enhancement, demonstrating that lignin nanoparticles (LNPs) represent a promising nanoformulation for bioactive compound encapsulation.},
	number = {1},
	urldate = {2025-06-13},
	journal = {BMC Plant Biology},
	author = {Faleiro, Rodrigo and Tessmer, Magda Andreia and Santo Pereira, Anderson Espirito and Fraceto, Leonardo Fernandes and Rampasso, Marcelle Sanches and Miranda, Marcela Trevenzoli and Pissolato, Maria Dolores and Cassola, Fábio and Ribeiro, Rafael Vasconcelos and Mayer, Juliana Lischka Sampaio},
	month = jun,
	year = {2025},
	keywords = {Crop science, Encapsulation, Nanotechnology, Plant growth regulators, Sustainability},
	pages = {768},
}

Polymeric nanoparticles have emerged as promising nanocarriers for plant growth regulators (PGRs) in agriculture, enhancing plant growth and boosting fruit and cereal yields. Among these, lignin nanoparticles (LNPs) stand out due to their biodegradability and low production cost. However, few studies have evaluated the biological effects of LNPs encapsulating PGRs — particularly their dose-dependent impacts across the entire plant life cycle. Therefore, our study aims to evaluate the efficiency of lignin nanoparticles (LNPs) encapsulating indole-3-acetic acid (IAA) compared with free application of the hormone. We employed a multidisciplinary approach to comprehensively assess the impacts of different LNPs-IAA concentrations. Germination tests and morphometric analyses were conducted, along with anatomical analyses of seeds, seedlings, and vegetative organs using light microscopy. Confocal microscopy analyses to examine LNP uptake and translocation. Additionally, leaf gas exchange parameters and photosynthetic pigment levels were measured. The lignin nanoparticles were also characterized in terms of length, polydispersity index, zeta potential and encapsulation efficiency. All variables were subjected to normality tests, variance analysis, and post-hoc tests. Structural analysis revealed that LNP application did not alter overall plant anatomy architecture, except for inducing differences in xylem area among vegetative organs. Additionally, LNPs were rapidly absorbed by seeds in less than 5 h and were transported exclusively via the apoplastic pathway. The composition of lignin nanoparticles influenced germination rates and time. Application with lower concentrations showed minimal statistical significance, whereas higher concentrations exhibited phytotoxic effects. Thus, our study highlights the critical importance of optimizing nanocarrier concentrations for plant growth enhancement, demonstrating that lignin nanoparticles (LNPs) represent a promising nanoformulation for bioactive compound encapsulation.

@article{gran_unravelling_2025,
	title = {Unravelling the dynamics of seed-stored {mRNAs} during seed priming},
	copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.70098},
	doi = {10.1111/nph.70098},
	abstract = {Seed priming is a pre-sowing treatment that enables more efficient and uniform seed germination; however, it negatively affects seed longevity. In this work, the mRNA dynamics underlying a hydropriming treatment have been investigated. Polysome profiling was performed on seeds during different stages of hydropriming. Ribosome nascent chain complex sequencing (RNC-seq) elucidated transcriptomic and translatomic changes during the priming treatment. In contrast to mature dry seeds, hydroprimed seeds contain more mRNA-ribosome complexes, suggesting that the mRNAs that need to be translated during germination are already associated with ribosomes in the primed seeds, leading to a quicker restart of translation and thus faster germination upon re-imbibition. As a result of priming, seeds lose part of their stress-related transcriptome. This work highlights genes that might play a role in increasing the rate of germination after priming.},
	language = {en},
	urldate = {2025-03-28},
	journal = {New Phytologist},
	author = {Gran, Patricija and Visscher, Tessa W. and Bai, Bing and Nijveen, Harm and Mahboubi, Amir and Bakermans, Lars L. and Willems, Leo A. J. and Bentsink, Leónie},
	month = mar,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.70098},
	keywords = {Arabidopsis thaliana, RNC-seq, germination, hydropriming, longevity, mRNA dynamics, polysome profiling, seeds},
}

Seed priming is a pre-sowing treatment that enables more efficient and uniform seed germination; however, it negatively affects seed longevity. In this work, the mRNA dynamics underlying a hydropriming treatment have been investigated. Polysome profiling was performed on seeds during different stages of hydropriming. Ribosome nascent chain complex sequencing (RNC-seq) elucidated transcriptomic and translatomic changes during the priming treatment. In contrast to mature dry seeds, hydroprimed seeds contain more mRNA-ribosome complexes, suggesting that the mRNAs that need to be translated during germination are already associated with ribosomes in the primed seeds, leading to a quicker restart of translation and thus faster germination upon re-imbibition. As a result of priming, seeds lose part of their stress-related transcriptome. This work highlights genes that might play a role in increasing the rate of germination after priming.

@article{holloway-phillips_is_2025,
	title = {Is {Photosynthesis}-{Derived} {NADPH} {Really} a {Source} of {2H}-{Depleted} {Hydrogen} in {Plant} {Compounds}?},
	volume = {48},
	copyright = {© 2025 John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.15403},
	doi = {10.1111/pce.15403},
	abstract = {statement We provide evidence that photosynthetically produced NADPH is not the major source of 2H-depletion in carbohydrates.},
	number = {6},
	urldate = {2025-05-23},
	journal = {Plant, Cell \& Environment},
	author = {Holloway-Phillips, Meisha and Tcherkez, Guillaume and Wieloch, Thomas and Lehmann, Marco M. and Werner, Roland A.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.15403},
	pages = {4083--4098},
}

statement We provide evidence that photosynthetically produced NADPH is not the major source of 2H-depletion in carbohydrates.

@article{di_fino_cellular_2025,
	title = {Cellular damage triggers mechano-chemical control of cell wall dynamics and patterned cell divisions in plant healing},
	volume = {60},
	issn = {1534-5807},
	url = {https://www.sciencedirect.com/science/article/pii/S1534580724007718},
	doi = {10.1016/j.devcel.2024.12.032},
	abstract = {Reactivation of cell division is crucial for the regeneration of damaged tissues, which is a fundamental process across all multicellular organisms. However, the mechanisms underlying the activation of cell division in plants during regeneration remain poorly understood. Here, we show that single-cell endodermal ablation generates a transient change in the local mechanical pressure on neighboring pericycle cells to activate patterned cell division that is crucial for tissue regeneration in Arabidopsis roots. Moreover, we provide strong evidence that this process relies on the phytohormone ethylene. Thus, our results highlight a previously unrecognized role of mechano-chemical control in patterned cell division during regeneration in plants.},
	number = {10},
	urldate = {2025-05-23},
	journal = {Developmental Cell},
	author = {Di Fino, Luciano Martín and Anjam, Muhammad Shahzad and Besten, Maarten and Mentzelopoulou, Andriani and Papadakis, Vassilis and Zahid, Nageena and Baez, Luis Alonso and Trozzi, Nicola and Majda, Mateusz and Ma, Xuemin and Hamann, Thorsten and Sprakel, Joris and Moschou, Panagiotis N. and Smith, Richard S. and Marhavý, Peter},
	month = may,
	year = {2025},
	keywords = {cell division, cell wall, ethylene, mechanobiology, pectin, regeneration, single-cell laser ablation, xylem-pole-pericycle},
	pages = {1411--1422.e6},
}

Reactivation of cell division is crucial for the regeneration of damaged tissues, which is a fundamental process across all multicellular organisms. However, the mechanisms underlying the activation of cell division in plants during regeneration remain poorly understood. Here, we show that single-cell endodermal ablation generates a transient change in the local mechanical pressure on neighboring pericycle cells to activate patterned cell division that is crucial for tissue regeneration in Arabidopsis roots. Moreover, we provide strong evidence that this process relies on the phytohormone ethylene. Thus, our results highlight a previously unrecognized role of mechano-chemical control in patterned cell division during regeneration in plants.

@article{moe_marked_2025,
	title = {Marked mucosal lipid shifts in treatment refractory inflammatory bowel disease: a lipidomic study},
	volume = {25},
	issn = {1471-230X},
	shorttitle = {Marked mucosal lipid shifts in treatment refractory inflammatory bowel disease},
	url = {https://doi.org/10.1186/s12876-025-03944-6},
	doi = {10.1186/s12876-025-03944-6},
	abstract = {Mechanisms causing non-response to biological agents in IBD remain to be fully understood. Thus, we aimed to characterize the lipid profile in treatment refractory non-immunogenic patients with adequate trough-levels.},
	number = {1},
	urldate = {2025-05-23},
	journal = {BMC Gastroenterology},
	author = {Moe, Øystein K. and Gao, Qian and Geng, Dawei and Jensen, Einar and Goll, Rasmus and Nestegard, Oddmund and Gundersen, Mona D. and Florholmen, Jon R. and Moritz, T.},
	month = may,
	year = {2025},
	keywords = {Biological therapy, Inflammatory bowel disease, Lipids, Non-response},
	pages = {389},
}

Mechanisms causing non-response to biological agents in IBD remain to be fully understood. Thus, we aimed to characterize the lipid profile in treatment refractory non-immunogenic patients with adequate trough-levels.

@article{liang_pan-genome_2025,
	title = {Pan-{Genome} {Analysis} {Reveals} {Local} {Adaptation} to {Climate} {Driven} by {Introgression} in {Oak} {Species}},
	volume = {42},
	issn = {1537-1719},
	url = {https://doi.org/10.1093/molbev/msaf088},
	doi = {10.1093/molbev/msaf088},
	abstract = {The genetic base of local adaptation has been extensively studied in natural populations. However, a comprehensive genome-wide perspective on the contribution of structural variants (SVs) and adaptive introgression to local adaptation remains limited. In this study, we performed de novo assembly and annotation of 22 representative accessions of Quercus variabilis, identifying a total of 543,372 SVs. These SVs play crucial roles in shaping genomic structure and influencing gene expression. By analyzing range-wide genomic data, we identified both SNPs and SVs associated with local adaptation in Q. variabilis and Quercus acutissima. Notably, SV-outliers exhibit selection signals that did not overlap with SNP-outliers, indicating that SNP-based analyses may not detect the same candidate genes associated with SV-outliers. Remarkably, 29\%−37\% of candidate SNPs were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF. This region contains 8 duplicated ethylene-responsive factor (ERF) genes, which may have contributed to local adaptation of Q. variabilis and Q. acutissima. We also found that a considerable number of candidate SNPs were shared between Q. variabilis and Q. acutissima in the Chr9-ERF region, suggesting a pattern of repeated selection. We further demonstrated that advantageous variants in this region were introgressed from western populations of Q. acutissima into Q. variabilis, providing compelling evidence that introgression facilitates local adaptation. This study offers a valuable genomic resource for future studies on oak species and highlights the importance of pan-genome analysis in understating mechanism driving adaptation and evolution.},
	number = {5},
	urldate = {2025-05-16},
	journal = {Molecular Biology and Evolution},
	author = {Liang, Yi-Ye and Liu, Hui and Lin, Qiong-Qiong and Shi, Yong and Zhou, Biao-Feng and Wang, Jing-Shu and Chen, Xue-Yan and Shen, Zhao and Qiao, Liang-Jing and Niu, Jing-Wei and Ling, Shao-Jun and Luo, Wen-Ji and Zhao, Wei and Liu, Jian-Feng and Kuang, Yuan-Wen and Ingvarsson, Pär K and Guo, Ya-Long and Wang, Baosheng},
	month = may,
	year = {2025},
	pages = {msaf088},
}

The genetic base of local adaptation has been extensively studied in natural populations. However, a comprehensive genome-wide perspective on the contribution of structural variants (SVs) and adaptive introgression to local adaptation remains limited. In this study, we performed de novo assembly and annotation of 22 representative accessions of Quercus variabilis, identifying a total of 543,372 SVs. These SVs play crucial roles in shaping genomic structure and influencing gene expression. By analyzing range-wide genomic data, we identified both SNPs and SVs associated with local adaptation in Q. variabilis and Quercus acutissima. Notably, SV-outliers exhibit selection signals that did not overlap with SNP-outliers, indicating that SNP-based analyses may not detect the same candidate genes associated with SV-outliers. Remarkably, 29%−37% of candidate SNPs were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF. This region contains 8 duplicated ethylene-responsive factor (ERF) genes, which may have contributed to local adaptation of Q. variabilis and Q. acutissima. We also found that a considerable number of candidate SNPs were shared between Q. variabilis and Q. acutissima in the Chr9-ERF region, suggesting a pattern of repeated selection. We further demonstrated that advantageous variants in this region were introgressed from western populations of Q. acutissima into Q. variabilis, providing compelling evidence that introgression facilitates local adaptation. This study offers a valuable genomic resource for future studies on oak species and highlights the importance of pan-genome analysis in understating mechanism driving adaptation and evolution.

@article{koehler_node_2025,
	title = {Node of origin matters: comparative analysis of soil water limitation effects on nodal root anatomy in maize ({Zea} mays {L}.)},
	issn = {0305-7364},
	shorttitle = {Node of origin matters},
	url = {https://doi.org/10.1093/aob/mcaf075},
	doi = {10.1093/aob/mcaf075},
	urldate = {2025-05-16},
	journal = {Annals of Botany},
	author = {Koehler, Tina and Kim, Yunhee and Tung, Shu-Yin and Heymans, Adrien and Tyborski, Nicolas and Steiner, Franziska and Wild, Andreas J and Pausch, Johanna and Ahmed, Mutez A and Schneider, Hannah M},
	month = may,
	year = {2025},
	pages = {mcaf075},
}

@article{biancucci_mutations_2025,
	title = {Mutations in {HEADING} {DATE} 1 affect transcription and cell wall composition in rice},
	volume = {197},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiaf120},
	doi = {10.1093/plphys/kiaf120},
	abstract = {Plants utilize environmental information to modify their developmental trajectories for optimal survival and reproduction. Over a century ago, day length (photoperiod) was identified as a major factor influencing developmental transitions, particularly the shift from vegetative to reproductive growth. In rice (Oryza sativa), exposure to day lengths shorter than a critical threshold accelerates flowering, while longer days inhibit this process. This response is mediated by HEADING DATE 1 (Hd1), a zinc finger transcription factor that is central in the photoperiodic flowering network. Hd1 acts as a repressor of flowering under long days but functions as a promoter of flowering under short days. However, how global transcription of genes downstream of Hd1 changes in response to the photoperiod is still not fully understood. Furthermore, it is unclear whether Hd1 target genes are solely involved in flowering time control or mediate additional functions. In this study, we utilized RNA-Seq to analyze the transcriptome of hd1 mutants under both long and short day conditions. We identified genes involved in the phenylpropanoid pathway that are deregulated under long days in the mutant. Quantitative profiling of cell wall components and abiotic stress assays suggested that Hd1 is involved in processes considered unrelated to flowering control. This indicates that day length perception and responses are intertwined with physiological processes beyond flowering.},
	number = {4},
	urldate = {2025-05-09},
	journal = {Plant Physiology},
	author = {Biancucci, Marco and Chirivì, Daniele and Baldini, Alessio and Badenhorst, Eugene and Dobetti, Fabio and Khahani, Bahman and Formentin, Elide and Eguen, Tenai and Turck, Franziska and Moore, John P and Tavakol, Elahe and Wenkel, Stephan and Lo Schiavo, Fiorella and Ezquer, Ignacio and Brambilla, Vittoria and Horner, David and Chiara, Matteo and Perrella, Giorgio and Betti, Camilla and Fornara, Fabio},
	month = apr,
	year = {2025},
	pages = {kiaf120},
}

Plants utilize environmental information to modify their developmental trajectories for optimal survival and reproduction. Over a century ago, day length (photoperiod) was identified as a major factor influencing developmental transitions, particularly the shift from vegetative to reproductive growth. In rice (Oryza sativa), exposure to day lengths shorter than a critical threshold accelerates flowering, while longer days inhibit this process. This response is mediated by HEADING DATE 1 (Hd1), a zinc finger transcription factor that is central in the photoperiodic flowering network. Hd1 acts as a repressor of flowering under long days but functions as a promoter of flowering under short days. However, how global transcription of genes downstream of Hd1 changes in response to the photoperiod is still not fully understood. Furthermore, it is unclear whether Hd1 target genes are solely involved in flowering time control or mediate additional functions. In this study, we utilized RNA-Seq to analyze the transcriptome of hd1 mutants under both long and short day conditions. We identified genes involved in the phenylpropanoid pathway that are deregulated under long days in the mutant. Quantitative profiling of cell wall components and abiotic stress assays suggested that Hd1 is involved in processes considered unrelated to flowering control. This indicates that day length perception and responses are intertwined with physiological processes beyond flowering.

@article{asao_leaf_2025,
	title = {Leaf nonstructural carbohydrate residence time, not concentration, correlates with leaf functional traits following the leaf economic spectrum in woody plants},
	volume = {246},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20315},
	doi = {10.1111/nph.20315},
	abstract = {Nonstructural carbohydrate (NSC) concentrations might reflect the strategies described in the leaf economic spectrum (LES) due to their dependence on photosynthesis and respiration. We examined if NSC concentrations correlate with leaf structure, chemistry, and physiology traits for 114 species from 19 sites and 5 biomes around the globe. Total leaf NSC concentrations varied greatly from 16 to 199 mg g−1 dry mass and were mostly independent of leaf gas exchange and the LES traits. By contrast, leaf NSC residence time was shorter in species with higher rates of photosynthesis, following the fast-slow strategies in the LES. An average leaf held an amount of NSCs that could sustain one night of leaf respiration and could be replenished in just a few hours of photosynthesis under saturating light, indicating that most daily carbon gain is exported. Our results suggest that NSC export is clearly linked to the economics of return on resource investment.},
	language = {en},
	number = {4},
	urldate = {2025-05-09},
	journal = {New Phytologist},
	author = {Asao, Shinichi and Way, Danielle A. and Turnbull, Matthew H. and Stitt, Mark and McDowell, Nate G. and Reich, Peter B. and Bloomfield, Keith J. and Zaragoza-Castells, Joana and Creek, Danielle and O'Sullivan, Odhran and Crous, Kristine Y. and Egerton, John J.G. and Mirotchnick, Nicholas and Weerasinghe, Lasantha K. and Griffin, Kevin L. and Hurry, Vaughan and Meir, Patrick and Sitch, Stephen and Atkin, Owen K.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20315},
	keywords = {export, leaf economic spectrum, leaf functional traits, nonstructural carbohydrate, residence time},
	pages = {1505--1519},
}

Nonstructural carbohydrate (NSC) concentrations might reflect the strategies described in the leaf economic spectrum (LES) due to their dependence on photosynthesis and respiration. We examined if NSC concentrations correlate with leaf structure, chemistry, and physiology traits for 114 species from 19 sites and 5 biomes around the globe. Total leaf NSC concentrations varied greatly from 16 to 199 mg g−1 dry mass and were mostly independent of leaf gas exchange and the LES traits. By contrast, leaf NSC residence time was shorter in species with higher rates of photosynthesis, following the fast-slow strategies in the LES. An average leaf held an amount of NSCs that could sustain one night of leaf respiration and could be replenished in just a few hours of photosynthesis under saturating light, indicating that most daily carbon gain is exported. Our results suggest that NSC export is clearly linked to the economics of return on resource investment.

@article{xiao_protein_2025,
	title = {The protein kinases {KIPK} and {KIPK}-{LIKE1} suppress overbending during negative hypocotyl gravitropic growth in {Arabidopsis}},
	volume = {37},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koaf056},
	doi = {10.1093/plcell/koaf056},
	abstract = {Plants use environmental cues to orient organ and plant growth, such as the direction of gravity or the direction, quantity, and quality of light. During the germination of Arabidopsis thaliana seeds in soil, negative gravitropism responses direct hypocotyl elongation such that the seedling can reach the light for photosynthesis and autotrophic growth. Similarly, hypocotyl elongation in the soil also requires mechanisms to efficiently grow around obstacles such as soil particles. Here, we identify KIPK (KINESIN-LIKE CALMODULIN-BINDING PROTEIN-INTERACTING PROTEIN KINASE) and the paralogous KIPKL1 (KIPK-LIKE1) as genetically redundant regulators of gravitropic hypocotyl bending. Moreover, we demonstrate that the homologous KIPKL2 (KIPK-LIKE2), which shows strong sequence similarity, must be functionally distinct. KIPK and KIPKL1 are polarly localized plasma membrane-associated proteins that can activate PIN-FORMED auxin transporters. KIPK and KIPKL1 are required to efficiently align hypocotyl growth with the gravity vector when seedling hypocotyls are grown on media plates or in soil, where contact with soil particles and obstacle avoidance impede direct negative gravitropic growth. Therefore, the polar KIPK and KIPKL1 kinases have different biological functions from the related AGC1 family kinases D6PK (D6 PROTEIN KINASE) or PAX (PROTEIN KINASE ASSOCIATED WITH BRX).},
	number = {4},
	urldate = {2025-04-25},
	journal = {The Plant Cell},
	author = {Xiao, Yao and Zourelidou, Melina and Bassukas, Alkistis E Lanassa and Weller, Benjamin and Janacek, Dorina P and Šimura, Jan and Ljung, Karin and Hammes, Ulrich Z and Li, Jia and Schwechheimer, Claus},
	month = apr,
	year = {2025},
	pages = {koaf056},
}

Plants use environmental cues to orient organ and plant growth, such as the direction of gravity or the direction, quantity, and quality of light. During the germination of Arabidopsis thaliana seeds in soil, negative gravitropism responses direct hypocotyl elongation such that the seedling can reach the light for photosynthesis and autotrophic growth. Similarly, hypocotyl elongation in the soil also requires mechanisms to efficiently grow around obstacles such as soil particles. Here, we identify KIPK (KINESIN-LIKE CALMODULIN-BINDING PROTEIN-INTERACTING PROTEIN KINASE) and the paralogous KIPKL1 (KIPK-LIKE1) as genetically redundant regulators of gravitropic hypocotyl bending. Moreover, we demonstrate that the homologous KIPKL2 (KIPK-LIKE2), which shows strong sequence similarity, must be functionally distinct. KIPK and KIPKL1 are polarly localized plasma membrane-associated proteins that can activate PIN-FORMED auxin transporters. KIPK and KIPKL1 are required to efficiently align hypocotyl growth with the gravity vector when seedling hypocotyls are grown on media plates or in soil, where contact with soil particles and obstacle avoidance impede direct negative gravitropic growth. Therefore, the polar KIPK and KIPKL1 kinases have different biological functions from the related AGC1 family kinases D6PK (D6 PROTEIN KINASE) or PAX (PROTEIN KINASE ASSOCIATED WITH BRX).

@article{aydin_probing_2025,
	title = {Probing substrate water access through the {O1} channel of {Photosystem} {II} by single site mutations and membrane inlet mass spectrometry},
	volume = {163},
	issn = {1573-5079},
	url = {https://doi.org/10.1007/s11120-025-01147-4},
	doi = {10.1007/s11120-025-01147-4},
	abstract = {Light-driven water oxidation by photosystem II sustains life on Earth by providing the electrons and protons for the reduction of CO2 to carbohydrates and the molecular oxygen we breathe. The inorganic core of the oxygen evolving complex is made of the earth-abundant elements manganese, calcium and oxygen (Mn4CaO5 cluster), and is situated in a binding pocket that is connected to the aqueous surrounding via water-filled channels that allow water intake and proton egress. Recent serial crystallography and infrared spectroscopy studies performed with PSII isolated from Thermosynechococcus vestitus (T. vestitus) support that one of these channels, the O1 channel, facilitates water access to the Mn4CaO5 cluster during its S2→S3 and S3→S4→S0 state transitions, while a subsequent CryoEM study concluded that this channel is blocked in the cyanobacterium Synechocystis sp. PCC 6803, questioning the role of the O1 channel in water delivery. Employing site-directed mutagenesis we modified the two O1 channel bottleneck residues D1-E329 and CP43-V410 (T. vestitus numbering) and probed water access and substrate exchange via time resolved membrane inlet mass spectrometry. Our data demonstrates that water reaches the Mn4CaO5 cluster via the O1 channel in both wildtype and mutant PSII. In addition, the detailed analysis provides functional insight into the intricate protein-water-cofactor network near the Mn4CaO5 cluster that includes the pentameric, near planar ‘water wheel’ of the O1 channel.},
	language = {en},
	number = {3},
	urldate = {2025-04-25},
	journal = {Photosynthesis Research},
	author = {Aydin, A. Orkun and de Lichtenberg, Casper and Liang, Feiyan and Forsman, Jack and Graça, André T. and Chernev, Petko and Zhu, Shaochun and Mateus, André and Magnuson, Ann and Cheah, Mun Hon and Schröder, Wolfgang P. and Ho, Felix and Lindblad, Peter and Debus, Richard J. and Mamedov, Fikret and Messinger, Johannes},
	month = apr,
	year = {2025},
	keywords = {CP43-V410, D1-E329, O1 channel, Oxygen evolving complex, Photosystem II, Substrate water exchange, Synechocystis sp. PCC 6803, Water delivery, Water oxidation, Water wheel},
	pages = {28},
}

Light-driven water oxidation by photosystem II sustains life on Earth by providing the electrons and protons for the reduction of CO2 to carbohydrates and the molecular oxygen we breathe. The inorganic core of the oxygen evolving complex is made of the earth-abundant elements manganese, calcium and oxygen (Mn4CaO5 cluster), and is situated in a binding pocket that is connected to the aqueous surrounding via water-filled channels that allow water intake and proton egress. Recent serial crystallography and infrared spectroscopy studies performed with PSII isolated from Thermosynechococcus vestitus (T. vestitus) support that one of these channels, the O1 channel, facilitates water access to the Mn4CaO5 cluster during its S2→S3 and S3→S4→S0 state transitions, while a subsequent CryoEM study concluded that this channel is blocked in the cyanobacterium Synechocystis sp. PCC 6803, questioning the role of the O1 channel in water delivery. Employing site-directed mutagenesis we modified the two O1 channel bottleneck residues D1-E329 and CP43-V410 (T. vestitus numbering) and probed water access and substrate exchange via time resolved membrane inlet mass spectrometry. Our data demonstrates that water reaches the Mn4CaO5 cluster via the O1 channel in both wildtype and mutant PSII. In addition, the detailed analysis provides functional insight into the intricate protein-water-cofactor network near the Mn4CaO5 cluster that includes the pentameric, near planar ‘water wheel’ of the O1 channel.

@article{mazumdar_damage_2025,
	title = {Damage activates \textit{{EXG1}} and \textit{{RLP44}} to suppress vascular differentiation during regeneration in \textit{{Arabidopsis}}},
	volume = {6},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S2590346225000185},
	doi = {10.1016/j.xplc.2025.101256},
	abstract = {Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients. To identify common factors that affect vascular formation upon stress, we searched for Arabidopsis thaliana genes differentially expressed upon Agrobacterium infection, nematode infection, and plant grafting. One such gene is cell wall-related and highly induced by all three stresses, which we named ENHANCED XYLEM AND GRAFTING1 (EXG1), since its mutations promote ectopic xylem formation in a vascular cell induction system and enhance graft formation. Further observations revealed that exg1 mutants show inhibited cambium development and callus formation but enhanced tissue attachment, syncytium size, phloem reconnection, and xylem formation. Given that brassinosteroids also promote xylem differentiation, we analyzed brassinosteroid-related genes and found that mutations in RLP44 encoding a receptor-like protein cause similar regeneration-related phenotypes as mutations in EXG1. Like EXG1, RLP44 expression is also induced by grafting and wounding. Mutations in EXG1 and RLP44 affect the expression of many genes in common, including those related to cell walls and genes important for vascular regeneration. Our results suggest that EXG1 integrates information from wounding or pathogen stress and functions with RLP44 to suppress vascular differentiation during regeneration and healing.},
	number = {4},
	urldate = {2025-04-22},
	journal = {Plant Communications},
	author = {Mazumdar, Shamik and Augstein, Frauke and Zhang, Ai and Musseau, Constance and Anjam, Muhammad Shahzad and Marhavy, Peter and Melnyk, Charles W.},
	month = apr,
	year = {2025},
	keywords = {Cell wall, Grafting, Regeneration, Stress, Wounding, Xylem, cell wall, grafting, regeneration, stress, wounding, xylem},
	pages = {101256},
}

Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients. To identify common factors that affect vascular formation upon stress, we searched for Arabidopsis thaliana genes differentially expressed upon Agrobacterium infection, nematode infection, and plant grafting. One such gene is cell wall-related and highly induced by all three stresses, which we named ENHANCED XYLEM AND GRAFTING1 (EXG1), since its mutations promote ectopic xylem formation in a vascular cell induction system and enhance graft formation. Further observations revealed that exg1 mutants show inhibited cambium development and callus formation but enhanced tissue attachment, syncytium size, phloem reconnection, and xylem formation. Given that brassinosteroids also promote xylem differentiation, we analyzed brassinosteroid-related genes and found that mutations in RLP44 encoding a receptor-like protein cause similar regeneration-related phenotypes as mutations in EXG1. Like EXG1, RLP44 expression is also induced by grafting and wounding. Mutations in EXG1 and RLP44 affect the expression of many genes in common, including those related to cell walls and genes important for vascular regeneration. Our results suggest that EXG1 integrates information from wounding or pathogen stress and functions with RLP44 to suppress vascular differentiation during regeneration and healing.

@article{bogacz_x-ray_2025,
	title = {X-ray {Absorption} {Spectroscopy} of {Dilute} {Metalloenzymes} at {X}-ray {Free}-{Electron} {Lasers} in a {Shot}-by-{Shot} {Mode}},
	volume = {16},
	url = {https://doi.org/10.1021/acs.jpclett.5c00399},
	doi = {10.1021/acs.jpclett.5c00399},
	abstract = {X-ray absorption spectroscopy (XAS) of 3d transition metals provides important electronic structure information for many fields. However, X-ray-induced radiation damage under physiological temperature has prevented using this method to study dilute aqueous systems, such as metalloenzymes, as the catalytic reaction proceeds. Here we present a new approach to enable operando XAS of dilute biological samples and demonstrate its feasibility with K-edge XAS spectra from the Mn cluster in photosystem II and the Fe–S centers in photosystem I. This approach combines highly efficient sample delivery strategies and a robust signal normalization method with high-transmission Bragg diffraction-based spectrometers at X-ray free-electron lasers (XFELs) in a damage-free, shot-by-shot mode. These photon-out spectrometers have been optimized for discriminating the metal Mn/Fe Kα fluorescence signals from the overwhelming scattering background present on currently available detectors for XFELs that lack suitable energy discrimination. We quantify the enhanced performance metrics of the spectrometer and discuss its potential applications for acquiring time-resolved XAS spectra of biological samples during their reactions at XFELs.},
	number = {15},
	urldate = {2025-04-22},
	journal = {The Journal of Physical Chemistry Letters},
	publisher = {American Chemical Society},
	author = {Bogacz, Isabel and Szilagyi, Erzsi and Makita, Hiroki and Simon, Philipp S. and Zhang, Miao and Doyle, Margaret D. and Chatterjee, Kuntal and Kretzschmar, Moritz and Chernev, Petko and Croy, Nicholas and Cheah, Mun-Hon and Dasgupta, Medhanjali and Nangca, Isabela and Fransson, Thomas and Bhowmick, Asmit and Brewster, Aaron S. and Sauter, Nicholas K. and Owada, Shigeki and Tono, Kensuke and Zerdane, Serhane and Oggenfuss, Alexander and Babich, Danylo and Sander, Mathias and Mankowsky, Roman and Lemke, Henrik T. and Gee, Leland B. and Sato, Takahiro and Kroll, Thomas and Messinger, Johannes and Alonso-Mori, Roberto and Bergmann, Uwe and Sokaras, Dimosthenis and Yachandra, Vittal K. and Kern, Jan and Yano, Junko},
	month = apr,
	year = {2025},
	pages = {3778--3787},
}

X-ray absorption spectroscopy (XAS) of 3d transition metals provides important electronic structure information for many fields. However, X-ray-induced radiation damage under physiological temperature has prevented using this method to study dilute aqueous systems, such as metalloenzymes, as the catalytic reaction proceeds. Here we present a new approach to enable operando XAS of dilute biological samples and demonstrate its feasibility with K-edge XAS spectra from the Mn cluster in photosystem II and the Fe–S centers in photosystem I. This approach combines highly efficient sample delivery strategies and a robust signal normalization method with high-transmission Bragg diffraction-based spectrometers at X-ray free-electron lasers (XFELs) in a damage-free, shot-by-shot mode. These photon-out spectrometers have been optimized for discriminating the metal Mn/Fe Kα fluorescence signals from the overwhelming scattering background present on currently available detectors for XFELs that lack suitable energy discrimination. We quantify the enhanced performance metrics of the spectrometer and discuss its potential applications for acquiring time-resolved XAS spectra of biological samples during their reactions at XFELs.

@article{nair_elf3_2025,
	title = {{ELF3} coordinates temperature and photoperiodic control of seasonal growth in hybrid aspen},
	volume = {35},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982225001903},
	doi = {10.1016/j.cub.2025.02.027},
	abstract = {Timely growth cessation before winter is crucial for the survival of perennial plants in temperate and boreal regions. Short photoperiod (SP) and low temperature (LT) are major seasonal cues regulating growth cessation. SP, sensed in the leaves, initiates growth cessation by downregulating FLOWERING LOCUS T 2 (FT2) expression, but how LT regulates seasonal growth is unclear. Genetic and cell biological approaches identified a hybrid aspen EARLY FLOWERING 3(ELF3) ortholog with a prion-like domain (PrLD) that undergoes LT-responsive phase separation as a key mediator of LT-induced growth cessation. In contrast with SP, LT acts independently of FT2 downregulation and targets the AIL1-BRC1 transcription factor network and hormonal pathways via ELF3 to induce growth cessation. Intriguingly, ELF3 also functions in SP-mediated growth cessation by downregulating FT2 in leaves. Our work thus reveals a previously unrecognized role of ELF3 in growth cessation and in coordinating temperature and photoperiodic pathways to enable robust adaptation to seasonal change.},
	number = {7},
	urldate = {2025-04-11},
	journal = {Current Biology},
	author = {Nair, Aswin and Maurya, Jay P. and Pandey, Shashank K. and Singh, Rajesh Kumar and Miskolczi, Pal C. and Aryal, Bibek and Bhalerao, Rishikesh P.},
	month = apr,
	year = {2025},
	keywords = {EARLY FLOWERING 3(ELF3), FLOWERING LOCUS T (FT), growth cessation, hybrid aspen, perennial trees, seasonal growth},
	pages = {1484--1494.e2},
}

Timely growth cessation before winter is crucial for the survival of perennial plants in temperate and boreal regions. Short photoperiod (SP) and low temperature (LT) are major seasonal cues regulating growth cessation. SP, sensed in the leaves, initiates growth cessation by downregulating FLOWERING LOCUS T 2 (FT2) expression, but how LT regulates seasonal growth is unclear. Genetic and cell biological approaches identified a hybrid aspen EARLY FLOWERING 3(ELF3) ortholog with a prion-like domain (PrLD) that undergoes LT-responsive phase separation as a key mediator of LT-induced growth cessation. In contrast with SP, LT acts independently of FT2 downregulation and targets the AIL1-BRC1 transcription factor network and hormonal pathways via ELF3 to induce growth cessation. Intriguingly, ELF3 also functions in SP-mediated growth cessation by downregulating FT2 in leaves. Our work thus reveals a previously unrecognized role of ELF3 in growth cessation and in coordinating temperature and photoperiodic pathways to enable robust adaptation to seasonal change.

@article{bag_photosynthetic_2025,
	title = {Photosynthetic advantages of conifers in the boreal forest},
	volume = {30},
	issn = {1360-1385},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138524003005},
	doi = {10.1016/j.tplants.2024.10.018},
	abstract = {Boreal conifers – the ‘Christmas trees’ – maintain their green needles over the winter by retaining their chlorophyll. These conifers face the toughest challenge in February and March, when subzero temperatures coincide with high solar radiation. To balance the light energy they harvest with the light energy they utilise, conifers deploy various mechanisms in parallel. These include, thylakoid destacking, which facilitates direct energy transfer from Photosystem II (PSII) to Photosystem I (PSI), and excess energy dissipation through sustained nonphotochemical quenching (NPQ). Additionally, they upregulate alternative electron transport pathways to safely reroute excess electrons while maintaining ATP production. From an evolutionary and ecological perspective, we consider these mechanisms as part of a comprehensive photosynthetic alteration, which enhances our understanding of winter acclimation in conifers and their dominance in the boreal forests.},
	number = {4},
	urldate = {2025-04-11},
	journal = {Trends in Plant Science},
	author = {Bag, Pushan and Ivanov, Alexander G. and Huner, Norman P. and Jansson, Stefan},
	month = apr,
	year = {2025},
	keywords = {alternative electron transport, conifers, direct energy transfer, flavodiiron proteins, nonphotochemical quenching (NPQ), photosystems},
	pages = {409--423},
}

Boreal conifers – the ‘Christmas trees’ – maintain their green needles over the winter by retaining their chlorophyll. These conifers face the toughest challenge in February and March, when subzero temperatures coincide with high solar radiation. To balance the light energy they harvest with the light energy they utilise, conifers deploy various mechanisms in parallel. These include, thylakoid destacking, which facilitates direct energy transfer from Photosystem II (PSII) to Photosystem I (PSI), and excess energy dissipation through sustained nonphotochemical quenching (NPQ). Additionally, they upregulate alternative electron transport pathways to safely reroute excess electrons while maintaining ATP production. From an evolutionary and ecological perspective, we consider these mechanisms as part of a comprehensive photosynthetic alteration, which enhances our understanding of winter acclimation in conifers and their dominance in the boreal forests.

@article{marien_natures_2025,
	title = {Nature’s {Master} of {Ceremony}: {The} {Populus} {Circadian} {Clock} as {Orchestrator} of {Tree} {Growth} and {Phenology}},
	volume = {2},
	copyright = {2025 The Author(s)},
	issn = {2948-281X},
	shorttitle = {Nature’s {Master} of {Ceremony}},
	url = {https://www.nature.com/articles/s44323-025-00034-4},
	doi = {10.1038/s44323-025-00034-4},
	abstract = {Understanding the timely regulation of plant growth and phenology is crucial for assessing a terrestrial ecosystem’s productivity and carbon budget. The circadian clock, a system of genetic oscillators, acts as ‘Master of Ceremony’ during plant physiological processes. The mechanism is particularly elusive in trees despite its relevance. The primary and secondary tree growth, leaf senescence, bud set, and bud burst timing were investigated in 68 constructs transformed into Populus hybrids and compared with untransformed or transformed controls grown in natural or controlled conditions. The results were analyzed using generalized additive models with ordered-factor-smooth interaction smoothers. This meta-analysis shows that several genetic components are associated with the clock. Especially core clock-regulated genes affected tree growth and phenology in both controlled and field conditions. Our results highlight the importance of field trials and the potential of using the clock to generate trees with improved characteristics for sustainable silviculture (e.g., reprogrammed to new photoperiodic regimes and increased growth).},
	language = {en},
	number = {1},
	urldate = {2025-04-11},
	journal = {npj Biological Timing and Sleep},
	publisher = {Nature Publishing Group},
	author = {Mariën, Bertold and Robinson, Kathryn M. and Jurca, Manuela and Michelson, Ingrid H. and Takata, Naoki and Kozarewa, Iwanka and Pin, Pierre A. and Ingvarsson, Pär K. and Moritz, Thomas and Ibáñez, Cristian and Nilsson, Ove and Jansson, Stefan and Penfield, Steve and Yu, Jun and Eriksson, Maria E.},
	month = apr,
	year = {2025},
	keywords = {Biological techniques, Plant sciences},
	pages = {1--19},
}

Understanding the timely regulation of plant growth and phenology is crucial for assessing a terrestrial ecosystem’s productivity and carbon budget. The circadian clock, a system of genetic oscillators, acts as ‘Master of Ceremony’ during plant physiological processes. The mechanism is particularly elusive in trees despite its relevance. The primary and secondary tree growth, leaf senescence, bud set, and bud burst timing were investigated in 68 constructs transformed into Populus hybrids and compared with untransformed or transformed controls grown in natural or controlled conditions. The results were analyzed using generalized additive models with ordered-factor-smooth interaction smoothers. This meta-analysis shows that several genetic components are associated with the clock. Especially core clock-regulated genes affected tree growth and phenology in both controlled and field conditions. Our results highlight the importance of field trials and the potential of using the clock to generate trees with improved characteristics for sustainable silviculture (e.g., reprogrammed to new photoperiodic regimes and increased growth).

@article{dikaya_arabidopsis_2025,
	title = {The {Arabidopsis} thaliana core splicing factor {PORCUPINE}/{SmE1} requires intron-mediated expression},
	volume = {20},
	doi = {10.1371/journal.pone.0318163},
	abstract = {Plants are prone to genome duplications and tend to preserve multiple gene copies. This is also the case for the genes encoding the Sm proteins of Arabidopsis thaliana (L). The Sm proteins are best known for their roles in RNA processing such as pre-mRNA splicing and nonsense-mediated mRNA decay. In this study, we have taken a closer look at the phylogeny and differential regulation of the SmE-coding genes found in A. thaliana, PCP/SmE1, best known for its cold-sensitive phenotype, and its paralog, PCPL/SmE2. The phylogeny of the PCP homologs in the green lineage shows that SmE duplications happened multiple times independently in different plant clades and that the duplication that gave rise to PCP and PCPL occurred only in the Brassicaceae family. Our analysis revealed that A. thaliana PCP and PCPL proteins, which only differ in two amino acids, exhibit a very high level of functional conservation and can perform the same function in the cell. However, our results indicate that PCP is the prevailing copy of the two SmE genes in A. thaliana as it is more highly expressed and that the main difference between PCP and PCPL resides in their transcriptional regulation, which is strongly linked to intronic sequences. Our results provide insight into the complex mechanisms that underlie the differentiation of the paralogous gene expression as an adaptation to stress. © 2025 Dikaya et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},
	number = {3 March},
	journal = {PLoS ONE},
	author = {Dikaya, V. and Rojas-Murcia, N. and Benstein, R.M. and Eiserhardt, W.L. and Schmid, M.},
	year = {2025},
	keywords = {Arabidopsis thaliana, Gene expression, Genomics, Introns, Phenotypes, Phylogenetic analysis, Seedlings, Sequence alignment},
}

Plants are prone to genome duplications and tend to preserve multiple gene copies. This is also the case for the genes encoding the Sm proteins of Arabidopsis thaliana (L). The Sm proteins are best known for their roles in RNA processing such as pre-mRNA splicing and nonsense-mediated mRNA decay. In this study, we have taken a closer look at the phylogeny and differential regulation of the SmE-coding genes found in A. thaliana, PCP/SmE1, best known for its cold-sensitive phenotype, and its paralog, PCPL/SmE2. The phylogeny of the PCP homologs in the green lineage shows that SmE duplications happened multiple times independently in different plant clades and that the duplication that gave rise to PCP and PCPL occurred only in the Brassicaceae family. Our analysis revealed that A. thaliana PCP and PCPL proteins, which only differ in two amino acids, exhibit a very high level of functional conservation and can perform the same function in the cell. However, our results indicate that PCP is the prevailing copy of the two SmE genes in A. thaliana as it is more highly expressed and that the main difference between PCP and PCPL resides in their transcriptional regulation, which is strongly linked to intronic sequences. Our results provide insight into the complex mechanisms that underlie the differentiation of the paralogous gene expression as an adaptation to stress. © 2025 Dikaya et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

@article{jiang_incorporating_2025,
	title = {Incorporating genetic load contributes to predicting {Arabidopsis} thaliana’s response to climate change},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-58021-z},
	doi = {10.1038/s41467-025-58021-z},
	abstract = {Understanding how species respond to climate change can facilitate species conservation and crop breeding. Current prediction frameworks about population vulnerability focused on predicting range shifts or local adaptation but ignored genetic load, which is also crucial for adaptation. By analyzing 1115 globally distributed Arabidopsis thaliana natural accessions, we find that effective population size (Ne) is the major contributor of genetic load variation, both along genome and among populations, and can explain 74-94\% genetic load variation in natural populations. Intriguingly, Ne affects genetic load by changing both effectiveness of purifying selection and GC biased gene conversion strength. In particular, by incorporating genetic load, genetic offset and species distribution models (SDM), we predict that, the populations at species’ range edge are generally at higher risk. The populations at the eastern range perform poorer in all aspects, southern range have higher genetic offset and lower SDM suitability, while northern range have higher genetic load. Among the diverse natural populations, the Yangtze River basin population is the most vulnerable population under future climate change. Overall, here we deciphered the driving forces of genetic load in A. thaliana, and incorporated SDM, local adaptation and genetic load to predict the fate of populations under future climate change.},
	language = {en},
	number = {1},
	urldate = {2025-04-04},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Jiang, Juan and Chen, Jia-Fu and Li, Xin-Tong and Wang, Li and Mao, Jian-Feng and Wang, Bao-Sheng and Guo, Ya-Long},
	month = mar,
	year = {2025},
	keywords = {Conservation biology, Evolutionary genetics, Molecular evolution, Population genetics},
	pages = {2752},
}

Understanding how species respond to climate change can facilitate species conservation and crop breeding. Current prediction frameworks about population vulnerability focused on predicting range shifts or local adaptation but ignored genetic load, which is also crucial for adaptation. By analyzing 1115 globally distributed Arabidopsis thaliana natural accessions, we find that effective population size (Ne) is the major contributor of genetic load variation, both along genome and among populations, and can explain 74-94% genetic load variation in natural populations. Intriguingly, Ne affects genetic load by changing both effectiveness of purifying selection and GC biased gene conversion strength. In particular, by incorporating genetic load, genetic offset and species distribution models (SDM), we predict that, the populations at species’ range edge are generally at higher risk. The populations at the eastern range perform poorer in all aspects, southern range have higher genetic offset and lower SDM suitability, while northern range have higher genetic load. Among the diverse natural populations, the Yangtze River basin population is the most vulnerable population under future climate change. Overall, here we deciphered the driving forces of genetic load in A. thaliana, and incorporated SDM, local adaptation and genetic load to predict the fate of populations under future climate change.

@article{casanova-saez_suitable_2025,
	title = {A suitable strategy to find {IAA} metabolism mutants},
	volume = {177},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70166},
	doi = {10.1111/ppl.70166},
	abstract = {Indole-3-acetic acid (IAA), the most common form of auxin, is involved in a great range of plant physiological processes. IAA is synthesized from the amino acid tryptophan and can be transported and inactivated in a myriad of ways. Despite intense research efforts, there are still dark corners in our comprehension of IAA metabolism and its interplays with other pathways. Genetic screens are a powerful tool for unbiasedly looking for new players in a given biological process. However, pleiotropism of auxin-related phenotypes and indirect effects make it necessary to incorporate additional screening steps to specifically find mutants affected in IAA homeostasis. We previously developed and validated a high-throughput methodology to simultaneously quantify IAA, key precursors, and inactive forms from as little as 10 mg of fresh tissue. We have carried out a genetic screening to identify mutants involved in IAA metabolism. Auxin reporters DR5pro:VENUS and 35Spro:DII-VENUS were EMS-mutagenized and subjected to a parallel morphological and reporter-signal pre-screen. We then obtained the auxin metabolite profile of 325 M3 selected lines and used multivariate data analysis to identify potential IAA-metabolism mutants. To test the screening design, we identified the causal mutations in three of the candidate lines by mapping-by-sequencing: dii365.3, dii571.1 and dr693. These carry new alleles of CYP83A1, MIAO, and SUPERROOT2, respectively, all of which have been previously involved in auxin homeostasis. Our results support the suitability of this approach to find new genes involved in IAA metabolism.},
	language = {en},
	number = {2},
	urldate = {2025-04-04},
	journal = {Physiologia Plantarum},
	author = {Casanova-Sáez, Rubén and Pěnčík, Aleš and Muñoz-Viana, Rafael and Brunoni, Federica and Pinto, Rui and Novák, Ondřej and Ljung, Karin and Mateo-Bonmatí, Eduardo},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70166},
	pages = {e70166},
}

Indole-3-acetic acid (IAA), the most common form of auxin, is involved in a great range of plant physiological processes. IAA is synthesized from the amino acid tryptophan and can be transported and inactivated in a myriad of ways. Despite intense research efforts, there are still dark corners in our comprehension of IAA metabolism and its interplays with other pathways. Genetic screens are a powerful tool for unbiasedly looking for new players in a given biological process. However, pleiotropism of auxin-related phenotypes and indirect effects make it necessary to incorporate additional screening steps to specifically find mutants affected in IAA homeostasis. We previously developed and validated a high-throughput methodology to simultaneously quantify IAA, key precursors, and inactive forms from as little as 10 mg of fresh tissue. We have carried out a genetic screening to identify mutants involved in IAA metabolism. Auxin reporters DR5pro:VENUS and 35Spro:DII-VENUS were EMS-mutagenized and subjected to a parallel morphological and reporter-signal pre-screen. We then obtained the auxin metabolite profile of 325 M3 selected lines and used multivariate data analysis to identify potential IAA-metabolism mutants. To test the screening design, we identified the causal mutations in three of the candidate lines by mapping-by-sequencing: dii365.3, dii571.1 and dr693. These carry new alleles of CYP83A1, MIAO, and SUPERROOT2, respectively, all of which have been previously involved in auxin homeostasis. Our results support the suitability of this approach to find new genes involved in IAA metabolism.

@article{wu_population_2025,
	title = {Population genomics of \textit{{Marchantia} polymorpha} subsp. \textit{ruderalis} reveals evidence of climate adaptation},
	volume = {35},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982225000089},
	doi = {10.1016/j.cub.2025.01.008},
	abstract = {Sexual reproduction results in the development of haploid and diploid cell states during the life cycle. In bryophytes, the dominant multicellular haploid phase produces motile sperm that swim through water to the egg to effect fertilization from which a relatively small diploid phase develops. In angiosperms, the reduced multicellular haploid phase produces non-motile sperm that is delivered to the egg through a pollen tube to effect fertilization from which the dominant diploid phase develops. These different life cycle characteristics are likely to impact the distribution of genetic variation among populations. However, little is known about the distribution of genetic variation among wild populations of bryophytes. To investigate how genetic variation is distributed among populations of a bryophyte and to establish the foundation for population genetics research in bryophytes, we described the genetic diversity of collections of Marchantia polymorpha subsp. ruderalis, a cosmopolitan ruderal liverwort. We identified 78 genetically unique (non-clonal) from a total of 209 sequenced accessions collected from 37 sites in Europe and Japan. There was no detectable population structure among European populations but significant genetic differentiation between Japanese and European populations. By associating genetic variation across the genome with global climate data, we showed that temperature and precipitation influence the frequency of potentially adaptive alleles. This collection establishes the core of an experimental platform that exploits natural genetic variation to answer diverse questions in biology.},
	number = {5},
	urldate = {2025-03-28},
	journal = {Current Biology},
	author = {Wu, Shuangyang and Jandrasits, Katharina and Swarts, Kelly and Roetzer, Johannes and Akimcheva, Svetlana and Shimamura, Masaki and Hisanaga, Tetsuya and Berger, Frédéric and Dolan, Liam},
	month = mar,
	year = {2025},
	pages = {970--980.e3},
}

Sexual reproduction results in the development of haploid and diploid cell states during the life cycle. In bryophytes, the dominant multicellular haploid phase produces motile sperm that swim through water to the egg to effect fertilization from which a relatively small diploid phase develops. In angiosperms, the reduced multicellular haploid phase produces non-motile sperm that is delivered to the egg through a pollen tube to effect fertilization from which the dominant diploid phase develops. These different life cycle characteristics are likely to impact the distribution of genetic variation among populations. However, little is known about the distribution of genetic variation among wild populations of bryophytes. To investigate how genetic variation is distributed among populations of a bryophyte and to establish the foundation for population genetics research in bryophytes, we described the genetic diversity of collections of Marchantia polymorpha subsp. ruderalis, a cosmopolitan ruderal liverwort. We identified 78 genetically unique (non-clonal) from a total of 209 sequenced accessions collected from 37 sites in Europe and Japan. There was no detectable population structure among European populations but significant genetic differentiation between Japanese and European populations. By associating genetic variation across the genome with global climate data, we showed that temperature and precipitation influence the frequency of potentially adaptive alleles. This collection establishes the core of an experimental platform that exploits natural genetic variation to answer diverse questions in biology.

@article{ranade_metabolomic_2025,
	title = {Metabolomic profiling of shade response and in silico analysis of {PAL} homologs imply the potential presence of bifunctional ammonia lyases in conifers},
	volume = {177},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70175},
	doi = {10.1111/ppl.70175},
	abstract = {Norway spruce and Scots pine show enhanced lignin synthesis under shade, along with differential expression of defense-related genes that render disease resilience. In general, phenylalanine (Phe) is the precursor for lignin synthesis in plants, and tyrosine (Tyr) forms an additional lignin precursor specifically in grasses. Phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) from the lignin biosynthesis pathway use either Phe or Tyr as precursors for lignin production, respectively. Grasses possess a bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) that potentially can use both Phe and Tyr for lignin biosynthesis. Metabolomic profiles of seedlings revealed higher levels of Phe and Tyr under shade in Scots pine, while Norway spruce showed differential regulation of only Tyr under shade. Sequence analysis and phylogeny of PAL homologs in the two conifers, coupled with correlation of up-regulation of precursors for lignin synthesis (Phe/Tyr) and enhanced lignin synthesis along with differential expression of PAL homologs under shade, suggest the potential presence of a bifunctional ammonia-lyases (BAL) in conifers. This finding is novel and comparable to PTALs in grasses. Exome sequence analysis revealed a latitudinal variation in allele frequencies of SNPs from coding regions of putative PAL and BAL in Norway spruce, which may impact enzyme activity affecting lignin synthesis. Metabolomic analysis additionally identified metabolites involved in plant immunity, defense and stress response.},
	language = {en},
	number = {2},
	urldate = {2025-03-28},
	journal = {Physiologia Plantarum},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70175},
	pages = {e70175},
}

Norway spruce and Scots pine show enhanced lignin synthesis under shade, along with differential expression of defense-related genes that render disease resilience. In general, phenylalanine (Phe) is the precursor for lignin synthesis in plants, and tyrosine (Tyr) forms an additional lignin precursor specifically in grasses. Phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) from the lignin biosynthesis pathway use either Phe or Tyr as precursors for lignin production, respectively. Grasses possess a bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) that potentially can use both Phe and Tyr for lignin biosynthesis. Metabolomic profiles of seedlings revealed higher levels of Phe and Tyr under shade in Scots pine, while Norway spruce showed differential regulation of only Tyr under shade. Sequence analysis and phylogeny of PAL homologs in the two conifers, coupled with correlation of up-regulation of precursors for lignin synthesis (Phe/Tyr) and enhanced lignin synthesis along with differential expression of PAL homologs under shade, suggest the potential presence of a bifunctional ammonia-lyases (BAL) in conifers. This finding is novel and comparable to PTALs in grasses. Exome sequence analysis revealed a latitudinal variation in allele frequencies of SNPs from coding regions of putative PAL and BAL in Norway spruce, which may impact enzyme activity affecting lignin synthesis. Metabolomic analysis additionally identified metabolites involved in plant immunity, defense and stress response.

@article{jonsson_asymmetry_2025,
	title = {The asymmetry engine: how plants harness asymmetries to shape their bodies},
	volume = {245},
	copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.},
	issn = {1469-8137},
	shorttitle = {The asymmetry engine},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20413},
	doi = {10.1111/nph.20413},
	abstract = {Plant development depends on growth asymmetry to establish body plans and adapt to environmental stimuli. We explore how plants initiate, propagate, and regulate organ-wide growth asymmetries. External cues, such as light and gravity, and internal signals, including stochastic cellular growth variability, drive these asymmetries. The plant hormone auxin orchestrates growth asymmetry through its distribution and transport. Mechanochemical feedback loops, exemplified by apical hook formation, further amplify growth asymmetries, illustrating the dynamic interplay between biochemical signals and physical forces. Growth asymmetry itself can serve as a continuous cue, influencing subsequent growth decisions. By examining specific cellular programs and their responses to asymmetric cues, we propose that the decision to either amplify or dampen these asymmetries is key to shaping plant organs.},
	language = {en},
	number = {6},
	urldate = {2025-01-31},
	journal = {New Phytologist},
	author = {Jonsson, Kristoffer and Routier-Kierzkowska, Anne-Lise and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20413},
	keywords = {auxin, cell wall, development, feedback mechanisms, growth coordination, mechanics, morphogenesis, tropism},
	pages = {2422--2427},
}

Plant development depends on growth asymmetry to establish body plans and adapt to environmental stimuli. We explore how plants initiate, propagate, and regulate organ-wide growth asymmetries. External cues, such as light and gravity, and internal signals, including stochastic cellular growth variability, drive these asymmetries. The plant hormone auxin orchestrates growth asymmetry through its distribution and transport. Mechanochemical feedback loops, exemplified by apical hook formation, further amplify growth asymmetries, illustrating the dynamic interplay between biochemical signals and physical forces. Growth asymmetry itself can serve as a continuous cue, influencing subsequent growth decisions. By examining specific cellular programs and their responses to asymmetric cues, we propose that the decision to either amplify or dampen these asymmetries is key to shaping plant organs.

@article{bhalerao_intercellular_2025,
	title = {Intercellular communication: {Regulation} of plasmodesmata},
	volume = {35},
	issn = {0960-9822},
	shorttitle = {Intercellular communication},
	url = {https://www.cell.com/current-biology/abstract/S0960-9822(24)01642-7},
	doi = {10.1016/j.cub.2024.12.002},
	language = {English},
	number = {4},
	urldate = {2025-02-28},
	journal = {Current Biology},
	publisher = {Elsevier},
	author = {Bhalerao, Rishikesh P.},
	month = feb,
	year = {2025},
	pages = {R143--R145},
}

@article{boussardon_atypical_2025,
	title = {The atypical proteome of mitochondria from mature pollen grains},
	volume = {35},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982224017056},
	doi = {10.1016/j.cub.2024.12.037},
	abstract = {To propagate their genetic material, flowering plants rely on the production of large amounts of pollen grains that are capable of germinating on a compatible stigma. Pollen germination and pollen tube growth are thought to be extremely energy-demanding processes. This raises the question of whether mitochondria from pollen grains are specifically tuned to support this developmental process. To address this question, we isolated mitochondria from both mature pollen and floral buds using the isolation of mitochondria tagged in specific cell-type (IMTACT) strategy and examined their respective proteomes. Strikingly, mitochondria from mature pollen grains have lost many proteins required for genome maintenance, gene expression, and translation. Conversely, a significant accumulation of proteins associated with the tricarboxylic acid (TCA) cycle, the electron transport chain (ETC), and Ca2+ homeostasis was observed. This supports the current model in which pollen requires large quantities of ATP for tube growth but also identifies an unexpected depletion of the gene expression machinery, aligned with the fact that the mitochondrial genome is actively degraded during pollen maturation. Altogether, our results uncover that mitochondria from mature pollen grains are strategically prepared for action by increasing their respiratory capacity and dismantling their gene expression machinery, which raises new questions about the assembly of respiratory complexes in pollen mitochondria, as they rely on the integration of proteins coded by the nuclear and mitochondrial genomes. In addition, the approach described here opens a new range of possibilities for studying mitochondria during pollen development and in pollen-specific mitochondrial events.},
	number = {4},
	urldate = {2025-02-28},
	journal = {Current Biology},
	author = {Boussardon, Clément and Simon, Matthieu and Carrie, Chris and Fuszard, Matthew and Meyer, Etienne H. and Budar, Françoise and Keech, Olivier},
	month = feb,
	year = {2025},
	pages = {776--787.e5},
}

To propagate their genetic material, flowering plants rely on the production of large amounts of pollen grains that are capable of germinating on a compatible stigma. Pollen germination and pollen tube growth are thought to be extremely energy-demanding processes. This raises the question of whether mitochondria from pollen grains are specifically tuned to support this developmental process. To address this question, we isolated mitochondria from both mature pollen and floral buds using the isolation of mitochondria tagged in specific cell-type (IMTACT) strategy and examined their respective proteomes. Strikingly, mitochondria from mature pollen grains have lost many proteins required for genome maintenance, gene expression, and translation. Conversely, a significant accumulation of proteins associated with the tricarboxylic acid (TCA) cycle, the electron transport chain (ETC), and Ca2+ homeostasis was observed. This supports the current model in which pollen requires large quantities of ATP for tube growth but also identifies an unexpected depletion of the gene expression machinery, aligned with the fact that the mitochondrial genome is actively degraded during pollen maturation. Altogether, our results uncover that mitochondria from mature pollen grains are strategically prepared for action by increasing their respiratory capacity and dismantling their gene expression machinery, which raises new questions about the assembly of respiratory complexes in pollen mitochondria, as they rely on the integration of proteins coded by the nuclear and mitochondrial genomes. In addition, the approach described here opens a new range of possibilities for studying mitochondria during pollen development and in pollen-specific mitochondrial events.

@article{petri_exploring_2025,
	series = {Special issue: {Microproteins}},
	title = {Exploring the world of small proteins in plant biology and bioengineering},
	volume = {41},
	issn = {0168-9525},
	url = {https://www.sciencedirect.com/science/article/pii/S0168952524002129},
	doi = {10.1016/j.tig.2024.09.004},
	abstract = {Small proteins are ubiquitous in all kingdoms of life. MicroProteins, initially characterized as small proteins with protein interaction domains that enable them to interact with larger multidomain proteins, frequently modulate the function of these proteins. The study of these small proteins has contributed to a greater comprehension of protein regulation. In addition to sequence homology, sequence-divergent small proteins have the potential to function as microProtein mimics, binding to structurally related proteins. Moreover, a multitude of other small proteins encoded by short open reading frames (sORFs) and peptides, derived from diverse sources such as long noncoding RNAs (lncRNAs) and miRNAs, contribute to a variety of biological processes. The potential of small proteins is evident, offering promising avenues for bioengineering that could revolutionize crop performance and reduce reliance on agrochemicals in future agriculture.},
	number = {2},
	urldate = {2025-02-28},
	journal = {Trends in Genetics},
	author = {Petri, Louise and Van Humbeeck, Anne and Niu, Huanying and Ter Waarbeek, Casper and Edwards, Ashleigh and Chiurazzi, Maurizio Junior and Vittozzi, Ylenia and Wenkel, Stephan},
	month = feb,
	year = {2025},
	keywords = {lncRNA, microProteins, sORFs, transcription factor},
	pages = {170--180},
}

Small proteins are ubiquitous in all kingdoms of life. MicroProteins, initially characterized as small proteins with protein interaction domains that enable them to interact with larger multidomain proteins, frequently modulate the function of these proteins. The study of these small proteins has contributed to a greater comprehension of protein regulation. In addition to sequence homology, sequence-divergent small proteins have the potential to function as microProtein mimics, binding to structurally related proteins. Moreover, a multitude of other small proteins encoded by short open reading frames (sORFs) and peptides, derived from diverse sources such as long noncoding RNAs (lncRNAs) and miRNAs, contribute to a variety of biological processes. The potential of small proteins is evident, offering promising avenues for bioengineering that could revolutionize crop performance and reduce reliance on agrochemicals in future agriculture.

@article{street_data-driven_2025,
	title = {Data-driven resources and computational tools in non-model plant species},
	volume = {177},
	copyright = {© 2025 Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70133},
	doi = {10.1111/ppl.70133},
	language = {en},
	number = {1},
	urldate = {2025-02-28},
	journal = {Physiologia Plantarum},
	author = {Street, Nathaniel R.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70133},
	pages = {e70133},
}

@article{hogberg_improved_2025,
	title = {Improved methodology for tracing a pulse of {13C}-labelled tree photosynthate carbon to ectomycorrhizal roots, other soil biota and soil processes in the field},
	volume = {45},
	issn = {1758-4469},
	url = {https://doi.org/10.1093/treephys/tpae169},
	doi = {10.1093/treephys/tpae169},
	abstract = {Isotopic pulse-labelling of photosynthate allows tracing of carbon (C) from tree canopies to below-ground biota and calculations of its turnover in roots and recipient soil microorganisms. A high concentration of label is desirable but is difficult to achieve in field studies of intact ecosystem patches with trees. Moreover, root systems of trees overlap considerably in most forests, which requires a large labelled area to minimize the impact of C allocated below-ground by un-labelled trees. We describe a method which combines a high level of labelling at ambient concentrations of CO2, [CO2], with undisturbed root systems and a model to account for root C and root-derived C from un-labelled trees. We raised 5-m-tall chambers, each covering 50 m2 of ground (volume 250 m3) in a young boreal Pinus sylvestris L. forest with up to 5 m tall trees. Rather than a conventional single release of 13CO2, we used five consecutive releases, each followed by a draw-down period, thus avoiding high [CO2]. Hence, we elevated successively the 13CO2 from 1.1 to 23 atom\% after the first release to 61 atom\% after the fifth, while maintaining [CO2] below 500 p.p.m. during 4–4.5 h of labelling. The average abundance of 13CO2 was as high as 42 atom\%. We used the central 10 m2 of the 50 m2 area for sampling of roots and other soil biota. We modelled the dilution of labelled C across the plots by un-labelled C from roots of trees outside the area. In the central 10 m2 area, {\textasciitilde}85\% of roots and root-associated biota received C from labelled trees. In summary, we elevated the labelling of roots and associated soil biota four-fold compared with previous studies and described the commonly overlooked impact of roots from un-labelled trees outside the labelled area.},
	number = {1},
	urldate = {2025-02-21},
	journal = {Tree Physiology},
	author = {Högberg, Peter and Klatt, Christian and Franklin, Oskar and Henriksson, Nils and Lim, Hyungwoo and Inselsbacher, Erich and Hurry, Vaughan and Näsholm, Torgny and Högberg, Mona N},
	month = jan,
	year = {2025},
	pages = {tpae169},
}

Isotopic pulse-labelling of photosynthate allows tracing of carbon (C) from tree canopies to below-ground biota and calculations of its turnover in roots and recipient soil microorganisms. A high concentration of label is desirable but is difficult to achieve in field studies of intact ecosystem patches with trees. Moreover, root systems of trees overlap considerably in most forests, which requires a large labelled area to minimize the impact of C allocated below-ground by un-labelled trees. We describe a method which combines a high level of labelling at ambient concentrations of CO2, [CO2], with undisturbed root systems and a model to account for root C and root-derived C from un-labelled trees. We raised 5-m-tall chambers, each covering 50 m2 of ground (volume 250 m3) in a young boreal Pinus sylvestris L. forest with up to 5 m tall trees. Rather than a conventional single release of 13CO2, we used five consecutive releases, each followed by a draw-down period, thus avoiding high [CO2]. Hence, we elevated successively the 13CO2 from 1.1 to 23 atom% after the first release to 61 atom% after the fifth, while maintaining [CO2] below 500 p.p.m. during 4–4.5 h of labelling. The average abundance of 13CO2 was as high as 42 atom%. We used the central 10 m2 of the 50 m2 area for sampling of roots and other soil biota. We modelled the dilution of labelled C across the plots by un-labelled C from roots of trees outside the area. In the central 10 m2 area, ~85% of roots and root-associated biota received C from labelled trees. In summary, we elevated the labelling of roots and associated soil biota four-fold compared with previous studies and described the commonly overlooked impact of roots from un-labelled trees outside the labelled area.

@article{kokla_long-distance_2025,
	title = {A long-distance inhibitory system regulates haustoria numbers in parasitic plants},
	volume = {122},
	url = {https://www.pnas.org/doi/10.1073/pnas.2424557122},
	doi = {10.1073/pnas.2424557122},
	abstract = {The ability of parasitic plants to withdraw nutrients from their hosts depends on the formation of an infective structure known as the haustorium. How parasites regulate their haustoria numbers is poorly understood, and here, we uncovered that existing haustoria in the facultative parasitic plants Phtheirospermum japonicum and Parentucellia viscosa suppressed the formation of new haustoria located on distant roots. Using Phtheirospermum, we found that this effect depended on the formation of mature haustoria and could be induced through the application of external nutrients. To understand the molecular basis of this root plasticity, we analyzed hormone response and found that existing infections upregulated cytokinin-responsive genes first at the haustoria and then more distantly in Phtheirospermum shoots. We observed that infections increased endogenous cytokinin levels in Phtheirospermum roots and shoots, and this increase appeared relevant since local treatments with exogenous cytokinins blocked the formation of both locally and distantly formed haustoria. In addition, local overexpression of a cytokinin-degrading enzyme in Phtheirospermum prevented this systemic interhaustoria repression and increased haustoria numbers locally. We propose that a long-distance signal produced by haustoria negatively regulates future haustoria, and in Phtheirospermum, such a signaling system is mediated by a local increase in cytokinin to regulate haustoria numbers and balance nutrient acquisition.},
	number = {8},
	urldate = {2025-02-21},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {Kokla, Anna and Leso, Martina and Šimura, Jan and Wärdig, Cecilia and Hayashi, Marina and Nishii, Naoshi and Tsuchiya, Yuichiro and Ljung, Karin and Melnyk, Charles W.},
	month = feb,
	year = {2025},
	pages = {e2424557122},
}

The ability of parasitic plants to withdraw nutrients from their hosts depends on the formation of an infective structure known as the haustorium. How parasites regulate their haustoria numbers is poorly understood, and here, we uncovered that existing haustoria in the facultative parasitic plants Phtheirospermum japonicum and Parentucellia viscosa suppressed the formation of new haustoria located on distant roots. Using Phtheirospermum, we found that this effect depended on the formation of mature haustoria and could be induced through the application of external nutrients. To understand the molecular basis of this root plasticity, we analyzed hormone response and found that existing infections upregulated cytokinin-responsive genes first at the haustoria and then more distantly in Phtheirospermum shoots. We observed that infections increased endogenous cytokinin levels in Phtheirospermum roots and shoots, and this increase appeared relevant since local treatments with exogenous cytokinins blocked the formation of both locally and distantly formed haustoria. In addition, local overexpression of a cytokinin-degrading enzyme in Phtheirospermum prevented this systemic interhaustoria repression and increased haustoria numbers locally. We propose that a long-distance signal produced by haustoria negatively regulates future haustoria, and in Phtheirospermum, such a signaling system is mediated by a local increase in cytokinin to regulate haustoria numbers and balance nutrient acquisition.

@article{jewaria_reduced_2025,
	title = {Reduced {RG}-{II} pectin dimerization disrupts differential growth by attenuating hormonal regulation},
	volume = {11},
	url = {https://www.science.org/doi/10.1126/sciadv.ads0760},
	doi = {10.1126/sciadv.ads0760},
	abstract = {Defects in cell wall integrity (CWI) profoundly affect plant growth, although, underlying mechanisms are not well understood. We show that in Arabidopsis mur1 mutant, CWI defects from compromising dimerization of RG-II pectin, a key component of cell wall, attenuate the expression of auxin response factors ARF7-ARF19. As a result, polar auxin transport components are misexpressed, disrupting auxin response asymmetry, leading to defective apical hook development. Accordingly, mur1 hook defects are suppressed by enhancing ARF7 expression. In addition, expression of brassinosteroid biosynthesis genes is down-regulated in mur1 mutant, and supplementing brassinosteroid or enhancing brassinosteroid signaling suppresses mur1 hook defects. Intriguingly, brassinosteroid enhances RG-II dimerization, showing hormonal feedback to the cell wall. Our results thus reveal a previously unrecognized link between cell wall defects from reduced RG-II dimerization and growth regulation mediated via modulation of auxin-brassinosteroid pathways in early seedling development.},
	number = {7},
	urldate = {2025-02-20},
	journal = {Science Advances},
	publisher = {American Association for the Advancement of Science},
	author = {Jewaria, Pawan Kumar and Aryal, Bibek and Begum, Rifat Ara and Wang, Yaowei and Sancho-Andrés, Gloria and Baba, Abu Imran and Yu, Meng and Li, Xiaojuan and Lin, Jinxing and Fry, Stephen C. and Verger, Stephane and Russinova, Eugenia and Jonsson, Kristoffer and Bhalerao, Rishikesh P.},
	month = feb,
	year = {2025},
	pages = {eads0760},
}

Defects in cell wall integrity (CWI) profoundly affect plant growth, although, underlying mechanisms are not well understood. We show that in Arabidopsis mur1 mutant, CWI defects from compromising dimerization of RG-II pectin, a key component of cell wall, attenuate the expression of auxin response factors ARF7-ARF19. As a result, polar auxin transport components are misexpressed, disrupting auxin response asymmetry, leading to defective apical hook development. Accordingly, mur1 hook defects are suppressed by enhancing ARF7 expression. In addition, expression of brassinosteroid biosynthesis genes is down-regulated in mur1 mutant, and supplementing brassinosteroid or enhancing brassinosteroid signaling suppresses mur1 hook defects. Intriguingly, brassinosteroid enhances RG-II dimerization, showing hormonal feedback to the cell wall. Our results thus reveal a previously unrecognized link between cell wall defects from reduced RG-II dimerization and growth regulation mediated via modulation of auxin-brassinosteroid pathways in early seedling development.

@article{jeong_spectral_2025,
	title = {Spectral unmixing of hyperspectral images revealed pine wilt disease sensitive endmembers},
	volume = {177},
	copyright = {© 2025 Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70090},
	doi = {10.1111/ppl.70090},
	abstract = {Throughout the entire cycle of leaf phenological events, leaf colour undergoes changes that are influenced by either abiotic stress or biotic infection. These changes in colouration are closely linked to the quantity and quality of photosynthetic pigments, which directly impact the primary productivity of plants. Therefore, monitoring and quantifying leaf colouration changes are crucial for distinguishing damage caused by pine wilt nematodes from natural tree senescence. In this study, a hyperspectral camera sensor was employed for the non-invasive and non-destructive evaluation of needle colour changes in coniferous trees grown in field tests. Three distinct needle colour variations of six coniferous tree species were selected and monitored using a hyperspectral sensor: those displaying seasonal autumn colours, undergoing nematode-infected necrosis processes, and experiencing natural death. To mitigate the inherently mixed spectral properties of hyperspectral data, endmembers were extracted from individual images using the Purity Pixel Index algorithm under the assumption of linear mixing of endmembers. From a total of 1,321 endmembers extracted from 378 hyperspectral images of six pine species, eight endmembers were ultimately chosen to reconstruct hyperspectral images and generate abundance maps. Among these eight endmembers, four represent varying levels of photosynthetic pigment contents—ranging from very low to high. Consequently, these coniferous endmembers hold promise for assessing seasonal leaf phenology and the extent of damage in pine trees infected by pine wilt nematodes. This comprehensive approach underscores the effectiveness of spectral unmixing of hyperspectral images in advancing precision forestry through meticulous coniferous needle trait analysis.},
	language = {en},
	number = {1},
	urldate = {2025-02-07},
	journal = {Physiologia Plantarum},
	author = {Jeong, Seok Won and Lee, Il Hwan and Kim, Yang-Gil and Kang, Kyu-Suk and Shim, Donghwan and Hurry, Vaughan and Ivanov, Alexander G. and Park, Youn-Il},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70090},
	pages = {e70090},
}

Throughout the entire cycle of leaf phenological events, leaf colour undergoes changes that are influenced by either abiotic stress or biotic infection. These changes in colouration are closely linked to the quantity and quality of photosynthetic pigments, which directly impact the primary productivity of plants. Therefore, monitoring and quantifying leaf colouration changes are crucial for distinguishing damage caused by pine wilt nematodes from natural tree senescence. In this study, a hyperspectral camera sensor was employed for the non-invasive and non-destructive evaluation of needle colour changes in coniferous trees grown in field tests. Three distinct needle colour variations of six coniferous tree species were selected and monitored using a hyperspectral sensor: those displaying seasonal autumn colours, undergoing nematode-infected necrosis processes, and experiencing natural death. To mitigate the inherently mixed spectral properties of hyperspectral data, endmembers were extracted from individual images using the Purity Pixel Index algorithm under the assumption of linear mixing of endmembers. From a total of 1,321 endmembers extracted from 378 hyperspectral images of six pine species, eight endmembers were ultimately chosen to reconstruct hyperspectral images and generate abundance maps. Among these eight endmembers, four represent varying levels of photosynthetic pigment contents—ranging from very low to high. Consequently, these coniferous endmembers hold promise for assessing seasonal leaf phenology and the extent of damage in pine trees infected by pine wilt nematodes. This comprehensive approach underscores the effectiveness of spectral unmixing of hyperspectral images in advancing precision forestry through meticulous coniferous needle trait analysis.

@article{ding_insights_2025,
	title = {Insights into \textit{{PeERF168}} gene in slash pine terpene biosynthesis: {Integrating} high-throughput phenotyping, {GWAS}, and transgenic studies},
	volume = {300},
	issn = {0141-8130},
	shorttitle = {Insights into \textit{{PeERF168}} gene in slash pine terpene biosynthesis},
	url = {https://www.sciencedirect.com/science/article/pii/S0141813025002776},
	doi = {10.1016/j.ijbiomac.2025.139728},
	abstract = {Resin biosynthesis in conifer is a complex process, controlled by multiple quantitative trait loci (QTLs). Quantifying resin components is traditionally expensive and labor-intensive. In this study, we employed near infrared (NIR) spectroscopy to quantify resin components in Slash pine using 240 genotypes. A partial least squares regression model was applied to identify the characteristic bands responsed to variations in Alpha and Beta pinene levels. Genome-wide association study (GWAS) identified 35 significant SNPs involved in terpenoid precursor biosynthesis, transport, modification, and abiotic stress resistance. eQTL mapping co-localized four candidate genes: PeCHITINASE (c166891.graph\_c0), PeGLYCOSYLTRANSFERASE (c160167.graph\_c0), PeASIL2 (c324347.graph\_c0), and PeERF168 (c311225.graph\_c0). Mutations in two SNPs increased the expression of PeASIL2 and PeERF168, leading to higher levels of Alpha and Beta pinene. Further heterologous transformation experiments confirmed that the PeERF168 gene regulates the concentration of both monoterpenes and sesquiterpenes. These findings provide valuable insights into the molecular mechanisms of resin biosynthesis, facilitating cost-effective gene discovery through high-throughput resin component detection and genomics integration, with substantial potential to enhance molecular breeding and improve resin yield and quality.},
	urldate = {2025-01-31},
	journal = {International Journal of Biological Macromolecules},
	author = {Ding, Xianyin and Diao, Shu and Zhang, Yini and Luan, Qifu and Li, Yanjie and Jiang, Jingmin and Wu, Harry X.},
	month = apr,
	year = {2025},
	keywords = {GWAS, High-throughput phenotyping, Slash pine, Terpene biosynthesis, eQTL mapping},
	pages = {139728},
}

Resin biosynthesis in conifer is a complex process, controlled by multiple quantitative trait loci (QTLs). Quantifying resin components is traditionally expensive and labor-intensive. In this study, we employed near infrared (NIR) spectroscopy to quantify resin components in Slash pine using 240 genotypes. A partial least squares regression model was applied to identify the characteristic bands responsed to variations in Alpha and Beta pinene levels. Genome-wide association study (GWAS) identified 35 significant SNPs involved in terpenoid precursor biosynthesis, transport, modification, and abiotic stress resistance. eQTL mapping co-localized four candidate genes: PeCHITINASE (c166891.graph_c0), PeGLYCOSYLTRANSFERASE (c160167.graph_c0), PeASIL2 (c324347.graph_c0), and PeERF168 (c311225.graph_c0). Mutations in two SNPs increased the expression of PeASIL2 and PeERF168, leading to higher levels of Alpha and Beta pinene. Further heterologous transformation experiments confirmed that the PeERF168 gene regulates the concentration of both monoterpenes and sesquiterpenes. These findings provide valuable insights into the molecular mechanisms of resin biosynthesis, facilitating cost-effective gene discovery through high-throughput resin component detection and genomics integration, with substantial potential to enhance molecular breeding and improve resin yield and quality.

@article{baral_typhon_2025,
	title = {{TYPHON} proteins are {RAB}-dependent mediators of the trans-{Golgi} network secretory pathway},
	volume = {37},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koae280},
	doi = {10.1093/plcell/koae280},
	abstract = {The trans-Golgi network (TGN), a key compartment in endomembrane trafficking, participates in both secretion to and endocytosis from the plasma membrane. Consequently, the TGN plays a key role in plant growth and development. Understanding how proteins are sorted for secretion or endocytic recycling at the TGN is critical for elucidating mechanisms of plant development. We previously showed that the protein ECHIDNA is essential for phytohormonal control of hypocotyl bending because it mediates secretion of cell wall components and the auxin influx carrier AUXIN RESISTANT 1 (AUX1) from the TGN. Despite the critical role of ECHIDNA in TGN-mediated trafficking, its mode of action remains unknown in Arabidopsis (Arabidopsis thaliana). We therefore performed a suppressor screen on the ech mutant. Here, we report the identification of TGN-localized TYPHON 1 (TPN1) and TPN2 proteins. A single amino acid change in either TPN protein causes dominant suppression of the ech mutant's defects in growth and AUX1 secretion, while also restoring wild-type (WT)-like ethylene-responsive hypocotyl bending. Importantly, genetic and cell biological evidence shows that TPN1 acts through RAS-ASSOCIATED BINDING H1b (RABH1b), a TGN-localized RAB-GTPase. These results provide insights into ECHIDNA-mediated secretory trafficking of cell wall and auxin carriers at the TGN, as well as its role in controlling plant growth.},
	number = {1},
	urldate = {2025-01-20},
	journal = {The Plant Cell},
	author = {Baral, Anirban and Gendre, Delphine and Aryal, Bibek and Fougère, Louise and Di Fino, Luciano Martin and Ohori, Chihiro and Sztojka, Bernadette and Uemura, Tomohiro and Ueda, Takashi and Marhavý, Peter and Boutté, Yohann and Bhalerao, Rishikesh P},
	month = jan,
	year = {2025},
	pages = {koae280},
}

The trans-Golgi network (TGN), a key compartment in endomembrane trafficking, participates in both secretion to and endocytosis from the plasma membrane. Consequently, the TGN plays a key role in plant growth and development. Understanding how proteins are sorted for secretion or endocytic recycling at the TGN is critical for elucidating mechanisms of plant development. We previously showed that the protein ECHIDNA is essential for phytohormonal control of hypocotyl bending because it mediates secretion of cell wall components and the auxin influx carrier AUXIN RESISTANT 1 (AUX1) from the TGN. Despite the critical role of ECHIDNA in TGN-mediated trafficking, its mode of action remains unknown in Arabidopsis (Arabidopsis thaliana). We therefore performed a suppressor screen on the ech mutant. Here, we report the identification of TGN-localized TYPHON 1 (TPN1) and TPN2 proteins. A single amino acid change in either TPN protein causes dominant suppression of the ech mutant's defects in growth and AUX1 secretion, while also restoring wild-type (WT)-like ethylene-responsive hypocotyl bending. Importantly, genetic and cell biological evidence shows that TPN1 acts through RAS-ASSOCIATED BINDING H1b (RABH1b), a TGN-localized RAB-GTPase. These results provide insights into ECHIDNA-mediated secretory trafficking of cell wall and auxin carriers at the TGN, as well as its role in controlling plant growth.

@article{wieloch_new_2025,
	title = {New insights into the mechanisms of plant isotope fractionation from combined analysis of intramolecular {13C} and deuterium abundances in {Pinus} nigra tree-ring glucose},
	volume = {245},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20113},
	doi = {10.1111/nph.20113},
	abstract = {Understanding isotope fractionation mechanisms is fundamental for analyses of plant ecophysiology and paleoclimate based on tree-ring isotope data. To gain new insights into isotope fractionation, we analysed intramolecular 13C discrimination in tree-ring glucose (Δi′, i = C-1 to C-6) and metabolic deuterium fractionation at H1 and H2 (εmet) combinedly. This dual-isotope approach was used for isotope-signal deconvolution. We found evidence for metabolic processes affecting Δ1′ and Δ3′, which respond to air vapour pressure deficit (VPD), and processes affecting Δ1′, Δ2′, and εmet, which respond to precipitation but not VPD. These relationships exhibit change points dividing a period of homeostasis (1961–1980) from a period of metabolic adjustment (1983–1995). Homeostasis may result from sufficient groundwater availability. Additionally, we found Δ5′ and Δ6′ relationships with radiation and temperature, which are temporally stable and consistent with previously proposed isotope fractionation mechanisms. Based on the multitude of climate covariables, intramolecular carbon isotope analysis has a remarkable potential for climate reconstruction. While isotope fractionation beyond leaves is currently considered to be constant, we propose significant parts of the carbon and hydrogen isotope variation in tree-ring glucose originate in stems (precipitation-dependent signals). As basis for follow-up studies, we propose mechanisms introducing Δ1′, Δ2′, Δ3′, and εmet variability.},
	language = {en},
	number = {3},
	urldate = {2025-01-10},
	journal = {New Phytologist},
	author = {Wieloch, Thomas and Holloway-Phillips, Meisha and Yu, Jun and Niittylä, Totte},
	month = feb,
	year = {2025},
	keywords = {carbon stable isotopes, hydrogen stable isotopes, intramolecular isotope analysis, isotope fractionation mechanisms, leaf water status, plant–environment interactions, stem water status, tree rings},
	pages = {1000--1017},
}

Understanding isotope fractionation mechanisms is fundamental for analyses of plant ecophysiology and paleoclimate based on tree-ring isotope data. To gain new insights into isotope fractionation, we analysed intramolecular 13C discrimination in tree-ring glucose (Δi′, i = C-1 to C-6) and metabolic deuterium fractionation at H1 and H2 (εmet) combinedly. This dual-isotope approach was used for isotope-signal deconvolution. We found evidence for metabolic processes affecting Δ1′ and Δ3′, which respond to air vapour pressure deficit (VPD), and processes affecting Δ1′, Δ2′, and εmet, which respond to precipitation but not VPD. These relationships exhibit change points dividing a period of homeostasis (1961–1980) from a period of metabolic adjustment (1983–1995). Homeostasis may result from sufficient groundwater availability. Additionally, we found Δ5′ and Δ6′ relationships with radiation and temperature, which are temporally stable and consistent with previously proposed isotope fractionation mechanisms. Based on the multitude of climate covariables, intramolecular carbon isotope analysis has a remarkable potential for climate reconstruction. While isotope fractionation beyond leaves is currently considered to be constant, we propose significant parts of the carbon and hydrogen isotope variation in tree-ring glucose originate in stems (precipitation-dependent signals). As basis for follow-up studies, we propose mechanisms introducing Δ1′, Δ2′, Δ3′, and εmet variability.

@article{sivan_modification_2025,
	title = {Modification of xylan in secondary walls alters cell wall biosynthesis and wood formation programs and improves saccharification},
	volume = {23},
	copyright = {© 2024 The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley \& Sons Ltd.},
	issn = {1467-7652},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.14487},
	doi = {10.1111/pbi.14487},
	abstract = {Wood of broad-leaf tree species is a valued source of renewable biomass for biorefinery and a target for genetic improvement efforts to reduce its recalcitrance. Glucuronoxylan (GX) plays a key role in recalcitrance through its interactions with cellulose and lignin. To reduce recalcitrance, we modified wood GX by expressing GH10 and GH11 endoxylanases from Aspergillus nidulans in hybrid aspen (Populus tremula L. × tremuloides Michx.) and targeting the enzymes to cell wall. The xylanases reduced tree height, modified cambial activity by increasing phloem and reducing xylem production, and reduced secondary wall deposition. Xylan molecular weight was decreased, and the spacing between acetyl and MeGlcA side chains was reduced in transgenic lines. The transgenic trees produced hypolignified xylem having thin secondary walls and deformed vessels. Glucose yields of enzymatic saccharification without pretreatment almost doubled indicating decreased recalcitrance. The transcriptomics, hormonomics and metabolomics data provided evidence for activation of cytokinin and ethylene signalling pathways, decrease in ABA levels, transcriptional suppression of lignification and a subset of secondary wall biosynthetic program, including xylan glucuronidation and acetylation machinery. Several candidate genes for perception of impairment in xylan integrity were detected. These candidates could provide a new target for uncoupling negative growth effects from reduced recalcitrance. In conclusion, our study supports the hypothesis that xylan modification generates intrinsic signals and evokes novel pathways regulating tree growth and secondary wall biosynthesis.},
	language = {en},
	number = {1},
	urldate = {2024-10-25},
	journal = {Plant Biotechnology Journal},
	author = {Sivan, Pramod and Urbancsok, János and Donev, Evgeniy N. and Derba-Maceluch, Marta and Barbut, Félix R. and Yassin, Zakiya and Gandla, Madhavi L. and Mitra, Madhusree and Heinonen, Saara E. and Šimura, Jan and Cermanová, Kateřina and Karady, Michal and Scheepers, Gerhard and Jönsson, Leif J. and Master, Emma R. and Vilaplana, Francisco and Mellerowicz, Ewa J.},
	month = jan,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.14487},
	keywords = {Glucuronoxylan, fungal xylanases, lignocellulose, secondary cell wall, transgenic aspen, wood development},
	pages = {174--197},
}

Wood of broad-leaf tree species is a valued source of renewable biomass for biorefinery and a target for genetic improvement efforts to reduce its recalcitrance. Glucuronoxylan (GX) plays a key role in recalcitrance through its interactions with cellulose and lignin. To reduce recalcitrance, we modified wood GX by expressing GH10 and GH11 endoxylanases from Aspergillus nidulans in hybrid aspen (Populus tremula L. × tremuloides Michx.) and targeting the enzymes to cell wall. The xylanases reduced tree height, modified cambial activity by increasing phloem and reducing xylem production, and reduced secondary wall deposition. Xylan molecular weight was decreased, and the spacing between acetyl and MeGlcA side chains was reduced in transgenic lines. The transgenic trees produced hypolignified xylem having thin secondary walls and deformed vessels. Glucose yields of enzymatic saccharification without pretreatment almost doubled indicating decreased recalcitrance. The transcriptomics, hormonomics and metabolomics data provided evidence for activation of cytokinin and ethylene signalling pathways, decrease in ABA levels, transcriptional suppression of lignification and a subset of secondary wall biosynthetic program, including xylan glucuronidation and acetylation machinery. Several candidate genes for perception of impairment in xylan integrity were detected. These candidates could provide a new target for uncoupling negative growth effects from reduced recalcitrance. In conclusion, our study supports the hypothesis that xylan modification generates intrinsic signals and evokes novel pathways regulating tree growth and secondary wall biosynthesis.

@article{wieloch_shining_2025,
	title = {Shining a new light on the classical concepts of carbon-isotope dendrochronology},
	volume = {245},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20258},
	doi = {10.1111/nph.20258},
	abstract = {Retrospective information about plant ecophysiology and the climate system are key inputs in Earth system and vegetation models. Dendrochronology provides such information with large spatiotemporal coverage, and carbon-isotope analysis across tree-ring series is among the most advanced dendrochronological tools. For the past 70 years, this analysis was performed on whole molecules and, to this day, 13C discrimination during carbon assimilation is invoked to explain isotope variation and associated climate signals. However, recently it was reported that tree-ring glucose exhibits multiple isotope signals at the intramolecular level (see Wieloch et al., 2025). Here, I estimated the signals' contribution to whole-molecule isotope variation and found that downstream processes in leaf and stem metabolism each introduce more variation than carbon assimilation. Moreover, downstream processes introduce most of the climate information. These findings are inconsistent with the classical concepts/practices of carbon-isotope dendrochronology. More importantly, intramolecular tree-ring isotope analysis promises novel insights into forest metabolism and the climate of the past.},
	language = {en},
	number = {3},
	urldate = {2025-01-10},
	journal = {New Phytologist},
	author = {Wieloch, Thomas},
	month = feb,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20258},
	keywords = {carbon stable isotopes, dendrochronology, intramolecular isotope analysis, paleoclimate reconstruction, plant carbon fluxes, tree rings, water-use efficiency, whole-molecule isotope analysis},
	pages = {939--944},
}

Retrospective information about plant ecophysiology and the climate system are key inputs in Earth system and vegetation models. Dendrochronology provides such information with large spatiotemporal coverage, and carbon-isotope analysis across tree-ring series is among the most advanced dendrochronological tools. For the past 70 years, this analysis was performed on whole molecules and, to this day, 13C discrimination during carbon assimilation is invoked to explain isotope variation and associated climate signals. However, recently it was reported that tree-ring glucose exhibits multiple isotope signals at the intramolecular level (see Wieloch et al., 2025). Here, I estimated the signals' contribution to whole-molecule isotope variation and found that downstream processes in leaf and stem metabolism each introduce more variation than carbon assimilation. Moreover, downstream processes introduce most of the climate information. These findings are inconsistent with the classical concepts/practices of carbon-isotope dendrochronology. More importantly, intramolecular tree-ring isotope analysis promises novel insights into forest metabolism and the climate of the past.

@article{renzi_epigenetic_2025,
	title = {Epigenetic suppression of creatine kinase {B} in adipocytes links endoplasmic reticulum stress to obesity-associated inflammation},
	volume = {92},
	issn = {2212-8778},
	url = {https://www.sciencedirect.com/science/article/pii/S2212877824002138},
	doi = {10.1016/j.molmet.2024.102082},
	abstract = {In white adipose tissue, disturbed creatine metabolism through reduced creatine kinase B (CKB) transcription contributes to obesity-related inflammation. However, the mechanisms regulating CKB expression in human white adipocytes remain unclear. By screening conditions perturbed in obesity, we identified endoplasmic reticulum (ER) stress as a key suppressor of CKB transcription across multiple cell types. Through follow-up studies, we found that ER stress through the IRE1–XBP1s pathway, promotes CKB promoter methylation via the methyltransferase DNMT3A. This epigenetic change represses CKB transcription, shifting metabolism towards glycolysis and increasing the production of the pro-inflammatory chemokine CCL2. We validated our findings in vivo, demonstrating that individuals living with obesity show an inverse relationship between CKB expression and promoter methylation in white adipocytes, along with elevated CCL2 secretion. Overall, our study uncovers a regulatory axis where ER stress drives inflammation in obesity by reducing CKB abundance, and consequently altering the bioenergetic state of the cell.},
	urldate = {2025-01-10},
	journal = {Molecular Metabolism},
	author = {Renzi, Gianluca and Vlassakev, Ivan and Hansen, Mattias and Higos, Romane and Lecoutre, Simon and Elmastas, Merve and Hodek, Ondrej and Moritz, Thomas and Alaeddine, Lynn M. and Frendo–Cumbo, Scott and Dahlman, Ingrid and Kerr, Alastair and Maqdasy, Salwan and Mejhert, Niklas and Rydén, Mikael},
	month = feb,
	year = {2025},
	keywords = {Chromatin remodeling, Creatine pathway, Glycolysis, Immunometabolism, Tunicamycin},
	pages = {102082},
}

In white adipose tissue, disturbed creatine metabolism through reduced creatine kinase B (CKB) transcription contributes to obesity-related inflammation. However, the mechanisms regulating CKB expression in human white adipocytes remain unclear. By screening conditions perturbed in obesity, we identified endoplasmic reticulum (ER) stress as a key suppressor of CKB transcription across multiple cell types. Through follow-up studies, we found that ER stress through the IRE1–XBP1s pathway, promotes CKB promoter methylation via the methyltransferase DNMT3A. This epigenetic change represses CKB transcription, shifting metabolism towards glycolysis and increasing the production of the pro-inflammatory chemokine CCL2. We validated our findings in vivo, demonstrating that individuals living with obesity show an inverse relationship between CKB expression and promoter methylation in white adipocytes, along with elevated CCL2 secretion. Overall, our study uncovers a regulatory axis where ER stress drives inflammation in obesity by reducing CKB abundance, and consequently altering the bioenergetic state of the cell.

@article{farci_characterization_2025,
	title = {Characterization of {SARS}-{CoV}-2 nucleocapsid protein oligomers},
	volume = {217},
	issn = {1047-8477},
	url = {https://www.sciencedirect.com/science/article/pii/S1047847724001023},
	doi = {10.1016/j.jsb.2024.108162},
	abstract = {Oligomers of the SARS-CoV-2 nucleocapsid (N) protein are characterized by pronounced instability resulting in fast degradation. This property likely relates to two contrasting behaviors of the N protein: genome stabilization through a compact nucleocapsid during cell evasion and genome release by nucleocapsid disassembling during infection. In vivo, the N protein forms rounded complexes of high molecular mass from its interaction with the viral genome. To study the N protein and understand its instability, we analyzed degradation profiles under different conditions by size-exclusion chromatography and characterized samples by mass spectrometry and cryo-electron microscopy. We identified self-cleavage properties of the N protein based on specific Proprotein convertases activities, with Cl- playing a key role in modulating stability and degradation. These findings allowed isolation of a stable oligomeric complex of N, for which we report the 3D structure at ∼6.8 Å resolution. Findings are discussed considering available knowledge about the coronaviruses’ infection cycle.},
	number = {1},
	urldate = {2025-01-10},
	journal = {Journal of Structural Biology},
	author = {Farci, Domenica and Graça, André T. and Hall, Michael and Haniewicz, Patrycja and Kereïche, Sami and Faull, Peter and Kirkpatrick, Joanna and Tramontano, Enzo and Schröder, Wolfgang P. and Piano, Dario},
	month = mar,
	year = {2025},
	keywords = {Covid-19, Cryo-electron microscopy, Furin, Nucleocapsid protein, Proprotein convertases, SARS-CoV-2, Self-cleavage},
	pages = {108162},
}

Oligomers of the SARS-CoV-2 nucleocapsid (N) protein are characterized by pronounced instability resulting in fast degradation. This property likely relates to two contrasting behaviors of the N protein: genome stabilization through a compact nucleocapsid during cell evasion and genome release by nucleocapsid disassembling during infection. In vivo, the N protein forms rounded complexes of high molecular mass from its interaction with the viral genome. To study the N protein and understand its instability, we analyzed degradation profiles under different conditions by size-exclusion chromatography and characterized samples by mass spectrometry and cryo-electron microscopy. We identified self-cleavage properties of the N protein based on specific Proprotein convertases activities, with Cl- playing a key role in modulating stability and degradation. These findings allowed isolation of a stable oligomeric complex of N, for which we report the 3D structure at ∼6.8 Å resolution. Findings are discussed considering available knowledge about the coronaviruses’ infection cycle.

@article{kleczkowski_adenylate-driven_2025,
	title = {Adenylate-driven equilibration of both ribo- and deoxyribonucleotides is under magnesium control: {Quantification} of the {Mg2}+-signal},
	volume = {304},
	issn = {0176-1617},
	shorttitle = {Adenylate-driven equilibration of both ribo- and deoxyribonucleotides is under magnesium control},
	url = {https://www.sciencedirect.com/science/article/pii/S0176161724002116},
	doi = {10.1016/j.jplph.2024.154380},
	abstract = {Nucleoside mono-, di- and triphosphates (NMP, NDP, and NTP) and their deoxy-counterparts (dNMP, dNDP, dNTP) are involved in energy metabolism and are the building blocks of RNA and DNA, respectively. The production of NTP and dNTP is carried out by several NMP kinases (NMPK) and NDP kinases (NDPK). All NMPKs are fully reversible and use defined Mg-free and Mg-complexed nucleotides in both directions of their reactions, with Mg2+ controlling the ratios of Mg-free and Mg-complexed reactants. Their activities are driven by adenylates produced by adenylate kinase which controls the direction of NMPK and NDPK reactions, depending on the energy status of a cell. This enzymatic machinery is localized in the cytosol, mitochondria, and plastids, i.e. compartments with high energy budgets and where (except for cytosol) RNA and DNA synthesis occur. Apparent equilibrium constants of NMPKs, based on total nucleotide contents, are [Mg2+]-dependent. This allows for an indirect estimation of internal [Mg2+], which constitutes a signal of the energetic status of a given tissue/cell/compartment. Adenylates contribute the most to this Mg2+-signal, followed by uridylates, guanylates, and cytidylates, with deoxynucleotides’ contribution deemed negligible. A method to quantify the Mg2+-signal, using nucleotide datasets, is discussed.},
	urldate = {2025-01-10},
	journal = {Journal of Plant Physiology},
	author = {Kleczkowski, Leszek A. and Igamberdiev, Abir U.},
	month = jan,
	year = {2025},
	keywords = {Adenylate kinase, Equilibrium constant, Guanylate kinase, Magnesium signaling, Thymidylate kinase, Uridylate-cytidylate kinase},
	pages = {154380},
}

Nucleoside mono-, di- and triphosphates (NMP, NDP, and NTP) and their deoxy-counterparts (dNMP, dNDP, dNTP) are involved in energy metabolism and are the building blocks of RNA and DNA, respectively. The production of NTP and dNTP is carried out by several NMP kinases (NMPK) and NDP kinases (NDPK). All NMPKs are fully reversible and use defined Mg-free and Mg-complexed nucleotides in both directions of their reactions, with Mg2+ controlling the ratios of Mg-free and Mg-complexed reactants. Their activities are driven by adenylates produced by adenylate kinase which controls the direction of NMPK and NDPK reactions, depending on the energy status of a cell. This enzymatic machinery is localized in the cytosol, mitochondria, and plastids, i.e. compartments with high energy budgets and where (except for cytosol) RNA and DNA synthesis occur. Apparent equilibrium constants of NMPKs, based on total nucleotide contents, are [Mg2+]-dependent. This allows for an indirect estimation of internal [Mg2+], which constitutes a signal of the energetic status of a given tissue/cell/compartment. Adenylates contribute the most to this Mg2+-signal, followed by uridylates, guanylates, and cytidylates, with deoxynucleotides’ contribution deemed negligible. A method to quantify the Mg2+-signal, using nucleotide datasets, is discussed.

@article{spitzer_aboveground_2025,
	title = {Aboveground and belowground trait coordination across twelve boreal forest tree species},
	volume = {15},
	copyright = {2024 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-024-84162-0},
	doi = {10.1038/s41598-024-84162-0},
	abstract = {The existence of trait coordination in roots and leaves has recently been debated, with studies reaching opposing conclusions. Here, we assessed trait coordination across twelve boreal tree species. We show that there is only partial evidence for above-belowground coordination for “fast-slow” economic traits across boreal tree species, i.e., while N content in leaves and roots were positively correlated, as well as dry matter content, root dry matter content and leaf N had no significant relationship. For resource acquisition traits (i.e. related to light capture and nutrient uptake) we did not find strong evidence for trait coordination, as specific root length and specific leaf area were not positively correlated. We further show that site only explained between 0 and 7\% of the total trait variation, while within-site variation contributed substantially to the total trait variation for a large number of traits (1.6–96\%), and more so for morphological root traits than leaf traits. This likely influences the strength of above-belowground trait coordination found across species in our study. Understanding sources of trait variation and above-belowground trait relationships can contribute to improving global and regional C cycling models. However, fine-scale environmental variability should be accounted for given its importance for driving trait variation.},
	language = {en},
	number = {1},
	urldate = {2025-01-10},
	journal = {Scientific Reports},
	publisher = {Nature Publishing Group},
	author = {Spitzer, Clydecia M. and Jämtgård, Sandra and Larsson, Marcus J. and Gundale, Michael J.},
	month = jan,
	year = {2025},
	keywords = {Ecology, Plant sciences},
	pages = {680},
}

The existence of trait coordination in roots and leaves has recently been debated, with studies reaching opposing conclusions. Here, we assessed trait coordination across twelve boreal tree species. We show that there is only partial evidence for above-belowground coordination for “fast-slow” economic traits across boreal tree species, i.e., while N content in leaves and roots were positively correlated, as well as dry matter content, root dry matter content and leaf N had no significant relationship. For resource acquisition traits (i.e. related to light capture and nutrient uptake) we did not find strong evidence for trait coordination, as specific root length and specific leaf area were not positively correlated. We further show that site only explained between 0 and 7% of the total trait variation, while within-site variation contributed substantially to the total trait variation for a large number of traits (1.6–96%), and more so for morphological root traits than leaf traits. This likely influences the strength of above-belowground trait coordination found across species in our study. Understanding sources of trait variation and above-belowground trait relationships can contribute to improving global and regional C cycling models. However, fine-scale environmental variability should be accounted for given its importance for driving trait variation.

@article{miranda-cervantes_pantothenate_2025,
	title = {Pantothenate kinase 4 controls skeletal muscle substrate metabolism},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-024-55036-w},
	doi = {10.1038/s41467-024-55036-w},
	abstract = {Metabolic flexibility in skeletal muscle is essential for maintaining healthy glucose and lipid metabolism, and its dysfunction is closely linked to metabolic diseases. Exercise enhances metabolic flexibility, making it an important tool for discovering mechanisms that promote metabolic health. Here we show that pantothenate kinase 4 (PanK4) is a new conserved exercise target with high abundance in muscle. Muscle-specific deletion of PanK4 impairs fatty acid oxidation which is related to higher intramuscular acetyl-CoA and malonyl-CoA levels. Elevated acetyl-CoA levels persist regardless of feeding state and are associated with whole-body glucose intolerance, reduced insulin-stimulated glucose uptake in glycolytic muscle, and impaired glucose uptake during exercise. Conversely, increasing PanK4 levels in glycolytic muscle lowers acetyl-CoA and enhances glucose uptake. Our findings highlight PanK4 as an important regulator of acetyl-CoA levels, playing a key role in both muscle lipid and glucose metabolism.},
	language = {en},
	number = {1},
	urldate = {2025-01-10},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Miranda-Cervantes, Adriana and Fritzen, Andreas M. and Raun, Steffen H. and Hodek, Ondřej and Møller, Lisbeth L. V. and Johann, Kornelia and Deisen, Luisa and Gregorevic, Paul and Gudiksen, Anders and Artati, Anna and Adamski, Jerzy and Andersen, Nicoline R. and Sigvardsen, Casper M. and Carl, Christian S. and Voldstedlund, Christian T. and Kjøbsted, Rasmus and Hauck, Stefanie M. and Schjerling, Peter and Jensen, Thomas E. and Cebrian-Serrano, Alberto and Jähnert, Markus and Gottmann, Pascal and Burtscher, Ingo and Lickert, Heiko and Pilegaard, Henriette and Schürmann, Annette and Tschöp, Matthias H. and Moritz, Thomas and Müller, Timo D. and Sylow, Lykke and Kiens, Bente and Richter, Erik A. and Kleinert, Maximilian},
	month = jan,
	year = {2025},
	keywords = {Diabetes, Fat metabolism, Homeostasis, Metabolomics},
	pages = {345},
}

Metabolic flexibility in skeletal muscle is essential for maintaining healthy glucose and lipid metabolism, and its dysfunction is closely linked to metabolic diseases. Exercise enhances metabolic flexibility, making it an important tool for discovering mechanisms that promote metabolic health. Here we show that pantothenate kinase 4 (PanK4) is a new conserved exercise target with high abundance in muscle. Muscle-specific deletion of PanK4 impairs fatty acid oxidation which is related to higher intramuscular acetyl-CoA and malonyl-CoA levels. Elevated acetyl-CoA levels persist regardless of feeding state and are associated with whole-body glucose intolerance, reduced insulin-stimulated glucose uptake in glycolytic muscle, and impaired glucose uptake during exercise. Conversely, increasing PanK4 levels in glycolytic muscle lowers acetyl-CoA and enhances glucose uptake. Our findings highlight PanK4 as an important regulator of acetyl-CoA levels, playing a key role in both muscle lipid and glucose metabolism.

@article{larsson_conversion_2025,
	title = {Conversion of unmanaged boreal forest to even-aged management has a stronger effect on carbon stocks in the organic layer than the mineral soil},
	volume = {578},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112724007709},
	doi = {10.1016/j.foreco.2024.122458},
	abstract = {Forest management can impact forest carbon stocks, above- and belowground. The even-aged management practice removes the aboveground carbon stock at harvest, which is thereafter restored as the new forest stand establishes. The effects of even-aged management on forest soils in earlier unmanaged stands are however less well understood, and it has been suggested that large carbon losses may occur. In this study we use a unique paired sampling approach of stands in north inland Sweden. Half of the sampled stands had been clear cut within the previous 54 years, and half were left unmanaged. Our results show that clear-cut harvesting and subsequent transformation of unmanaged stands into even-aged management resulted in lower aboveground carbon stock in the living trees. For the soil there was weak evidence for a loss of c. 15 \% of the carbon stock in the organic layer. No evidence of an effect in the more stabilized soil organic carbon within the mineral soil layers was found.},
	urldate = {2025-01-10},
	journal = {Forest Ecology and Management},
	author = {Larsson, Marcus and Dahl, Jenny and Lundmark, Tomas and Gundale, Michael J. and Lim, Hyungwoo and Nordin, Annika},
	month = feb,
	year = {2025},
	keywords = {Boreal forest, Carbon sink, Ecosystem carbon stock, Forest management, Soil organic carbon, Unmanaged forests},
	pages = {122458},
}

Forest management can impact forest carbon stocks, above- and belowground. The even-aged management practice removes the aboveground carbon stock at harvest, which is thereafter restored as the new forest stand establishes. The effects of even-aged management on forest soils in earlier unmanaged stands are however less well understood, and it has been suggested that large carbon losses may occur. In this study we use a unique paired sampling approach of stands in north inland Sweden. Half of the sampled stands had been clear cut within the previous 54 years, and half were left unmanaged. Our results show that clear-cut harvesting and subsequent transformation of unmanaged stands into even-aged management resulted in lower aboveground carbon stock in the living trees. For the soil there was weak evidence for a loss of c. 15 % of the carbon stock in the organic layer. No evidence of an effect in the more stabilized soil organic carbon within the mineral soil layers was found.

@article{yu_integration_2025,
	title = {Integration of {Mitoflash} and {Time}-{Series} {Transcriptomics} {Facilitates} {Energy} {Dynamics} {Tracking} and {Substrate} {Supply} {Analysis} of {Floral} {Thermogenesis} in {Lotus}},
	volume = {48},
	copyright = {© 2024 John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.15185},
	doi = {10.1111/pce.15185},
	abstract = {The high biosynthetic and energetic demands of floral thermogenesis render thermogenic plants the ideal systems to characterize energy metabolism in plants, but real-time tracking of energy metabolism in plant cells remains challenging. In this study, a new method was developed for tracking the mitochondrial energy metabolism at the single mitochondria level by real-time imaging of mitochondrial superoxide production (i.e., mitoflash). Using this method, we observed the increased mitoflash frequencies in the receptacles of Nelumbo nucifera Gaertn. at the thermogenic stages. This increase, combined with the higher expression of antioxidant response-related genes identified through time-series transcriptomics at the same stages, shows us a new regulatory mechanism for plant redox balance. Furthermore, we found that the upregulation of respiratory metabolism-related genes during the thermogenic stages not only correlates with changes in mitoflash frequency but also underscores the critical roles of these pathways in ensuring adequate substrate supply for thermogenesis. Metabolite analysis revealed that sugars are likely one of the substrates for thermogenesis and may be transported over long distances by sugar transporters. Taken together, our findings demonstrate that mitoflash is a reliable tool for tracking energy metabolism in thermogenic plants and contributes to our understanding of the regulatory mechanisms underlying floral thermogenesis.},
	language = {en},
	number = {1},
	urldate = {2024-12-06},
	journal = {Plant, Cell \& Environment},
	author = {Yu, Miao and Wang, Siqin and Gu, Ge and Shi, Tian-Le and Zhang, Jin and Jia, Yaping and Ma, Qi and Porth, Ilga and Mao, Jian-Feng and Wang, Ruohan},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.15185},
	keywords = {Nelumbo nucifera, energy metabolism, floral thermogenesis, mitochondrial flash, respiratory substrate, time-series transcriptomics},
	pages = {893--906},
}

The high biosynthetic and energetic demands of floral thermogenesis render thermogenic plants the ideal systems to characterize energy metabolism in plants, but real-time tracking of energy metabolism in plant cells remains challenging. In this study, a new method was developed for tracking the mitochondrial energy metabolism at the single mitochondria level by real-time imaging of mitochondrial superoxide production (i.e., mitoflash). Using this method, we observed the increased mitoflash frequencies in the receptacles of Nelumbo nucifera Gaertn. at the thermogenic stages. This increase, combined with the higher expression of antioxidant response-related genes identified through time-series transcriptomics at the same stages, shows us a new regulatory mechanism for plant redox balance. Furthermore, we found that the upregulation of respiratory metabolism-related genes during the thermogenic stages not only correlates with changes in mitoflash frequency but also underscores the critical roles of these pathways in ensuring adequate substrate supply for thermogenesis. Metabolite analysis revealed that sugars are likely one of the substrates for thermogenesis and may be transported over long distances by sugar transporters. Taken together, our findings demonstrate that mitoflash is a reliable tool for tracking energy metabolism in thermogenic plants and contributes to our understanding of the regulatory mechanisms underlying floral thermogenesis.

@article{bas_influence_2025,
	title = {Influence of {TEMPO} on preparation of softwood nanofibrils and their hydrogel network properties},
	volume = {348},
	issn = {0144-8617},
	url = {https://www.sciencedirect.com/science/article/pii/S0144861724010385},
	doi = {10.1016/j.carbpol.2024.122812},
	abstract = {From an economic and environmental perspective, the use of less chemicals in the production of cellulose nanofibrils (CNFs) is advantageous. In this study, we investigated the oxidation (TEMPO/NaClO2/NaClO, pH 6.8) of softwood (SW) particles with varying amounts of TEMPO (16, 8 or 0 mg g−1 of wood). Following, TEMPO-oxidized SW nanofibrils (TO-SWNFs) were obtained by nanofibrillation and their size, morphology, and crystallite size were assessed. Hydrogel networks of TO-SWNFs were prepared and mechanical properties were measured in dH2O and phosphate buffered saline (PBS) to compare their performance for possible biomedical applications such as wound dressings. The results reveal that the presence of TEMPO is of importance for TO-SWNF network properties, presenting higher eq. H2O absorption (≈2500 \%) and elongation at break (≈10 \%) with good wet strength (≈180 kPa). In addition, a decrease in use of TEMPO catalyst from 16 to 8 mg g−1 of wood is possible, without detrimental effects on hydrogel network properties (dH2O absorption ≈ 2000 \%, elongation at break ≈ 13 \%, wet strength ≈ 190 kPa) related to applications as wound dressings.},
	urldate = {2024-10-18},
	journal = {Carbohydrate Polymers},
	author = {Baş, Yağmur and Berglund, Linn and Stevanic, Jasna S. and Scheepers, Gerhard and Niittylä, Totte and Oksman, Kristiina},
	month = jan,
	year = {2025},
	keywords = {Absorption, Cellulose nanofibrils, Hydrogel network, TEMPO-oxidation, Wood},
	pages = {122812},
}

From an economic and environmental perspective, the use of less chemicals in the production of cellulose nanofibrils (CNFs) is advantageous. In this study, we investigated the oxidation (TEMPO/NaClO2/NaClO, pH 6.8) of softwood (SW) particles with varying amounts of TEMPO (16, 8 or 0 mg g−1 of wood). Following, TEMPO-oxidized SW nanofibrils (TO-SWNFs) were obtained by nanofibrillation and their size, morphology, and crystallite size were assessed. Hydrogel networks of TO-SWNFs were prepared and mechanical properties were measured in dH2O and phosphate buffered saline (PBS) to compare their performance for possible biomedical applications such as wound dressings. The results reveal that the presence of TEMPO is of importance for TO-SWNF network properties, presenting higher eq. H2O absorption (≈2500 %) and elongation at break (≈10 %) with good wet strength (≈180 kPa). In addition, a decrease in use of TEMPO catalyst from 16 to 8 mg g−1 of wood is possible, without detrimental effects on hydrogel network properties (dH2O absorption ≈ 2000 %, elongation at break ≈ 13 %, wet strength ≈ 190 kPa) related to applications as wound dressings.

@article{feng_plant_2024,
	series = {Focus {Issue} on “{Unique} {Aspects} of {Plant} {Sciences}”},
	title = {Plant grafting: {Molecular} mechanisms and applications},
	volume = {17},
	issn = {1674-2052},
	shorttitle = {Plant grafting},
	url = {https://www.sciencedirect.com/science/article/pii/S1674205223004008},
	doi = {10.1016/j.molp.2023.12.006},
	abstract = {People have grafted plants since antiquity for propagation, to increase yields, and to improve stress tolerance. This cutting and joining of tissues activates an incredible regenerative ability as different plants fuse and grow as one. For over a hundred years, people have studied the scientific basis for how plants graft. Today, new techniques and a deepening knowledge of the molecular basis for graft formation have allowed a range of previously ungraftable combinations to emerge. Here, we review recent developments in our understanding of graft formation, including the attachment and vascular formation steps. We analyze why plants graft and how biotic and abiotic factors influence successful grafting. We also discuss the ability and inability of plants to graft, and how grafting has transformed both horticulture and fundamental plant science. As our knowledge about plant grafting improves, new combinations and techniques will emerge to allow an expanded use of grafting for horticultural applications and to address fundamental research questions.},
	number = {1},
	urldate = {2026-09-07},
	journal = {Molecular Plant},
	author = {Feng, Ming and Augstein, Frauke and Kareem, Abdul and Melnyk, Charles W.},
	month = jan,
	year = {2024},
	keywords = {mobile molecules, plant grafting, regeneration, stress tolerance, tissue adhesion, vascular differentiation},
	pages = {75--91},
}

People have grafted plants since antiquity for propagation, to increase yields, and to improve stress tolerance. This cutting and joining of tissues activates an incredible regenerative ability as different plants fuse and grow as one. For over a hundred years, people have studied the scientific basis for how plants graft. Today, new techniques and a deepening knowledge of the molecular basis for graft formation have allowed a range of previously ungraftable combinations to emerge. Here, we review recent developments in our understanding of graft formation, including the attachment and vascular formation steps. We analyze why plants graft and how biotic and abiotic factors influence successful grafting. We also discuss the ability and inability of plants to graft, and how grafting has transformed both horticulture and fundamental plant science. As our knowledge about plant grafting improves, new combinations and techniques will emerge to allow an expanded use of grafting for horticultural applications and to address fundamental research questions.

@article{serivichyaswat_auxin_2024,
	title = {Auxin signaling in the cambium promotes tissue adhesion and vascular formation during {Arabidopsis} graft healing},
	volume = {196},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiae257},
	doi = {10.1093/plphys/kiae257},
	abstract = {The strong ability of plants to regenerate wounds is exemplified by grafting when two plants are cut and joined together to grow as one. During graft healing, tissues attach, cells proliferate, and the vasculatures connect to form a graft union. The plant hormone auxin plays a central role, and auxin-related mutants perturb grafting success. Here, we investigated the role of individual cell types and their response to auxin during Arabidopsis (Arabidopsis thaliana) graft formation. By employing a cell-specific inducible misexpression system, we blocked auxin response in individual cell types using the bodenlos mutation. We found that auxin signaling in procambial tissues was critical for successful tissue attachment and vascular differentiation. In addition, we found that auxin signaling was required for cell divisions of the procambial cells during graft formation. Loss of function mutants in cambial pathways also perturbed attachment and phloem reconnection. We propose that cambial and procambial tissues drive tissue attachment and vascular differentiation during successful grafting. Our study thus refines our knowledge of graft development and furthers our understanding of the regenerative role of the cambium.},
	number = {2},
	urldate = {2026-09-07},
	journal = {Plant Physiology},
	author = {Serivichyaswat, Phanu T and Kareem, Abdul and Feng, Ming and Melnyk, Charles W},
	month = oct,
	year = {2024},
	pages = {754--762},
}

The strong ability of plants to regenerate wounds is exemplified by grafting when two plants are cut and joined together to grow as one. During graft healing, tissues attach, cells proliferate, and the vasculatures connect to form a graft union. The plant hormone auxin plays a central role, and auxin-related mutants perturb grafting success. Here, we investigated the role of individual cell types and their response to auxin during Arabidopsis (Arabidopsis thaliana) graft formation. By employing a cell-specific inducible misexpression system, we blocked auxin response in individual cell types using the bodenlos mutation. We found that auxin signaling in procambial tissues was critical for successful tissue attachment and vascular differentiation. In addition, we found that auxin signaling was required for cell divisions of the procambial cells during graft formation. Loss of function mutants in cambial pathways also perturbed attachment and phloem reconnection. We propose that cambial and procambial tissues drive tissue attachment and vascular differentiation during successful grafting. Our study thus refines our knowledge of graft development and furthers our understanding of the regenerative role of the cambium.

@article{liu_telomere--telomere_2024,
	title = {Telomere-to-telomere, gap-free assembly of the \textit{{Rosa} rugosa} reference genome},
	issn = {2468-0141},
	url = {https://www.sciencedirect.com/science/article/pii/S2468014124001584},
	doi = {10.1016/j.hpj.2024.06.005},
	abstract = {Rosa, a genus esteemed worldwide for its ornamental plants, has encountered barriers in functional genomic studies and further genetic enhancement due to incomplete sequences and floating regions in previously sequenced genomes. Our groundbreaking study introduced a meticulously assembled, continuous, and fully bridged reference genome for Rosa rugosa, constructed through a sophisticated combination of PacBio High-Fidelity, ONT ultra-long reads, and Hi-C data. This robust assembly spanned 444.55 Mb and encompassed 34 109 protein-coding genes. We have uniquely assembled each chromosome into single, gap-free structures, successfully identifying all 14 telomeres and seven centromeres, a feat not achieved previously. The centromeric regions were distinguished by tandem repeats, primarily composed of centromere-specific 159-bp monomers, and a significant enrichment of ATHILA/Gypsy long terminal repeat retrotransposons in proximal regions. Our research highlighted recent tandem duplications as instrumental in bolstering R. rugosa's stress tolerance, environmental adaptability, and enhanced anthocyanin synthesis. Furthermore, our study ventured into uncharted territory by predicting transcription factors potentially regulating anthocyanin biosynthesis through the employment of gene co-expression networks, providing new avenues for research. This comprehensive reference genome not only serves as a cornerstone for in-depth exploration of genomic architecture and functionalities in R. rugosa but also acts as a catalyst for innovative breeding strategies and genetic refinement within the genus.},
	urldate = {2026-05-29},
	journal = {Horticultural Plant Journal},
	author = {Liu, Dan and Liu, Kun and Tong, Boqiang and Guo, Haili and Qu, Kai and Xu, Ting and Zhang, Rengang and Zhao, Wei and Xie, Xiaoman and Wang, Longxin and Jia, Kaihua},
	month = sep,
	year = {2024},
	keywords = {Anthocyanin biosynthesis, Telomere-to-telomere genome assembly},
}

Rosa, a genus esteemed worldwide for its ornamental plants, has encountered barriers in functional genomic studies and further genetic enhancement due to incomplete sequences and floating regions in previously sequenced genomes. Our groundbreaking study introduced a meticulously assembled, continuous, and fully bridged reference genome for Rosa rugosa, constructed through a sophisticated combination of PacBio High-Fidelity, ONT ultra-long reads, and Hi-C data. This robust assembly spanned 444.55 Mb and encompassed 34 109 protein-coding genes. We have uniquely assembled each chromosome into single, gap-free structures, successfully identifying all 14 telomeres and seven centromeres, a feat not achieved previously. The centromeric regions were distinguished by tandem repeats, primarily composed of centromere-specific 159-bp monomers, and a significant enrichment of ATHILA/Gypsy long terminal repeat retrotransposons in proximal regions. Our research highlighted recent tandem duplications as instrumental in bolstering R. rugosa's stress tolerance, environmental adaptability, and enhanced anthocyanin synthesis. Furthermore, our study ventured into uncharted territory by predicting transcription factors potentially regulating anthocyanin biosynthesis through the employment of gene co-expression networks, providing new avenues for research. This comprehensive reference genome not only serves as a cornerstone for in-depth exploration of genomic architecture and functionalities in R. rugosa but also acts as a catalyst for innovative breeding strategies and genetic refinement within the genus.

@article{feng_dual-trait_2024,
	title = {Dual-trait genomic analysis in highly stratified {Arabidopsis} thaliana populations using genome-wide association summary statistics},
	volume = {133},
	copyright = {2024 The Author(s), under exclusive licence to The Genetics Society},
	issn = {1365-2540},
	url = {https://www.nature.com/articles/s41437-024-00688-z},
	doi = {10.1038/s41437-024-00688-z},
	abstract = {Genome-wide association study (GWAS) is a powerful tool to identify genomic loci underlying complex traits. However, the application in natural populations comes with challenges, especially power loss due to population stratification. Here, we introduce a bivariate analysis approach to a GWAS dataset of Arabidopsis thaliana. We demonstrate the efficiency of dual-phenotype analysis to uncover hidden genetic loci masked by population structure via a series of simulations. In real data analysis, a common allele, strongly confounded with population structure, is discovered to be associated with late flowering and slow maturation of the plant. The discovered genetic effect on flowering time is further replicated in independent datasets. Using Mendelian randomization analysis based on summary statistics from our GWAS and expression QTL scans, we predicted and replicated a candidate gene AT1G11560 that potentially causes this association. Further analysis indicates that this locus is co-selected with flowering-time-related genes. The discovered pleiotropic genotype-phenotype map provides new insights into understanding the genetic correlation of complex traits.},
	language = {en},
	number = {1},
	urldate = {2026-05-19},
	journal = {Heredity},
	publisher = {Nature Publishing Group},
	author = {Feng, Xiao and Zan, Yanjun and Li, Ting and Yao, Yue and Ning, Zheng and Li, Jiabei and Charati, Hadi and Xu, Weilin and Wan, Qianhui and Zeng, Dongyu and Zeng, Ziyi and Liu, Yang and Shen, Xia},
	month = jul,
	year = {2024},
	keywords = {Genome-wide association studies, Population genetics, Quantitative trait},
	pages = {11--20},
}

Genome-wide association study (GWAS) is a powerful tool to identify genomic loci underlying complex traits. However, the application in natural populations comes with challenges, especially power loss due to population stratification. Here, we introduce a bivariate analysis approach to a GWAS dataset of Arabidopsis thaliana. We demonstrate the efficiency of dual-phenotype analysis to uncover hidden genetic loci masked by population structure via a series of simulations. In real data analysis, a common allele, strongly confounded with population structure, is discovered to be associated with late flowering and slow maturation of the plant. The discovered genetic effect on flowering time is further replicated in independent datasets. Using Mendelian randomization analysis based on summary statistics from our GWAS and expression QTL scans, we predicted and replicated a candidate gene AT1G11560 that potentially causes this association. Further analysis indicates that this locus is co-selected with flowering-time-related genes. The discovered pleiotropic genotype-phenotype map provides new insights into understanding the genetic correlation of complex traits.

@article{yu_shinygsgraphical_2024,
	title = {{ShinyGS}—a graphical toolkit with a serial of genetic and machine learning models for genomic selection: application, benchmarking, and recommendations},
	volume = {15},
	issn = {1664-462X},
	shorttitle = {{ShinyGS}—a graphical toolkit with a serial of genetic and machine learning models for genomic selection},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1480902/full},
	doi = {10.3389/fpls.2024.1480902},
	abstract = {Genomic prediction is a powerful approach for improving genetic gain and shortening the breeding cycles in animal and crop breeding programs. A series of statistical and machine learning models has been developed to increase the prediction performance continuously. However, the application of these models requires advanced R programming skills and command-line tools to perform quality control, format input files, and install packages and dependencies, posing challenges for breeders. Here, we present ShinyGS, a stand-alone R Shiny application with a user-friendly interface that allows breeders to perform genomic selection through simple point-and-click actions. This toolkit incorporates 16 methods, including linear models from maximum likelihood and Bayesian framework (BA, BB, BC, BL, and BRR), machine learning models, and a data visualization function. In addition, we benchmarked the performance of all 16 models using multiple populations and traits with varying populations and genetic architecture. Recommendations were given for specific breeding applications. Overall, ShinyGS is a platform-independent software that can be run on all operating systems with a Docker container for quick installation. It is freely available to non-commercial users at Docker Hub (https://hub.docker.com/r/yfd2/ags).},
	language = {English},
	urldate = {2026-05-19},
	journal = {Frontiers in Plant Science},
	publisher = {Frontiers},
	author = {Yu, Le and Dai, Yifei and Zhu, Mingjia and Guo, Linjie and Ji, Yan and Si, Huan and Cheng, Lirui and Zhao, Tao and Zan, Yanjun},
	month = dec,
	year = {2024},
	keywords = {BLUP, breeding, genomic prediction, graphical toolkit, machine learning},
}

Genomic prediction is a powerful approach for improving genetic gain and shortening the breeding cycles in animal and crop breeding programs. A series of statistical and machine learning models has been developed to increase the prediction performance continuously. However, the application of these models requires advanced R programming skills and command-line tools to perform quality control, format input files, and install packages and dependencies, posing challenges for breeders. Here, we present ShinyGS, a stand-alone R Shiny application with a user-friendly interface that allows breeders to perform genomic selection through simple point-and-click actions. This toolkit incorporates 16 methods, including linear models from maximum likelihood and Bayesian framework (BA, BB, BC, BL, and BRR), machine learning models, and a data visualization function. In addition, we benchmarked the performance of all 16 models using multiple populations and traits with varying populations and genetic architecture. Recommendations were given for specific breeding applications. Overall, ShinyGS is a platform-independent software that can be run on all operating systems with a Docker container for quick installation. It is freely available to non-commercial users at Docker Hub (https://hub.docker.com/r/yfd2/ags).

@article{wang_neighbourhood_2024,
	title = {Neighbourhood diversity effects on insect herbivory: {Plant} leaf traits mediate associational resistance},
	volume = {112},
	copyright = {© 2024 The Author(s). Journal of Ecology © 2024 British Ecological Society.},
	issn = {1365-2745},
	shorttitle = {Neighbourhood diversity effects on insect herbivory},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2745.14405},
	doi = {10.1111/1365-2745.14405},
	abstract = {The vulnerability of trees to insect herbivory can be influenced by forest structure and diversity. Associational resistance theory posits that trees surrounded by diverse neighbours are likely to suffer reduced herbivory. However, the underlying mechanisms of this effect are debated, with accumulating evidence suggesting that leaf traits could mediate the strength and direction of the diversity-herbivory relationships. To determine the role of tree trait variation in mediating this relationship, we measured leaf herbivory and nine morphological and nutritional leaf traits known to influence herbivory on 394 focal trees of twelve species cultivated in monocultures and mixtures of four, eight, and sixteen species in a 4-year-old large-scale manipulated tree diversity experiment. A reduction in the proportion of focal trees in species-rich neighbourhoods resulted in increased leaf carbon: nitrogen ratio of focal trees, which mediated a reduction in insect herbivory. Moreover, an increase in plant height apparency, defined as the disparity in total height between a focal tree and its closest neighbours, indirectly amplified herbivory by reducing leaf phosphorus concentration. Synthesis: The study suggests that neighbourhood diversity and physical structure can indirectly affect herbivory on a focal plant by modifying its leaf trait. Accounting for the functional differences between forests could enhance our understanding of diversity–herbivory relationships.},
	language = {en},
	number = {11},
	urldate = {2026-03-18},
	journal = {Journal of Ecology},
	author = {Wang, Zhenyu and Feng, Lixuan and Frew, Adam and Lu, Anqi and Yu, Zaipeng and Huang, Zhiqun},
	year = {2024},
	note = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2745.14405},
	keywords = {NaBEF experiment, associational resistance, biodiversity and ecosystem functioning, plant apparency, plant functional traits, plant-herbivore interactions, subtropical forest},
	pages = {2613--2623},
}

The vulnerability of trees to insect herbivory can be influenced by forest structure and diversity. Associational resistance theory posits that trees surrounded by diverse neighbours are likely to suffer reduced herbivory. However, the underlying mechanisms of this effect are debated, with accumulating evidence suggesting that leaf traits could mediate the strength and direction of the diversity-herbivory relationships. To determine the role of tree trait variation in mediating this relationship, we measured leaf herbivory and nine morphological and nutritional leaf traits known to influence herbivory on 394 focal trees of twelve species cultivated in monocultures and mixtures of four, eight, and sixteen species in a 4-year-old large-scale manipulated tree diversity experiment. A reduction in the proportion of focal trees in species-rich neighbourhoods resulted in increased leaf carbon: nitrogen ratio of focal trees, which mediated a reduction in insect herbivory. Moreover, an increase in plant height apparency, defined as the disparity in total height between a focal tree and its closest neighbours, indirectly amplified herbivory by reducing leaf phosphorus concentration. Synthesis: The study suggests that neighbourhood diversity and physical structure can indirectly affect herbivory on a focal plant by modifying its leaf trait. Accounting for the functional differences between forests could enhance our understanding of diversity–herbivory relationships.

@inproceedings{heuck_elevated_2024,
	address = {Australia},
	title = {Elevated {CO2} concentrations play a major role in influencing the functionality of {AM} fungal communities in agroecosystems},
	url = {https://esa2024.org.au/},
	abstract = {Arbuscular mycorrhizal (AM) fungi are important symbionts of most plants that can enhance nutrient uptake and resistance to abiotic stressors. Considering the potential benefits they offer plants, AM fungi could significantly contribute to sustainable agriculture, particularly as we face new challenges associated with climate change. However, our limited understanding of how agricultural practices affect the diversity and functions of AM fungi under climate change obstructs their effective use. We assessed how AM fungal communities, shaped by organic and conventional farming, influenced Sorghum bicolor performance under elevated CO2 (eCO2), water limitation, and their combination. Plant growth and development was analysed alongside AM fungal community composition using DNA metabarcoding.
Under both, water-limited and non-water-limited conditions, we observed considerable differences between eCO2 and ambient CO2 (aCO2) concentrations. Plants associated with AM fungi from conventional management produced 63\% more biomass under eCO2, while those with AM fungi from organic management produced 39\% more biomass under aCO2. Phosphorus concentrations followed a similar trend, increasing by 48\% under eCO2 and 25\% under aCO2.
Our findings suggest that AM fungi shaped by conventional management offer greater benefits to plants under eCO2, while the reverse is true under aCO2. This may be due to the fast-colonizing fungi of conventional systems more efficiently capitalising on higher carbon availability from plants under eCO2. Our study underscores the pivotal role of agricultural management in shaping the functionality of AM fungal communities for crops under climate change, emphasising the impact of eCO2 on the AM symbiosis.},
	language = {en},
	urldate = {2026-03-17},
	author = {Heuck, Meike Katharina and Powell, Jeff and Kath, Jarrod and Birnbaum, Christina and Frew, Adam},
	month = jan,
	year = {2024},
	note = {Num Pages: 1},
	pages = {319--319},
}

Arbuscular mycorrhizal (AM) fungi are important symbionts of most plants that can enhance nutrient uptake and resistance to abiotic stressors. Considering the potential benefits they offer plants, AM fungi could significantly contribute to sustainable agriculture, particularly as we face new challenges associated with climate change. However, our limited understanding of how agricultural practices affect the diversity and functions of AM fungi under climate change obstructs their effective use. We assessed how AM fungal communities, shaped by organic and conventional farming, influenced Sorghum bicolor performance under elevated CO2 (eCO2), water limitation, and their combination. Plant growth and development was analysed alongside AM fungal community composition using DNA metabarcoding. Under both, water-limited and non-water-limited conditions, we observed considerable differences between eCO2 and ambient CO2 (aCO2) concentrations. Plants associated with AM fungi from conventional management produced 63% more biomass under eCO2, while those with AM fungi from organic management produced 39% more biomass under aCO2. Phosphorus concentrations followed a similar trend, increasing by 48% under eCO2 and 25% under aCO2. Our findings suggest that AM fungi shaped by conventional management offer greater benefits to plants under eCO2, while the reverse is true under aCO2. This may be due to the fast-colonizing fungi of conventional systems more efficiently capitalising on higher carbon availability from plants under eCO2. Our study underscores the pivotal role of agricultural management in shaping the functionality of AM fungal communities for crops under climate change, emphasising the impact of eCO2 on the AM symbiosis.

@article{frew_herbivory-driven_2024,
	title = {Herbivory-driven shifts in arbuscular mycorrhizal fungal community assembly: increased fungal competition and plant phosphorus benefits},
	volume = {241},
	copyright = {© 2023 The Authors. New Phytologist © 2023 New Phytologist Foundation},
	issn = {1469-8137},
	shorttitle = {Herbivory-driven shifts in arbuscular mycorrhizal fungal community assembly},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19474},
	doi = {10.1111/nph.19474},
	language = {en},
	number = {5},
	urldate = {2026-03-17},
	journal = {New Phytologist},
	author = {Frew, Adam and Öpik, Maarja and Oja, Jane and Vahter, Tanel and Hiiesalu, Inga and Aguilar-Trigueros, Carlos A.},
	year = {2024},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19474},
	keywords = {arbuscular mycorrhizal fungal diversity, competition, insect herbivores, microbial communities, phylogenetic diversity},
	pages = {1891--1899},
}

@article{birnbaum_integrating_2024,
	title = {Integrating soil microbial communities into fundamental ecology, conservation, and restoration: examples from {Australia}},
	volume = {241},
	copyright = {© 2023 The Authors. New Phytologist © 2023 New Phytologist Foundation},
	issn = {1469-8137},
	shorttitle = {Integrating soil microbial communities into fundamental ecology, conservation, and restoration},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19440},
	doi = {10.1111/nph.19440},
	language = {en},
	number = {3},
	urldate = {2026-03-17},
	journal = {New Phytologist},
	author = {Birnbaum, Christina and Dearnaley, John and Egidi, Eleonora and Frew, Adam and Hopkins, Anna and Powell, Jeff and Aguilar-Trigueros, Carlos and Liddicoat, Craig and Albornoz, Felipe and Heuck, Meike K. and Dadzie, Frederick A. and Florence, Luke and Singh, Pankaj and Mansfield, Tomas and Rajapaksha, Kumari and Stewart, Jana and Rallo, Paola and Peddle, Shawn D. and Chiarenza, Giancarlo},
	year = {2024},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19440},
	keywords = {Australia, conservation, mycorrhizal fungi, restoration, soil microbes},
	pages = {974--981},
}

@article{frew_community_2024,
	title = {Community assembly of root-colonizing arbuscular mycorrhizal fungi: beyond carbon and into defence?},
	volume = {18},
	issn = {1751-7362},
	shorttitle = {Community assembly of root-colonizing arbuscular mycorrhizal fungi},
	url = {https://doi.org/10.1093/ismejo/wrae007},
	doi = {10.1093/ismejo/wrae007},
	abstract = {The arbuscular mycorrhizal (AM) fungi form symbiotic associations with the majority of terrestrial plants in a relationship estimated to be at least 470 million years old [1]. This symbiosis supported the terrestrialization of plants by facilitating their access to belowground nutrients, such as phosphorus. Today, AM fungi associate with most land plants where, as obligate symbionts, they rely entirely on their hosts for access to carbon as carbohydrates and lipids [2]. Yet the AM symbiosis does not exist in isolation. Simultaneous to AM fungal colonization, almost all plant hosts are subject to foliar damage from herbivores and pathogens. These antagonistic relationships are as ubiquitous as the AM symbiosis itself and have had significant impacts on the evolution and diversification of vegetation [3, 4]. Thus, this complex interplay among AM fungi, plants, and their herbivorous and pathogenic antagonists serves as a key driver in the ecological and evolutionary dynamics not only of the individual partners but also of global ecosystems.},
	number = {1},
	urldate = {2026-03-17},
	journal = {The ISME Journal},
	author = {Frew, Adam and Weinberger, Natascha and Powell, Jeff R and Watts-Williams, Stephanie J and Aguilar-Trigueros, Carlos A},
	month = jan,
	year = {2024},
	pages = {wrae007},
}

The arbuscular mycorrhizal (AM) fungi form symbiotic associations with the majority of terrestrial plants in a relationship estimated to be at least 470 million years old [1]. This symbiosis supported the terrestrialization of plants by facilitating their access to belowground nutrients, such as phosphorus. Today, AM fungi associate with most land plants where, as obligate symbionts, they rely entirely on their hosts for access to carbon as carbohydrates and lipids [2]. Yet the AM symbiosis does not exist in isolation. Simultaneous to AM fungal colonization, almost all plant hosts are subject to foliar damage from herbivores and pathogens. These antagonistic relationships are as ubiquitous as the AM symbiosis itself and have had significant impacts on the evolution and diversification of vegetation [3, 4]. Thus, this complex interplay among AM fungi, plants, and their herbivorous and pathogenic antagonists serves as a key driver in the ecological and evolutionary dynamics not only of the individual partners but also of global ecosystems.

@article{luo_mechanisms_2024,
	title = {Mechanisms of soil organic carbon stabilization and its response to conversion of primary natural broadleaf forests to secondary forests and plantation forests},
	volume = {240},
	issn = {0341-8162},
	url = {https://www.sciencedirect.com/science/article/pii/S0341816224002182},
	doi = {10.1016/j.catena.2024.108021},
	abstract = {Soil organic carbon (SOC) is highly susceptible to land cover change. The assessment of SOC stabilization mechanisms is therefore crucial to understand the carbon (C) dynamic in terrestrial ecosystems. However, the mechanisms underlying the stabilization of SOC following forest conversion of primary natural broadleaf forests (BF) to secondary forests (SF) and plantation forests (PF) remain unclear. Here, we investigated the soil aggregate distribution and associated SOC concentration, and the dynamics of iron (Fe) and aluminum (Al) oxides in BF (24 sites), SF (25 sites), and PF (16 sites) soils in subtropical China. Results showed that SOC concentrations both in the bulk soil and within aggregates significantly decreased when BF were converted to SF and PF, and these reductions were more pronounced in the topsoil (0–10 cm) than those in the subsoil (10–30 cm). Soil macroaggregates ({\textgreater}250 μm) accounted for the largest proportions of aggregate fractions by mass (40.3 \%, 38.9 \%, and 39.4 \%) and their associated SOC decreased with forest conversion and contributed the greatest proportions of C (11.1 g kg−1, 10.2 g kg−1, and 9.6 g kg−1) to the bulk soil C in BF, SF, and PF, respectively, suggesting that the SOC within macroaggregate contributed to the largest decrease in SOC. The decreases in SOC within macroaggregate, especially with the conversion of BF to PF, were mainly ascribed to the reductions of tree biomass, C stocks of litter and root, and the decreases in the concentration of the Fed/Ald and Fep/Alp oxides but not the concentration of total Fe/Al oxides in gravel and soil. These findings recommend that mixtures of suitable native broadleaf species (e.g., BF species) with plantation species to enhance SOC stabilization in PF, thereby improving the stabilization and sequestration of SOC. Overall, these results help explain why soil C stabilization decreases following forest conversion, and propose an approach for the rehabilitation of plantation forests.},
	urldate = {2026-03-17},
	journal = {CATENA},
	author = {Luo, Xianzhen and Zhang, Rui and Zhang, Lingling and Frew, Adam and Yu, Hanxia and Hou, Enqing and Wen, Dazhi},
	month = may,
	year = {2024},
	keywords = {Aggregates, Forest conversion, Iron or aluminum oxides, Organic carbon sequestration, Subtropical forests},
	pages = {108021},
}

Soil organic carbon (SOC) is highly susceptible to land cover change. The assessment of SOC stabilization mechanisms is therefore crucial to understand the carbon (C) dynamic in terrestrial ecosystems. However, the mechanisms underlying the stabilization of SOC following forest conversion of primary natural broadleaf forests (BF) to secondary forests (SF) and plantation forests (PF) remain unclear. Here, we investigated the soil aggregate distribution and associated SOC concentration, and the dynamics of iron (Fe) and aluminum (Al) oxides in BF (24 sites), SF (25 sites), and PF (16 sites) soils in subtropical China. Results showed that SOC concentrations both in the bulk soil and within aggregates significantly decreased when BF were converted to SF and PF, and these reductions were more pronounced in the topsoil (0–10 cm) than those in the subsoil (10–30 cm). Soil macroaggregates (\textgreater250 μm) accounted for the largest proportions of aggregate fractions by mass (40.3 %, 38.9 %, and 39.4 %) and their associated SOC decreased with forest conversion and contributed the greatest proportions of C (11.1 g kg−1, 10.2 g kg−1, and 9.6 g kg−1) to the bulk soil C in BF, SF, and PF, respectively, suggesting that the SOC within macroaggregate contributed to the largest decrease in SOC. The decreases in SOC within macroaggregate, especially with the conversion of BF to PF, were mainly ascribed to the reductions of tree biomass, C stocks of litter and root, and the decreases in the concentration of the Fed/Ald and Fep/Alp oxides but not the concentration of total Fe/Al oxides in gravel and soil. These findings recommend that mixtures of suitable native broadleaf species (e.g., BF species) with plantation species to enhance SOC stabilization in PF, thereby improving the stabilization and sequestration of SOC. Overall, these results help explain why soil C stabilization decreases following forest conversion, and propose an approach for the rehabilitation of plantation forests.

@article{yu_upgrade_2024,
	title = {Upgrade from aerated static pile to agitated bed systems promotes lignocellulose degradation in large-scale composting through enhanced microbial functional diversity},
	volume = {144},
	issn = {1001-0742},
	url = {https://www.sciencedirect.com/science/article/pii/S1001074223004060},
	doi = {10.1016/j.jes.2023.09.008},
	abstract = {Composting presents a viable management solution for lignocellulose-rich municipal solid waste. However, our understanding about the microbial metabolic mechanisms involved in the biodegradation of lignocellulose, particularly in industrial-scale composting plants, remains limited. This study employed metaproteomics to compare the impact of upgrading from aerated static pile (ASP) to agitated bed (AB) systems on physicochemical parameters, lignocellulose biodegradation, and microbial metabolic pathways during large-scale biowaste composting process, marking the first investigation of its kind. The degradation rates of lignocellulose including cellulose, hemicellulose, and lignin were significantly higher in AB (8.21\%-32.54\%, 10.21\%-39.41\%, and 6.21\%-26.78\%) than those (5.72\%-23.15\%, 7.01\%-33.26\%, and 4.79\%-19.76\%) in ASP at three thermal stages, respectively. The AB system in comparison to ASP increased the carbohydrate-active enzymes (CAZymes) abundance and production of the three essential enzymes required for lignocellulose decomposition involving a mixture of bacteria and fungi (i.e., Actinobacteria, Bacilli, Sordariomycetes and Eurotiomycetes). Conversely, ASP primarily produced exoglucanase and β-glucosidase via fungi (i.e., Ascomycota). Moreover, AB effectively mitigated microbial stress caused by acetic acid accumulation by regulating the key enzymes involved in acetate conversion, including acetyl-coenzyme A synthetase and acetate kinase. Overall, the AB upgraded from ASP facilitated the lignocellulose degradation and fostered more diverse functional microbial communities in large-scale composting. Our findings offer a valuable scientific basis to guide the engineering feasibility and environmental sustainability for large-scale industrial composting plants for treating lignocellulose-rich waste. These findings have important implications for establishing green sustainable development models (e.g., a circular economy based on material recovery) and for achieving sustainable development goals.},
	urldate = {2026-03-17},
	journal = {Journal of Environmental Sciences},
	author = {Yu, Hanxia and Xiao, Haoyan and Deng, Huiyu and Frew, Adam and Hossain, Md. Akhter and Tan, Wenbing and Xi, Beidou},
	month = oct,
	year = {2024},
	keywords = {Bacterial and fungal community, Large-scale composting, Lignocellulose degradation, Metaproteomic analysis, Microbial metabolism},
	pages = {55--66},
}

Composting presents a viable management solution for lignocellulose-rich municipal solid waste. However, our understanding about the microbial metabolic mechanisms involved in the biodegradation of lignocellulose, particularly in industrial-scale composting plants, remains limited. This study employed metaproteomics to compare the impact of upgrading from aerated static pile (ASP) to agitated bed (AB) systems on physicochemical parameters, lignocellulose biodegradation, and microbial metabolic pathways during large-scale biowaste composting process, marking the first investigation of its kind. The degradation rates of lignocellulose including cellulose, hemicellulose, and lignin were significantly higher in AB (8.21%-32.54%, 10.21%-39.41%, and 6.21%-26.78%) than those (5.72%-23.15%, 7.01%-33.26%, and 4.79%-19.76%) in ASP at three thermal stages, respectively. The AB system in comparison to ASP increased the carbohydrate-active enzymes (CAZymes) abundance and production of the three essential enzymes required for lignocellulose decomposition involving a mixture of bacteria and fungi (i.e., Actinobacteria, Bacilli, Sordariomycetes and Eurotiomycetes). Conversely, ASP primarily produced exoglucanase and β-glucosidase via fungi (i.e., Ascomycota). Moreover, AB effectively mitigated microbial stress caused by acetic acid accumulation by regulating the key enzymes involved in acetate conversion, including acetyl-coenzyme A synthetase and acetate kinase. Overall, the AB upgraded from ASP facilitated the lignocellulose degradation and fostered more diverse functional microbial communities in large-scale composting. Our findings offer a valuable scientific basis to guide the engineering feasibility and environmental sustainability for large-scale industrial composting plants for treating lignocellulose-rich waste. These findings have important implications for establishing green sustainable development models (e.g., a circular economy based on material recovery) and for achieving sustainable development goals.

@article{field_innovation_2024,
	title = {Innovation in plant and soil sciences to tackle critical global challenges},
	volume = {6},
	copyright = {© 2024 The Authors. Plants, People, Planet published by John Wiley \& Sons Ltd on behalf of New Phytologist Foundation.},
	issn = {2572-2611},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ppp3.10520},
	doi = {10.1002/ppp3.10520},
	abstract = {Innovations in plant and soil sciences are revolutionising our approach to sustainability, offering solutions with broad societal impacts. Discoveries in these fields hold great potential for combatting, mitigating and adapting to climate change; enhancing food security; and revitalising urban environments. By harnessing the power of plants and the soils they grow in, it is possible to cultivate resilience in the face of environmental challenges, informing policy and practice, and thereby guiding us towards a more sustainable future.},
	number = {6},
	urldate = {2026-03-17},
	journal = {PLANTS, PEOPLE, PLANET},
	author = {Field, Katie J. and Carrillo, Yolima and Campbell, Stuart A. and Ton, Jurriaan and Frew, Adam},
	year = {2024},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1002/ppp3.10520},
	keywords = {adaptation, climate change, global challenges, mitigation, plant science, soil science, sustainability},
	pages = {1153--1158},
}

Innovations in plant and soil sciences are revolutionising our approach to sustainability, offering solutions with broad societal impacts. Discoveries in these fields hold great potential for combatting, mitigating and adapting to climate change; enhancing food security; and revitalising urban environments. By harnessing the power of plants and the soils they grow in, it is possible to cultivate resilience in the face of environmental challenges, informing policy and practice, and thereby guiding us towards a more sustainable future.

@article{heuck_evaluating_2024,
	title = {Evaluating the {Usefulness} of the {C}-{S}-{R} {Framework} for {Understanding} {AM} {Fungal} {Responses} to {Climate} {Change} in {Agroecosystems}},
	volume = {30},
	copyright = {© 2024 John Wiley \& Sons Ltd.},
	issn = {1365-2486},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.17566},
	doi = {10.1111/gcb.17566},
	abstract = {Arbuscular mycorrhizal (AM) fungi play a key role in terrestrial ecosystems by forming symbiotic relationships with plants and may confer benefits for sustainable agriculture, by reducing reliance on harmful fertiliser and pesticide inputs and enhancing plant resilience against insect herbivores. Despite their ecological importance, critical gaps in understanding AM fungal ecology limit predictions of their responses to global change in agroecosystems. However, predicting climate change impacts on AM fungi is important for maintaining crop productivity and ecosystem stability. Efforts to classify AM fungi based on functional traits, such as the competitor, stress-tolerator, ruderal (C-S-R) framework, aim to address these gaps but face challenges due to the obligate symbiotic nature of the fungi. As the framework is still widely used, we evaluate its applicability in predicting global change impacts on AM fungal communities in agroecosystems. Chagnon's adaptation of the C-S-R framework for AM fungi aligns with some study outcomes (e.g., under the context of water limitation) but faces challenges when used in complex climate change scenarios, varying agricultural conditions and/or extreme climatic conditions. The reliance on a limited dataset to classify AM fungal families further limits accurate predictions of AM fungal community dynamics. Trait data collection could support a nuanced understanding of AM fungi and leveraging AM fungal databases could streamline data management and analysis, enhancing efforts to clarify AM fungal responses to environmental change and guide ecosystem management practices. Thus, while the C-S-R framework holds promise, it requires additional AM fungal trait data for validation and improvement of its predictive power. Conclusively, before designing experiments based on life-history strategies and developing new frameworks tailored to AM fungi a critical first step is to gain a comprehensive understanding of their traits.},
	language = {en},
	number = {11},
	urldate = {2026-03-17},
	journal = {Global Change Biology},
	author = {Heuck, Meike Katharina and Powell, Jeff R. and Kath, Jarrod and Birnbaum, Christina and Frew, Adam},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.17566},
	keywords = {AM fungal traits, Arbuscular mycorrhizal fungi, C-S-R framework, agriculture, climate change, life-history strategies},
	pages = {e17566},
}

Arbuscular mycorrhizal (AM) fungi play a key role in terrestrial ecosystems by forming symbiotic relationships with plants and may confer benefits for sustainable agriculture, by reducing reliance on harmful fertiliser and pesticide inputs and enhancing plant resilience against insect herbivores. Despite their ecological importance, critical gaps in understanding AM fungal ecology limit predictions of their responses to global change in agroecosystems. However, predicting climate change impacts on AM fungi is important for maintaining crop productivity and ecosystem stability. Efforts to classify AM fungi based on functional traits, such as the competitor, stress-tolerator, ruderal (C-S-R) framework, aim to address these gaps but face challenges due to the obligate symbiotic nature of the fungi. As the framework is still widely used, we evaluate its applicability in predicting global change impacts on AM fungal communities in agroecosystems. Chagnon's adaptation of the C-S-R framework for AM fungi aligns with some study outcomes (e.g., under the context of water limitation) but faces challenges when used in complex climate change scenarios, varying agricultural conditions and/or extreme climatic conditions. The reliance on a limited dataset to classify AM fungal families further limits accurate predictions of AM fungal community dynamics. Trait data collection could support a nuanced understanding of AM fungi and leveraging AM fungal databases could streamline data management and analysis, enhancing efforts to clarify AM fungal responses to environmental change and guide ecosystem management practices. Thus, while the C-S-R framework holds promise, it requires additional AM fungal trait data for validation and improvement of its predictive power. Conclusively, before designing experiments based on life-history strategies and developing new frameworks tailored to AM fungi a critical first step is to gain a comprehensive understanding of their traits.

@article{frew_increasing_2024,
	title = {Increasing {Phylogenetic} {Clustering} of {Arbuscular} {Mycorrhizal} {Fungal} {Communities} in {Roots} {Explains} {Enhanced} {Plant} {Growth} and {Phosphorus} {Uptake}},
	volume = {87},
	issn = {1432-184X},
	url = {https://doi.org/10.1007/s00248-024-02457-1},
	doi = {10.1007/s00248-024-02457-1},
	abstract = {Temporal variation during the assembly of arbuscular mycorrhizal (AM) fungal communities within plant roots have been posited as critical drivers of the plant-fungal symbiotic outcomes. However, functional implications of these dynamics for the host plant remain poorly understood. We conducted a controlled pot experiment with Sorghum bicolor to investigate how temporal shifts in AM fungal community composition and phylogenetic diversity influence plant growth and phosphorus responses to the symbiosis. We characterised the root-colonising AM fungal communities across three time points and explored their community assembly processes by analysing their phylogenetic diversity and employing joint species distribution modelling with the Hierarchical Modelling of Species Communities (HMSC) framework. We found strong AM fungal turnover through time with a high phylogenetic signal, indicating recruitment of phylogenetically clustered AM fungal species in the host. This temporal phylogenetic clustering of communities coincided with marked increases in plant biomass and phosphorus responses to the AM fungal symbiosis, suggesting that host selection for specific fungi may be a key determinant of these benefits.},
	language = {en},
	number = {1},
	urldate = {2026-03-17},
	journal = {Microbial Ecology},
	author = {Frew, Adam and Aguilar-Trigueros, Carlos A.},
	month = nov,
	year = {2024},
	keywords = {Arbuscular mycorrhiza, Community assembly, Phylogenetic diversity, Sorghum bicolor},
	pages = {139},
}

Temporal variation during the assembly of arbuscular mycorrhizal (AM) fungal communities within plant roots have been posited as critical drivers of the plant-fungal symbiotic outcomes. However, functional implications of these dynamics for the host plant remain poorly understood. We conducted a controlled pot experiment with Sorghum bicolor to investigate how temporal shifts in AM fungal community composition and phylogenetic diversity influence plant growth and phosphorus responses to the symbiosis. We characterised the root-colonising AM fungal communities across three time points and explored their community assembly processes by analysing their phylogenetic diversity and employing joint species distribution modelling with the Hierarchical Modelling of Species Communities (HMSC) framework. We found strong AM fungal turnover through time with a high phylogenetic signal, indicating recruitment of phylogenetically clustered AM fungal species in the host. This temporal phylogenetic clustering of communities coincided with marked increases in plant biomass and phosphorus responses to the AM fungal symbiosis, suggesting that host selection for specific fungi may be a key determinant of these benefits.

@article{mcevoy_reference_2024,
	title = {The reference genome of an endangered {Asteraceae}, {Deinandra} increscens subsp. villosa, endemic to the {Central} {Coast} of {California}},
	volume = {14},
	issn = {2160-1836},
	url = {https://doi.org/10.1093/g3journal/jkae117},
	doi = {10.1093/g3journal/jkae117},
	abstract = {We present a reference genome for the federally endangered Gaviota tarplant, Deinandra increscens subsp. villosa (Madiinae, Asteraceae), an annual herb endemic to the Central California coast. Generating PacBio HiFi, Oxford Nanopore Technologies, and Dovetail Omni-C data, we assembled a haploid consensus genome of 1.67 Gb as 28.7 K scaffolds with a scaffold N50 of 74.9 Mb. We annotated repeat content in 74.8\% of the genome. Long terminal repeats (LTRs) covered 44.0\% of the genome with Copia families predominant at 22.9\% followed by Gypsy at 14.2\%. Both Gypsy and Copia elements were common in ancestral peaks of LTRs, and the most abundant element was a Gypsy element containing nested Copia/Angela sequence similarity, reflecting a complex evolutionary history of repeat activity. Gene annotation produced 33,257 genes and 68,942 transcripts, of which 99\% were functionally annotated. BUSCO scores for the annotated proteins were 96.0\% complete of which 77.6\% was single copy and 18.4\% duplicates. Whole genome duplication synonymous mutation rates of Gaviota tarplant and sunflower (Helianthus annuus) shared peaks that correspond to the last Asteraceae polyploidization event and subsequent divergence from a common ancestor at ∼27 MYA. Regions of high-density tandem genes were identified, pointing to potentially important loci of environmental adaptation in this species.},
	number = {8},
	urldate = {2025-11-12},
	journal = {G3 Genes Genomes Genetics},
	author = {McEvoy, Susan L and Meyer, Rachel S and Hasenstab-Lehman, Kristen E and Guilliams, C Matt},
	month = aug,
	year = {2024},
	pages = {jkae117},
}

We present a reference genome for the federally endangered Gaviota tarplant, Deinandra increscens subsp. villosa (Madiinae, Asteraceae), an annual herb endemic to the Central California coast. Generating PacBio HiFi, Oxford Nanopore Technologies, and Dovetail Omni-C data, we assembled a haploid consensus genome of 1.67 Gb as 28.7 K scaffolds with a scaffold N50 of 74.9 Mb. We annotated repeat content in 74.8% of the genome. Long terminal repeats (LTRs) covered 44.0% of the genome with Copia families predominant at 22.9% followed by Gypsy at 14.2%. Both Gypsy and Copia elements were common in ancestral peaks of LTRs, and the most abundant element was a Gypsy element containing nested Copia/Angela sequence similarity, reflecting a complex evolutionary history of repeat activity. Gene annotation produced 33,257 genes and 68,942 transcripts, of which 99% were functionally annotated. BUSCO scores for the annotated proteins were 96.0% complete of which 77.6% was single copy and 18.4% duplicates. Whole genome duplication synonymous mutation rates of Gaviota tarplant and sunflower (Helianthus annuus) shared peaks that correspond to the last Asteraceae polyploidization event and subsequent divergence from a common ancestor at ∼27 MYA. Regions of high-density tandem genes were identified, pointing to potentially important loci of environmental adaptation in this species.

@incollection{pesquet_bulk_2024,
	address = {New York, NY},
	title = {Bulk and {In} {Situ} {Quantification} of {Coniferaldehyde} {Residues} in {Lignin}},
	isbn = {978-1-0716-3477-6},
	url = {https://doi.org/10.1007/978-1-0716-3477-6_14},
	doi = {10.1007/978-1-0716-3477-6_14},
	abstract = {Lignin is a group of cell wall localised heterophenolic polymers varying in the chemistry of the aromatic and aliphatic parts of its units. The lignin residues common to all vascular plants have an aromatic ring with one para hydroxy group and one meta methoxy group, also called guaiacyl (G). The terminal function of the aliphatic part of these G units, however, varies from alcohols, which are generally abundant, to aldehydes, which represent a smaller proportion of lignin monomers. The proportions of aldehyde to alcohol G units in lignin are, nevertheless, precisely controlled to respond to environmental and development cues. These G aldehyde to alcohol unit proportions differ between each cell wall layer of each cell type to fine-tune the cell wall biomechanical and physico-chemical properties. To precisely determine changes in lignin composition, we, herein, describe the various methods to detect and quantify the levels and positions of G aldehyde units, also called coniferaldehyde residues, of lignin polymers in ground plant samples as well as in situ in histological cross-sections.},
	language = {en},
	urldate = {2026-01-30},
	booktitle = {Xylem: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Pesquet, Edouard and Blaschek, Leonard and Takahashi, Junko and Yamamoto, Masanobu and Champagne, Antoine and {Nuoendagula} and Subbotina, Elena and Dimotakis, Charilaos and Bacisk, Zoltán and Kajita, Shinya},
	editor = {Agusti, Javier},
	year = {2024},
	keywords = {Coniferaldehyde residues, In situ quantitative chemical imaging, Lignin, Pyrolysis-GC/MS, Raman microspectroscopy, Thioacidolysis-GC/MS, Wiesner test, Xylem cell types},
	pages = {201--226},
}

Lignin is a group of cell wall localised heterophenolic polymers varying in the chemistry of the aromatic and aliphatic parts of its units. The lignin residues common to all vascular plants have an aromatic ring with one para hydroxy group and one meta methoxy group, also called guaiacyl (G). The terminal function of the aliphatic part of these G units, however, varies from alcohols, which are generally abundant, to aldehydes, which represent a smaller proportion of lignin monomers. The proportions of aldehyde to alcohol G units in lignin are, nevertheless, precisely controlled to respond to environmental and development cues. These G aldehyde to alcohol unit proportions differ between each cell wall layer of each cell type to fine-tune the cell wall biomechanical and physico-chemical properties. To precisely determine changes in lignin composition, we, herein, describe the various methods to detect and quantify the levels and positions of G aldehyde units, also called coniferaldehyde residues, of lignin polymers in ground plant samples as well as in situ in histological cross-sections.

@article{mudgal_cyclic_2024,
	title = {Cyclic di-{AMP} regulates genome stability and drug resistance in {Mycobacterium} through {RecA}-dependent and {RecA}-independent recombination},
	volume = {3},
	issn = {2752-6542},
	url = {https://doi.org/10.1093/pnasnexus/pgae555},
	doi = {10.1093/pnasnexus/pgae555},
	abstract = {In Escherichia coli, RecA plays a central role in the rescue of stalled replication forks, double-strand break (DSB) repair, homologous recombination (HR), and induction of the SOS response. While the RecA-dependent pathway is dominant, alternative HR pathways that function independently of RecA do exist, but relatively little is known about the underlying mechanism. Several studies have documented that a variety of proteins act as either positive or negative regulators of RecA to ensure high-fidelity HR and genomic stability. Along these lines, we previously demonstrated that the second messenger cyclic di-AMP (c-di-AMP) binds to mycobacterial RecA proteins, but not to E. coli RecA, and inhibits its DNA strand exchange activity in vitro via the disassembly of RecA nucleoprotein filaments. Herein, we demonstrate that Mycobacterium smegmatis ΔdisA cells, which lack c-di-AMP, exhibit increased DNA recombination, higher frequency of mutation, and gene duplications during RecA-dependent and RecA-independent DSB repair. We also found that c-di-AMP regulates SOS response by inhibiting RecA-mediated self-cleavage of LexA repressor and its absence enhances drug resistance in M. smegmatis ΔdisA cells. Together, our results uncover a role of c-di-AMP in the maintenance of genomic stability through modulation of DSB repair in M. smegmatis.},
	number = {12},
	urldate = {2025-12-05},
	journal = {PNAS Nexus},
	author = {Mudgal, Sudhanshu and Goyal, Nisha and Kasi, Manikandan and Saginela, Rahul and Singhal, Anusha and Nandi, Soumyadeep and Mahmud, A K M Firoj and Muniyappa, Kalappa and Sinha, Krishna Murari},
	month = dec,
	year = {2024},
	pages = {pgae555},
}

In Escherichia coli, RecA plays a central role in the rescue of stalled replication forks, double-strand break (DSB) repair, homologous recombination (HR), and induction of the SOS response. While the RecA-dependent pathway is dominant, alternative HR pathways that function independently of RecA do exist, but relatively little is known about the underlying mechanism. Several studies have documented that a variety of proteins act as either positive or negative regulators of RecA to ensure high-fidelity HR and genomic stability. Along these lines, we previously demonstrated that the second messenger cyclic di-AMP (c-di-AMP) binds to mycobacterial RecA proteins, but not to E. coli RecA, and inhibits its DNA strand exchange activity in vitro via the disassembly of RecA nucleoprotein filaments. Herein, we demonstrate that Mycobacterium smegmatis ΔdisA cells, which lack c-di-AMP, exhibit increased DNA recombination, higher frequency of mutation, and gene duplications during RecA-dependent and RecA-independent DSB repair. We also found that c-di-AMP regulates SOS response by inhibiting RecA-mediated self-cleavage of LexA repressor and its absence enhances drug resistance in M. smegmatis ΔdisA cells. Together, our results uncover a role of c-di-AMP in the maintenance of genomic stability through modulation of DSB repair in M. smegmatis.

@article{mcevoy_profiling_2024,
	title = {Profiling genome-wide methylation in two maples: {Fine}-scale approaches to detection with nanopore technology},
	volume = {17},
	copyright = {© 2024 The Authors. Evolutionary Applications published by John Wiley \& Sons Ltd.},
	issn = {1752-4571},
	shorttitle = {Profiling genome-wide methylation in two maples},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.13669},
	doi = {10.1111/eva.13669},
	abstract = {DNA methylation is critical to the regulation of transposable elements and gene expression and can play an important role in the adaptation of stress response mechanisms in plants. Traditional methods of methylation quantification rely on bisulfite conversion that can compromise accuracy. Recent advances in long-read sequencing technologies allow for methylation detection in real time. The associated algorithms that interpret these modifications have evolved from strictly statistical approaches to Hidden Markov Models and, recently, deep learning approaches. Much of the existing software focuses on methylation in the CG context, but methylation in other contexts is important to quantify, as it is extensively leveraged in plants. Here, we present methylation profiles for two maple species across the full range of 5mC sequence contexts using Oxford Nanopore Technologies (ONT) long-reads. Hybrid and reference-guided assemblies were generated for two new Acer accessions: Acer negundo (box elder; 65x ONT and 111X Illumina) and Acer saccharum (sugar maple; 93x ONT and 148X Illumina). The ONT reads generated for these assemblies were re-basecalled, and methylation detection was conducted in a custom pipeline with the published Acer references (PacBio assemblies) and hybrid assemblies reported herein to generate four epigenomes. Examination of the transposable element landscape revealed the dominance of LTR Copia elements and patterns of methylation associated with different classes of TEs. Methylation distributions were examined at high resolution across gene and repeat density and described within the broader angiosperm context, and more narrowly in the context of gene family dynamics and candidate nutrient stress genes.},
	language = {en},
	number = {4},
	urldate = {2025-11-12},
	journal = {Evolutionary Applications},
	author = {McEvoy, Susan L. and Grady, Patrick G. S. and Pauloski, Nicole and O'Neill, Rachel J. and Wegrzyn, Jill L.},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.13669},
	keywords = {Acer negundo, Acer saccharum, methylome, nanopore, nutrient stress, transposable elements},
	pages = {e13669},
}

DNA methylation is critical to the regulation of transposable elements and gene expression and can play an important role in the adaptation of stress response mechanisms in plants. Traditional methods of methylation quantification rely on bisulfite conversion that can compromise accuracy. Recent advances in long-read sequencing technologies allow for methylation detection in real time. The associated algorithms that interpret these modifications have evolved from strictly statistical approaches to Hidden Markov Models and, recently, deep learning approaches. Much of the existing software focuses on methylation in the CG context, but methylation in other contexts is important to quantify, as it is extensively leveraged in plants. Here, we present methylation profiles for two maple species across the full range of 5mC sequence contexts using Oxford Nanopore Technologies (ONT) long-reads. Hybrid and reference-guided assemblies were generated for two new Acer accessions: Acer negundo (box elder; 65x ONT and 111X Illumina) and Acer saccharum (sugar maple; 93x ONT and 148X Illumina). The ONT reads generated for these assemblies were re-basecalled, and methylation detection was conducted in a custom pipeline with the published Acer references (PacBio assemblies) and hybrid assemblies reported herein to generate four epigenomes. Examination of the transposable element landscape revealed the dominance of LTR Copia elements and patterns of methylation associated with different classes of TEs. Methylation distributions were examined at high resolution across gene and repeat density and described within the broader angiosperm context, and more narrowly in the context of gene family dynamics and candidate nutrient stress genes.

@article{alonso-serra_water_2024,
	title = {Water fluxes pattern growth and identity in shoot meristems},
	volume = {15},
	copyright = {2024 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-024-51099-x},
	doi = {10.1038/s41467-024-51099-x},
	abstract = {In multicellular organisms, tissue outgrowth creates a new water sink, modifying local hydraulic patterns. Although water fluxes are often considered passive by-products of development, their contribution to morphogenesis remains largely unexplored. Here, we mapped cell volumetric growth across the shoot apex in Arabidopsis thaliana. We found that, as organs grow, a subpopulation of cells at the organ-meristem boundary shrinks. Growth simulations using a model that integrates hydraulics and mechanics revealed water fluxes and predicted a water deficit for boundary cells. In planta, a water-soluble dye preferentially allocated to fast-growing tissues and failed to enter the boundary domain. Cell shrinkage next to fast-growing domains was also robust to different growth conditions and different topographies. Finally, a molecular signature of water deficit at the boundary confirmed our conclusion. Taken together, we propose that the differential sink strength of emerging organs prescribes the hydraulic patterns that define boundary domains at the shoot apex.},
	language = {en},
	number = {1},
	urldate = {2025-10-08},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Alonso-Serra, Juan and Cheddadi, Ibrahim and Kiss, Annamaria and Cerutti, Guillaume and Lang, Marianne and Dieudonné, Sana and Lionnet, Claire and Godin, Christophe and Hamant, Olivier},
	month = aug,
	year = {2024},
	keywords = {Computational biophysics, Patterning, Plant morphogenesis},
	pages = {6944},
}

In multicellular organisms, tissue outgrowth creates a new water sink, modifying local hydraulic patterns. Although water fluxes are often considered passive by-products of development, their contribution to morphogenesis remains largely unexplored. Here, we mapped cell volumetric growth across the shoot apex in Arabidopsis thaliana. We found that, as organs grow, a subpopulation of cells at the organ-meristem boundary shrinks. Growth simulations using a model that integrates hydraulics and mechanics revealed water fluxes and predicted a water deficit for boundary cells. In planta, a water-soluble dye preferentially allocated to fast-growing tissues and failed to enter the boundary domain. Cell shrinkage next to fast-growing domains was also robust to different growth conditions and different topographies. Finally, a molecular signature of water deficit at the boundary confirmed our conclusion. Taken together, we propose that the differential sink strength of emerging organs prescribes the hydraulic patterns that define boundary domains at the shoot apex.

@article{routier_investigating_2024,
	title = {Investigating the {Effect} of {Syringe} {Infiltration} on {Nicotiana} tabacum ({Tobacco})},
	volume = {5},
	issn = {2692-1952},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11752493/},
	doi = {10.1021/acsagscitech.4c00170},
	abstract = {, Plant infiltration techniques, particularly agroinfiltration,
have
transformed plant science and biotechnology by enabling transient
gene expression for genetic engineering of plants or genomic studies.
Recently, the use of infiltration has expanded to introduce nanomaterials
and polymers in plants to enable nonnative functionalities. Despite
its wide use, the impact of the infiltration process per se on plant physiology needs to be better understood. This study investigates
the effect of syringe infiltration, a commonly employed technique
in plants, using a typical infiltration buffer solution. Noninvasive
and real-time monitoring methods, including high-resolution thermal
imaging and a porometer/fluorometer, were used to study the physiological
responses and stress levels of the infiltrated plants. Our results
revealed localized cell damage at the infiltration site due to syringe
compression, but the overall cell viability and tissue integrity were
largely unaffected. Thermography showed a temporary temperature increase
of the leaves and stomatal conductance alterations postinfiltration,
with leaf recovery in 3–6 days. Additionally, fluorescence
measurements indicated a 6\% decrease in maximum quantum efficiency
(Fv/Fm) and
a 34\% decrease in photosystem II (ΦPSII) quantum yield, persisting
for 5 days after infiltration, suggesting sustained photosystem efficiency
changes. Our work highlights the need to consider the effect of infiltration
when performing biological studies and aims to facilitate the optimization
of protocols commonly used in plant science and biotechnology.},
	number = {1},
	urldate = {2025-01-31},
	journal = {ACS Agricultural Science \& Technology},
	author = {Routier, Cyril and Hermida-Carrera, Carmen and Stavrinidou, Eleni},
	month = dec,
	year = {2024},
	pages = {28--35},
}

, Plant infiltration techniques, particularly agroinfiltration, have transformed plant science and biotechnology by enabling transient gene expression for genetic engineering of plants or genomic studies. Recently, the use of infiltration has expanded to introduce nanomaterials and polymers in plants to enable nonnative functionalities. Despite its wide use, the impact of the infiltration process per se on plant physiology needs to be better understood. This study investigates the effect of syringe infiltration, a commonly employed technique in plants, using a typical infiltration buffer solution. Noninvasive and real-time monitoring methods, including high-resolution thermal imaging and a porometer/fluorometer, were used to study the physiological responses and stress levels of the infiltrated plants. Our results revealed localized cell damage at the infiltration site due to syringe compression, but the overall cell viability and tissue integrity were largely unaffected. Thermography showed a temporary temperature increase of the leaves and stomatal conductance alterations postinfiltration, with leaf recovery in 3–6 days. Additionally, fluorescence measurements indicated a 6% decrease in maximum quantum efficiency (Fv/Fm) and a 34% decrease in photosystem II (ΦPSII) quantum yield, persisting for 5 days after infiltration, suggesting sustained photosystem efficiency changes. Our work highlights the need to consider the effect of infiltration when performing biological studies and aims to facilitate the optimization of protocols commonly used in plant science and biotechnology.

@article{li_unravelling_2024,
	title = {Unravelling the novel sex determination genotype with ‘{ZY}’ and a distinctive 2.15–2.95 {Mb} inversion among poplar species through haplotype-resolved genome assembly and comparative genomics analysis},
	volume = {24},
	copyright = {© 2024 John Wiley \& Sons Ltd.},
	issn = {1755-0998},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.14002},
	doi = {10.1111/1755-0998.14002},
	abstract = {Populus tomentosa, an indigenous tree species, is widely distributed and cultivated over 1,000,000 km2 in China, contributing significantly to forest production, ecological conservation and urban–rural greening. Although a reference genome is available for P. tomentosa, the intricate interspecific hybrid origins, chromosome structural variations (SVs) and sex determination mechanisms remain confusion and unclear due to its broad and even overlapping geographical distribution, extensive morphological variations and cross infiltration among white poplar species. We conducted a haplotype-resolved de novo assembly of P. tomentosa elite individual GM107, which comprises subgenomes a and b with a total genome size of 714.9 Mb. We then analysed the formation of hybrid species and the phylogenetic evolution and sex differentiation across the entire genus. Phylogenomic analyses suggested that GM107 likely originated from a hybridisation event between P. alba (♀) and P. davidiana (♂) which diverged at approximately 3.8 Mya. A total of 1551 chromosome SVs were identified between the two subgenomes. More noteworthily, a distinctive inversion structure spanning 2.15–2.95 Mb was unveiled among Populus, Tacamahaca, Turaga, Aigeiros poplar species and Salix, highlighting a unique evolutionary feature. Intriguingly, a novel sex genotype of the ZY type, which represents a crossover between XY and ZW systems, was identified and confirmed through both natural and artificial hybrids populations. These novel insights offer significant theoretical value for the study of the species' evolutionary origins and serve as a valuable resource for ecological genetics and forest biotechnology.},
	language = {en},
	number = {7},
	urldate = {2024-08-09},
	journal = {Molecular Ecology Resources},
	author = {Li, Juan and Chen, Tingting and Gao, Kai and Xue, Yinxuan and Wu, Ruqian and Guo, Bin and Chen, Zhong and Li, Shanwen and Zhang, Ren-Gang and Jia, Kai-Hua and Mao, Jian-Feng and An, Xinmin},
	month = oct,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.14002},
	keywords = {Populus tomentosa, chromosome structural variations, haplotype-resolved genome assembly, interspecific hybrid, parental origin, sex determination},
	pages = {e14002},
}

Populus tomentosa, an indigenous tree species, is widely distributed and cultivated over 1,000,000 km2 in China, contributing significantly to forest production, ecological conservation and urban–rural greening. Although a reference genome is available for P. tomentosa, the intricate interspecific hybrid origins, chromosome structural variations (SVs) and sex determination mechanisms remain confusion and unclear due to its broad and even overlapping geographical distribution, extensive morphological variations and cross infiltration among white poplar species. We conducted a haplotype-resolved de novo assembly of P. tomentosa elite individual GM107, which comprises subgenomes a and b with a total genome size of 714.9 Mb. We then analysed the formation of hybrid species and the phylogenetic evolution and sex differentiation across the entire genus. Phylogenomic analyses suggested that GM107 likely originated from a hybridisation event between P. alba (♀) and P. davidiana (♂) which diverged at approximately 3.8 Mya. A total of 1551 chromosome SVs were identified between the two subgenomes. More noteworthily, a distinctive inversion structure spanning 2.15–2.95 Mb was unveiled among Populus, Tacamahaca, Turaga, Aigeiros poplar species and Salix, highlighting a unique evolutionary feature. Intriguingly, a novel sex genotype of the ZY type, which represents a crossover between XY and ZW systems, was identified and confirmed through both natural and artificial hybrids populations. These novel insights offer significant theoretical value for the study of the species' evolutionary origins and serve as a valuable resource for ecological genetics and forest biotechnology.

@article{tunnermann_plant_2024,
	title = {Plant organic nitrogen nutrition: costs, benefits, and carbon use efficiency},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	shorttitle = {Plant organic nitrogen nutrition},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20285},
	doi = {10.1111/nph.20285},
	abstract = {Differences in soil mobility and assimilation costs between organic and inorganic nitrogen (N) compounds would hypothetically induce plant phenotypic plasticity to optimize acquisition of, and performance on, the different N forms. Here we evaluated this hypothesis experimentally and theoretically. We grew Arabidopsis in split-root setups combined with stable isotope labelling to study uptake and distribution of carbon (C) and N from l-glutamine (l-gln) and NO3− and assessed the effect of the N source on biomass partitioning and carbon use efficiency (CUE). Analyses of stable isotopes showed that 40–48\% of C acquired from l-gln resided in plants, contributing 7–8\% to total C of both shoots and roots. Plants grown on l-gln exhibited increased root mass fraction and root hair length and a significantly lower N uptake rate per unit root biomass but displayed significantly enhanced CUE. Our data suggests that organic N nutrition is linked to a particular phenotype with extensive growth of roots and root hairs that optimizes for uptake of less mobile N forms. Increased CUE and lower N uptake per unit root growth may be key facets linked to the organic N phenotype.},
	language = {en},
	urldate = {2024-11-22},
	journal = {New Phytologist},
	author = {Tünnermann, Laura and Aguetoni Cambui, Camila and Franklin, Oskar and Merkel, Patrizia and Näsholm, Torgny and Gratz, Regina},
	month = nov,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20285},
	keywords = {Arabidopsis thaliana, amino acids, carbon use efficiency, glutamine, organic nitrogen, root hair},
}

Differences in soil mobility and assimilation costs between organic and inorganic nitrogen (N) compounds would hypothetically induce plant phenotypic plasticity to optimize acquisition of, and performance on, the different N forms. Here we evaluated this hypothesis experimentally and theoretically. We grew Arabidopsis in split-root setups combined with stable isotope labelling to study uptake and distribution of carbon (C) and N from l-glutamine (l-gln) and NO3− and assessed the effect of the N source on biomass partitioning and carbon use efficiency (CUE). Analyses of stable isotopes showed that 40–48% of C acquired from l-gln resided in plants, contributing 7–8% to total C of both shoots and roots. Plants grown on l-gln exhibited increased root mass fraction and root hair length and a significantly lower N uptake rate per unit root biomass but displayed significantly enhanced CUE. Our data suggests that organic N nutrition is linked to a particular phenotype with extensive growth of roots and root hairs that optimizes for uptake of less mobile N forms. Increased CUE and lower N uptake per unit root growth may be key facets linked to the organic N phenotype.

@article{stal_potential_2024,
	title = {Potential consequences of a rapid transition from rotation forestry to continous cover forestry in {Sweden}},
	volume = {0},
	issn = {0282-7581},
	url = {https://doi.org/10.1080/02827581.2024.2437409},
	doi = {10.1080/02827581.2024.2437409},
	abstract = {In the EU Forest Strategy for 2030 continuous cover forestry (CCF) is promoted, while rotation forestry (RF) is recommended only if required by forest health or environmental reasons. RF is the current practice on about two thirds of the EU forests. The envisioned shift toward CCF will have significant implications for Europe's forests and the industries. Using Sweden as a case, we simulated two scenarios: RF as a continued practice and a rapid transition to CCF. The results show that RF would ensure an even wood flow and slightly increasing harvest levels over the 50 years period. In contrast, the annual harvest in CCF exhibited significant variation, ranging from 50\% to 108\% of the RF harvest in the same year. This variation in harvest outcomes for CCF can be largely attributed to both economic and legal constraints during the transition from RF to CCF. As a result, the growing stock in CCF increased, allowing the forest to serve as a significant carbon sink. During the transition period, the ratio of pulpwood to sawlogs fluctuated for CCF, while it remained stable for RF. Consequently, the volume of sawlogs harvested under CCF was 86\% of that harvested under RF.},
	number = {0},
	urldate = {2025-01-10},
	journal = {Scandinavian Journal of Forest Research},
	publisher = {Taylor \& Francis},
	author = {Stål, Gustav and Nordin, Annika and Wikberg, Per-Erik and Arnesson Ceder, Lina and Lundmark, Tomas},
	month = dec,
	year = {2024},
	note = {\_eprint: https://doi.org/10.1080/02827581.2024.2437409},
	keywords = {Continuous cover forestry, EU forest strategy, closer to nature, forest management, rotation forestry, transition},
	pages = {1--10},
}

In the EU Forest Strategy for 2030 continuous cover forestry (CCF) is promoted, while rotation forestry (RF) is recommended only if required by forest health or environmental reasons. RF is the current practice on about two thirds of the EU forests. The envisioned shift toward CCF will have significant implications for Europe's forests and the industries. Using Sweden as a case, we simulated two scenarios: RF as a continued practice and a rapid transition to CCF. The results show that RF would ensure an even wood flow and slightly increasing harvest levels over the 50 years period. In contrast, the annual harvest in CCF exhibited significant variation, ranging from 50% to 108% of the RF harvest in the same year. This variation in harvest outcomes for CCF can be largely attributed to both economic and legal constraints during the transition from RF to CCF. As a result, the growing stock in CCF increased, allowing the forest to serve as a significant carbon sink. During the transition period, the ratio of pulpwood to sawlogs fluctuated for CCF, while it remained stable for RF. Consequently, the volume of sawlogs harvested under CCF was 86% of that harvested under RF.

@article{pawlowski_frankia_2024,
	title = {Frankia [{NiFe}] uptake hydrogenases and genome reduction: different lineages of loss},
	volume = {100},
	issn = {0168-6496},
	shorttitle = {Frankia [{NiFe}] uptake hydrogenases and genome reduction},
	url = {https://doi.org/10.1093/femsec/fiae147},
	doi = {10.1093/femsec/fiae147},
	abstract = {Uptake hydrogenase (Hup) recycles H2 formed by nitrogenase during nitrogen fixation, thereby preserving energy. Among root nodule bacteria, most rhizobial strains examined are Hup−, while only one Hup−  Frankia inoculum had been identified. Previous analyses had led to the identification of two different [NiFe] hydrogenase syntons. We analysed the distribution of different types of [NiFe] hydrogenase in the genomes of different Frankia species. Our results show that Frankia strains can contain four different [NiFe] hydrogenase syntons representing groups 1f, 1h, 2a, and 3b according to Søndergaard, Pedersen, and Greening (HydDB: a web tool for hydrogenase classification and analysis. Sci Rep 2016;6:34212. https://doi.org/10.1038/srep34212.); no more than three types were found in any individual genome. The phylogeny of the structural proteins of groups 1f, 1h, and 2a follows Frankia phylogeny; the phylogeny of the accessory proteins does not consistently. An analysis of different [NiFe] hydrogenase types in Actinomycetia shows that under the most parsimonious assumption, all four types were present in the ancestral Frankia strain. Based on Hup activities analysed and the losses of syntons in different lineages of genome reduction, we can conclude that groups 1f and 2a are involved in recycling H2 formed by nitrogenase while group 1 h and group 3b are not.},
	number = {12},
	urldate = {2025-01-10},
	journal = {FEMS Microbiology Ecology},
	author = {Pawlowski, Katharina and Wibberg, Daniel and Mehrabi, Sara and Obaid, Nadia Binte and Patyi, András and Berckx, Fede and Nguyen, Han and Hagen, Michelle and Lundin, Daniel and Brachmann, Andreas and Blom, Jochen and Herrera-Belaroussi, Aude and Abrouk, Danis and Pujic, Petar and Hahlin, Ann-Sofi and Kalinowski, Jörn and Normand, Philippe and Sellstedt, Anita},
	month = dec,
	year = {2024},
	pages = {fiae147},
}

Uptake hydrogenase (Hup) recycles H2 formed by nitrogenase during nitrogen fixation, thereby preserving energy. Among root nodule bacteria, most rhizobial strains examined are Hup−, while only one Hup−  Frankia inoculum had been identified. Previous analyses had led to the identification of two different [NiFe] hydrogenase syntons. We analysed the distribution of different types of [NiFe] hydrogenase in the genomes of different Frankia species. Our results show that Frankia strains can contain four different [NiFe] hydrogenase syntons representing groups 1f, 1h, 2a, and 3b according to Søndergaard, Pedersen, and Greening (HydDB: a web tool for hydrogenase classification and analysis. Sci Rep 2016;6:34212. https://doi.org/10.1038/srep34212.); no more than three types were found in any individual genome. The phylogeny of the structural proteins of groups 1f, 1h, and 2a follows Frankia phylogeny; the phylogeny of the accessory proteins does not consistently. An analysis of different [NiFe] hydrogenase types in Actinomycetia shows that under the most parsimonious assumption, all four types were present in the ancestral Frankia strain. Based on Hup activities analysed and the losses of syntons in different lineages of genome reduction, we can conclude that groups 1f and 2a are involved in recycling H2 formed by nitrogenase while group 1 h and group 3b are not.

@article{bhat_nuclear_2024,
	title = {The nuclear exosome subunit {HEN2} acts independently of the core exosome to assist transcription in {Arabidopsis}},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiae503},
	doi = {10.1093/plphys/kiae503},
	abstract = {Regulation of gene expression is at the frontier of plant responses to various external stimuli including stress. RNA polymerase-based transcription and post-transcriptional degradation of RNA play vital roles in this regulation. Here, we show that HUA ENHANCER 2 (HEN2), a co-factor of the nuclear exosome complex, influences RNAPII transcription elongation in Arabidopsis (Arabidopsis thaliana) under cold conditions. Our results demonstrate that a hen2 mutant is cold sensitive and undergoes substantial transcriptional changes compared to wild type when exposed to cold conditions. We found an accumulation of 5’ fragments from a subset of genes (including C-repeat binding factors 1-3 [CBF1-3]) that do not carry over to their 3’ ends. In fact, hen2 mutants have lower levels of full-length mRNA for a subset of genes. This distinct 5’-end accumulation and 3’-end depletion was not observed in other NEXT complex members or core exosome mutants, highlighting HEN2’s distinctive role. We further used RNAPII-associated nascent RNA to confirm the transcriptional phenotype is a result of lower active transcription specifically at the 3’-end of these genes in a hen2 mutant. Taken together, our data point to the unique role of HEN2 in maintaining RNAPII transcription dynamics especially highlighted under cold stress.},
	urldate = {2024-09-27},
	journal = {Plant Physiology},
	author = {Bhat, Susheel Sagar and Asgari, Mishaneh and Mermet, Sarah and Mishra, Priyanka and Kindgren, Peter},
	month = sep,
	year = {2024},
	pages = {kiae503},
}

Regulation of gene expression is at the frontier of plant responses to various external stimuli including stress. RNA polymerase-based transcription and post-transcriptional degradation of RNA play vital roles in this regulation. Here, we show that HUA ENHANCER 2 (HEN2), a co-factor of the nuclear exosome complex, influences RNAPII transcription elongation in Arabidopsis (Arabidopsis thaliana) under cold conditions. Our results demonstrate that a hen2 mutant is cold sensitive and undergoes substantial transcriptional changes compared to wild type when exposed to cold conditions. We found an accumulation of 5’ fragments from a subset of genes (including C-repeat binding factors 1-3 [CBF1-3]) that do not carry over to their 3’ ends. In fact, hen2 mutants have lower levels of full-length mRNA for a subset of genes. This distinct 5’-end accumulation and 3’-end depletion was not observed in other NEXT complex members or core exosome mutants, highlighting HEN2’s distinctive role. We further used RNAPII-associated nascent RNA to confirm the transcriptional phenotype is a result of lower active transcription specifically at the 3’-end of these genes in a hen2 mutant. Taken together, our data point to the unique role of HEN2 in maintaining RNAPII transcription dynamics especially highlighted under cold stress.

@article{dufil_glucose-sensitive_2024,
	title = {Glucose-{Sensitive} {Biohybrid} {Roots} for {Supercapacitive} {Bioanodes}},
	volume = {7},
	url = {https://doi.org/10.1021/acsabm.4c01425},
	doi = {10.1021/acsabm.4c01425},
	abstract = {Plants as living organisms, as well as their material–structural components and physiological processes, offer promising elements for developing more sustainable technologies. Previously, we demonstrated that plants could acquire electronic functionality, as their enzymatic activity catalyzes the in vivo polymerization of water-soluble conjugated oligomers. We then leveraged plant-integrated conductors to develop biohybrid energy storage devices and circuits. Here, we extend the concept of plant biohybrids to develop plant-based energy-harvesting devices. We demonstrate plant biohybrids with modified roots that can convert common root exudates, such as glucose, to electricity. To do so, we developed a simple one-step approach to convert living roots to glucose-sensitive electrodes by dipping the root in a solution of the conjugated trimer ETE-S and the enzyme glucose dehydrogenase flavin adenine dinucleotide. The biohybrid device responds to glucose concentrations down to 100 μM while it saturates at 100 mM. The performance of our approach was compared with a classic mediator-based glucose biosensor functionalization method. While the latter method increases the stability of the sensor, it results in less sensitivity and damages the root structure. Finally, we show that glucose oxidation can be combined with the volumetric capacitance of p(ETE-S)-forming devices that generate current in the presence of glucose and store it in the same biohybrid root electrodes. The plant biohybrid devices open a pathway to biologically integrated technology that finds application in low-power devices, for example, sensors for agriculture or the environment.},
	number = {12},
	urldate = {2025-01-10},
	journal = {ACS Applied Bio Materials},
	publisher = {American Chemical Society},
	author = {Dufil, Gwennaël and Pham, Julie and Diacci, Chiara and Daguerre, Yohann and Mantione, Daniele and Zrig, Samia and Näsholm, Torgny and Donahue, Mary J. and Oikonomou, Vasileios K. and Noël, Vincent and Piro, Benoit and Stavrinidou, Eleni},
	month = dec,
	year = {2024},
	pages = {8632--8641},
}

Plants as living organisms, as well as their material–structural components and physiological processes, offer promising elements for developing more sustainable technologies. Previously, we demonstrated that plants could acquire electronic functionality, as their enzymatic activity catalyzes the in vivo polymerization of water-soluble conjugated oligomers. We then leveraged plant-integrated conductors to develop biohybrid energy storage devices and circuits. Here, we extend the concept of plant biohybrids to develop plant-based energy-harvesting devices. We demonstrate plant biohybrids with modified roots that can convert common root exudates, such as glucose, to electricity. To do so, we developed a simple one-step approach to convert living roots to glucose-sensitive electrodes by dipping the root in a solution of the conjugated trimer ETE-S and the enzyme glucose dehydrogenase flavin adenine dinucleotide. The biohybrid device responds to glucose concentrations down to 100 μM while it saturates at 100 mM. The performance of our approach was compared with a classic mediator-based glucose biosensor functionalization method. While the latter method increases the stability of the sensor, it results in less sensitivity and damages the root structure. Finally, we show that glucose oxidation can be combined with the volumetric capacitance of p(ETE-S)-forming devices that generate current in the presence of glucose and store it in the same biohybrid root electrodes. The plant biohybrid devices open a pathway to biologically integrated technology that finds application in low-power devices, for example, sensors for agriculture or the environment.

@article{bhalerao_getting_2024,
	title = {Getting it right: suppression and leveraging of noise in robust decision-making},
	volume = {5},
	issn = {2632-8828},
	shorttitle = {Getting it right},
	url = {https://www.cambridge.org/core/journals/quantitative-plant-biology/article/getting-it-right-suppression-and-leveraging-of-noise-in-robust-decisionmaking/7EEB3D489D6F92FA179A22DFFDC55C49#},
	doi = {10.1017/qpb.2024.10},
	abstract = {, Noise is a ubiquitous feature for all organisms growing in nature. Noise (defined here as stochastic variation) in the availability of nutrients, water and light profoundly impacts their growth and development. Not only is noise present as an external factor but cellular processes themselves are noisy. Therefore, it is remarkable that organisms can display robust control of growth and development despite noise. To survive, various mechanisms to suppress noise have evolved. However, it is also becoming apparent that noise is not just a nuisance that organisms must suppress but can be beneficial as low noise can facilitate the response of an organism to a sub-threshold input signal in a stochastic resonance mechanism. This review discusses mechanisms capable of noise suppression or noise leveraging that might play a significant role in robust temporal regulation of an organism’s response to their noisy environment.},
	language = {en},
	urldate = {2025-01-10},
	journal = {Quantitative Plant Biology},
	author = {Bhalerao, Rishikesh P.},
	month = jan,
	year = {2024},
	keywords = {Noise, robustness, stochastic resonance},
	pages = {e10},
}

, Noise is a ubiquitous feature for all organisms growing in nature. Noise (defined here as stochastic variation) in the availability of nutrients, water and light profoundly impacts their growth and development. Not only is noise present as an external factor but cellular processes themselves are noisy. Therefore, it is remarkable that organisms can display robust control of growth and development despite noise. To survive, various mechanisms to suppress noise have evolved. However, it is also becoming apparent that noise is not just a nuisance that organisms must suppress but can be beneficial as low noise can facilitate the response of an organism to a sub-threshold input signal in a stochastic resonance mechanism. This review discusses mechanisms capable of noise suppression or noise leveraging that might play a significant role in robust temporal regulation of an organism’s response to their noisy environment.

@article{stojkovic_transcriptome_2024,
	title = {A transcriptome atlas of zygotic and somatic embryogenesis in {Norway} spruce},
	volume = {120},
	copyright = {© 2024 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.17087},
	doi = {10.1111/tpj.17087},
	abstract = {Somatic embryogenesis (SE) is a powerful model system for studying embryo development and an important method for scaling up availability of elite and climate-adapted genetic material of Norway spruce (Picea abies L. Karst). However, there are several steps during the development of the somatic embryo (Sem) that are suboptimal compared to zygotic embryo (Zem) development. These differences are poorly understood and result in substantial yield losses during plant production, which limits cost-effective large-scale production of SE plants. This study presents a comprehensive data resource profiling gene expression during zygotic and somatic embryo development to support studies aiming to advance understanding of gene regulatory programmes controlling embryo development. Transcriptome expression patterns were analysed during zygotic embryogenesis (ZE) in Norway spruce, including separated samples of the female gametophytes and Zem, and at multiple stages during SE. Expression data from eight developmental stages of SE, starting with pro-embryogenic masses (PEMs) up until germination, revealed extensive modulation of the transcriptome between the early and mid-stage maturing embryos and at the transition of desiccated embryos to germination. Comparative analysis of gene expression changes during ZE and SE identified differences in the pattern of gene expression changes and functional enrichment of these provided insight into the associated biological processes. Orthologs of transcription factors known to regulate embryo development in angiosperms were differentially regulated during Zem and Sem development and in the different zygotic embryo tissues, providing clues to the differences in development observed between Zem and Sem. This resource represents the most comprehensive dataset available for exploring embryo development in conifers.},
	language = {en},
	number = {5},
	urldate = {2024-12-13},
	journal = {The Plant Journal},
	author = {Stojkovič, Katja and Canovi, Camilla and Le, Kim-Cuong and Ahmad, Iftikhar and Gaboreanu, Ioana and Johansson, Sofie and Delhomme, Nicolas and Egertsdotter, Ulrika and Street, Nathaniel R.},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.17087},
	keywords = {Norway spruce, Picea abies, differential expression, embryo, embryogenesis, transcriptome},
	pages = {2238--2252},
}

Somatic embryogenesis (SE) is a powerful model system for studying embryo development and an important method for scaling up availability of elite and climate-adapted genetic material of Norway spruce (Picea abies L. Karst). However, there are several steps during the development of the somatic embryo (Sem) that are suboptimal compared to zygotic embryo (Zem) development. These differences are poorly understood and result in substantial yield losses during plant production, which limits cost-effective large-scale production of SE plants. This study presents a comprehensive data resource profiling gene expression during zygotic and somatic embryo development to support studies aiming to advance understanding of gene regulatory programmes controlling embryo development. Transcriptome expression patterns were analysed during zygotic embryogenesis (ZE) in Norway spruce, including separated samples of the female gametophytes and Zem, and at multiple stages during SE. Expression data from eight developmental stages of SE, starting with pro-embryogenic masses (PEMs) up until germination, revealed extensive modulation of the transcriptome between the early and mid-stage maturing embryos and at the transition of desiccated embryos to germination. Comparative analysis of gene expression changes during ZE and SE identified differences in the pattern of gene expression changes and functional enrichment of these provided insight into the associated biological processes. Orthologs of transcription factors known to regulate embryo development in angiosperms were differentially regulated during Zem and Sem development and in the different zygotic embryo tissues, providing clues to the differences in development observed between Zem and Sem. This resource represents the most comprehensive dataset available for exploring embryo development in conifers.

@article{pandey_regulatory_2024,
	title = {A regulatory module mediating temperature control of cell-cell communication facilitates tree bud dormancy release},
	volume = {43},
	issn = {0261-4189},
	url = {https://www.embopress.org/doi/full/10.1038/s44318-024-00256-5},
	doi = {10.1038/s44318-024-00256-5},
	abstract = {The control of cell–cell communication via plasmodesmata (PD) plays a key role in plant development. In tree buds, low-temperature conditions (LT) induce a switch in plasmodesmata from a closed to an open state, which restores cell-to-cell communication in the shoot apex and releases dormancy. Using genetic and cell-biological approaches, we have identified a previously uncharacterized transcription factor, Low-temperature-Induced MADS-box 1 (LIM1), as an LT-induced, direct upstream activator of the gibberellic acid (GA) pathway. The LIM1-GA module mediates low temperature-induced plasmodesmata opening, by negatively regulating callose accumulation to promote dormancy release. LIM1 also activates expression of FT1 (FLOWERING LOCUS T), another LT-induced factor, with LIM1-FT1 forming a coherent feedforward loop converging on low-temperature regulation of gibberellin signaling in dormancy release. Mathematical modeling and experimental validation suggest that negative feedback regulation of LIM1 by gibberellin could play a crucial role in maintaining the robust temporal regulation of bud responses to low temperature. These results reveal genetic factors linking temperature control of cell–cell communication with regulation of seasonally-aligned growth crucial for adaptation of trees.},
	number = {23},
	urldate = {2024-12-06},
	journal = {The EMBO Journal},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Pandey, Shashank K and Maurya, Jay Prakash and Aryal, Bibek and Drynda, Kamil and Nair, Aswin and Miskolczi, Pal and Singh, Rajesh Kumar and Wang, Xiaobin and Ma, Yujiao and de Souza Moraes, Tatiana and Bayer, Emmanuelle M and Farcot, Etienne and Bassel, George W and Band, Leah R and Bhalerao, Rishikesh P},
	month = dec,
	year = {2024},
	note = {Num Pages: 5812},
	keywords = {Callose, Dormancy, Gibberellins, Plasmodesmata, Temperature},
	pages = {5793--5812},
}

The control of cell–cell communication via plasmodesmata (PD) plays a key role in plant development. In tree buds, low-temperature conditions (LT) induce a switch in plasmodesmata from a closed to an open state, which restores cell-to-cell communication in the shoot apex and releases dormancy. Using genetic and cell-biological approaches, we have identified a previously uncharacterized transcription factor, Low-temperature-Induced MADS-box 1 (LIM1), as an LT-induced, direct upstream activator of the gibberellic acid (GA) pathway. The LIM1-GA module mediates low temperature-induced plasmodesmata opening, by negatively regulating callose accumulation to promote dormancy release. LIM1 also activates expression of FT1 (FLOWERING LOCUS T), another LT-induced factor, with LIM1-FT1 forming a coherent feedforward loop converging on low-temperature regulation of gibberellin signaling in dormancy release. Mathematical modeling and experimental validation suggest that negative feedback regulation of LIM1 by gibberellin could play a crucial role in maintaining the robust temporal regulation of bud responses to low temperature. These results reveal genetic factors linking temperature control of cell–cell communication with regulation of seasonally-aligned growth crucial for adaptation of trees.

@article{lazaro-gimeno_circadian_2024,
	title = {The circadian clock participates in seasonal growth in {Norway} spruce ({Picea} abies)},
	volume = {44},
	issn = {1758-4469},
	url = {https://doi.org/10.1093/treephys/tpae139},
	doi = {10.1093/treephys/tpae139},
	abstract = {The boreal forest ecosystems of the northern hemisphere are dominated by conifers, of which Norway spruce (Picea abies [L.] H. Karst.) is one of the most common species. Due to its economic interest to the agroforestry industry, as well as its ecological significance, it is important to understand seasonal growth and biomass production in Norway spruce. Solid evidence that the circadian clock regulates growth in conifers has proved elusive, however, resulting in significant gaps in our knowledge of clock function in these trees. Here, we reassess the impact of the circadian clock on growth in Norway spruce. Using a combination of approaches monitoring the physiology of vegetative growth, transcriptomics and bioinformatics, we determined that the clock could be playing a decisive role in enabling growth, acting in specific developmental processes influenced by season and geographical location to guide bud burst and growth. Thus, the evidence indicates that there is time for spruce.},
	number = {11},
	urldate = {2024-11-29},
	journal = {Tree Physiology},
	author = {Lázaro-Gimeno, David and Ferrari, Camilla and Delhomme, Nico and Johansson, Mikael and Sjölander, Johan and Singh, Rajesh Kumar and Mutwil, Marek and Eriksson, Maria E},
	month = nov,
	year = {2024},
	pages = {tpae139},
}

The boreal forest ecosystems of the northern hemisphere are dominated by conifers, of which Norway spruce (Picea abies [L.] H. Karst.) is one of the most common species. Due to its economic interest to the agroforestry industry, as well as its ecological significance, it is important to understand seasonal growth and biomass production in Norway spruce. Solid evidence that the circadian clock regulates growth in conifers has proved elusive, however, resulting in significant gaps in our knowledge of clock function in these trees. Here, we reassess the impact of the circadian clock on growth in Norway spruce. Using a combination of approaches monitoring the physiology of vegetative growth, transcriptomics and bioinformatics, we determined that the clock could be playing a decisive role in enabling growth, acting in specific developmental processes influenced by season and geographical location to guide bud burst and growth. Thus, the evidence indicates that there is time for spruce.

@article{carneiro_schinus_2024,
	title = {Schinus terebinthifolia {Raddi}—{Untargeted} {Metabolomics} {Approach} to {Investigate} the {Chemical} {Variation} in {Volatile} and {Non}-{Volatile} {Compounds}},
	volume = {14},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2218-1989},
	url = {https://www.mdpi.com/2218-1989/14/11/612},
	doi = {10.3390/metabo14110612},
	abstract = {Context: Schinus terebinthifolia Raddi is used in Brazilian folk medicine due to the wound healing and antiseptic properties of its bark, and its fruit are used as a condiment. However, the aerial parts of this plant have been studied and present some bioactive compounds as well. Objectives: The aim of this study was to investigate the variation in volatile and non-volatile composition of S. terebinthifolia leaves using untargeted metabolomics. Material and Methods: The leaves of four trees were collected over one year; ethanolic extracts were analyzed by UHPLC-MS and fresh leaves were analyzed by GC-MS using HS-SPME. The data were processed using online software. Results: The results suggest seasonality interfered little with the chemical composition of leaves. On the other hand, the sex of the plant clearly determined the chemical composition of both volatile and non-volatile compounds. Discussion and conclusions: Chemical variability between plants with male and female flowers is fundamental information for the standardized use of its leaves. Compounds with important biological activities were putatively identified, confirming the potential use of S. terebinthifolia leaves as a source of bioactive compounds, reducing waste and increasing economic gains for local farmers throughout the year.},
	language = {en},
	number = {11},
	urldate = {2024-11-29},
	journal = {Metabolites},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Carneiro, Mara Junqueira and Pinheiro, Guilherme Perez and Antunes, Elisa Ribeiro Miranda and Hantao, Leandro Wang and Moritz, Thomas and Sawaya, Alexandra Christine Helena Frankland},
	month = nov,
	year = {2024},
	note = {Number: 11},
	keywords = {\textit{Aroeira}, GC-MS, UHPLC-MS, pink pepper, plant sex, seasonality},
	pages = {612},
}

Context: Schinus terebinthifolia Raddi is used in Brazilian folk medicine due to the wound healing and antiseptic properties of its bark, and its fruit are used as a condiment. However, the aerial parts of this plant have been studied and present some bioactive compounds as well. Objectives: The aim of this study was to investigate the variation in volatile and non-volatile composition of S. terebinthifolia leaves using untargeted metabolomics. Material and Methods: The leaves of four trees were collected over one year; ethanolic extracts were analyzed by UHPLC-MS and fresh leaves were analyzed by GC-MS using HS-SPME. The data were processed using online software. Results: The results suggest seasonality interfered little with the chemical composition of leaves. On the other hand, the sex of the plant clearly determined the chemical composition of both volatile and non-volatile compounds. Discussion and conclusions: Chemical variability between plants with male and female flowers is fundamental information for the standardized use of its leaves. Compounds with important biological activities were putatively identified, confirming the potential use of S. terebinthifolia leaves as a source of bioactive compounds, reducing waste and increasing economic gains for local farmers throughout the year.

@article{parker_biohybrid_2024,
	title = {Biohybrid {Energy} {Storage} {Circuits} {Based} on {Electronically} {Functionalized} {Plant} {Roots}},
	volume = {16},
	issn = {1944-8244},
	url = {https://doi.org/10.1021/acsami.3c16861},
	doi = {10.1021/acsami.3c16861},
	abstract = {Biohybrid systems based on plants integrate plant structures and processes into technological components targeting more sustainable solutions. Plants’ biocatalytic machinery, for example, has been leveraged for the organization of electronic materials directly in the vasculature and roots of living plants, resulting in biohybrid electrochemical devices. Among other applications, energy storage devices were demonstrated where the charge storage electrodes were seamlessly integrated into the plant tissue. However, the capacitance and the voltage output of a single biohybrid supercapacitor are limited. Here, we developed biohybrid circuits based on functionalized conducting roots, extending the performance of plant based biohybrid energy storage systems. We show that root-supercapacitors can be combined in series and in parallel configuration, achieving up to 1.5 V voltage output or up to 11 mF capacitance, respectively. We further demonstrate that the supercapacitors circuit can be charged with an organic photovoltaic cell, and that the stored charge can be used to power an electrochromic display or a bioelectronic device. Furthermore, the functionalized roots degrade in composting similarly to native roots. The proof-of-concept demonstrations illustrate the potential of this technology to achieve more sustainable solutions for powering low consumption devices such as bioelectronics for agriculture or IoT applications.},
	number = {45},
	urldate = {2024-11-22},
	journal = {ACS Applied Materials \& Interfaces},
	publisher = {American Chemical Society},
	author = {Parker, Daniela and Dar, Abdul Manan and Armada-Moreira, Adam and Bernacka Wojcik, Iwona and Rai, Rajat and Mantione, Daniele and Stavrinidou, Eleni},
	month = nov,
	year = {2024},
	pages = {61475--61483},
}

Biohybrid systems based on plants integrate plant structures and processes into technological components targeting more sustainable solutions. Plants’ biocatalytic machinery, for example, has been leveraged for the organization of electronic materials directly in the vasculature and roots of living plants, resulting in biohybrid electrochemical devices. Among other applications, energy storage devices were demonstrated where the charge storage electrodes were seamlessly integrated into the plant tissue. However, the capacitance and the voltage output of a single biohybrid supercapacitor are limited. Here, we developed biohybrid circuits based on functionalized conducting roots, extending the performance of plant based biohybrid energy storage systems. We show that root-supercapacitors can be combined in series and in parallel configuration, achieving up to 1.5 V voltage output or up to 11 mF capacitance, respectively. We further demonstrate that the supercapacitors circuit can be charged with an organic photovoltaic cell, and that the stored charge can be used to power an electrochromic display or a bioelectronic device. Furthermore, the functionalized roots degrade in composting similarly to native roots. The proof-of-concept demonstrations illustrate the potential of this technology to achieve more sustainable solutions for powering low consumption devices such as bioelectronics for agriculture or IoT applications.

@article{hermida-carrera_cdk8_2024,
	title = {{CDK8} of the mediator kinase module connects leaf development to the establishment of correct stomata patterning by regulating the levels of the transcription factor {SPEECHLESS} ({SPCH})},
	volume = {47},
	copyright = {© 2024 The Author(s). Plant, Cell \& Environment published by John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.15102},
	doi = {10.1111/pce.15102},
	abstract = {The components of the mediator kinase module are highly conserved across all eukaryotic lineages, and cyclin-dependent kinase 8 (CDK8) is essential for correct cell proliferation and differentiation in diverse eukaryotic systems. We show that CDK8 couples leaf development with the establishment of correct stomata patterning for prevailing CO2 conditions. In Arabidopsis, the basic helix-loop-helix (bHLH) transcription factor SPEECHLESS (SPCH) controls cellular entry into the stomatal cell lineage, and CDK8 interacts with and phosphorylates SPCH, controlling SPCH protein levels and thereby also expression of the SPCH target genes encoding key regulators of cell fate and asymmetric cell divisions. The lack of the CDK8-mediated control of SPCH results in an increased number of meristemoid and guard mother cells, and increased stomata index in the cdk8 mutants. Increasing atmospheric CO2 concentrations trigger a developmental programme controlling cell entry into stomatal lineage by limiting the asymmetric divisions. In cdk8, the number of meristemoids and guard mother cells remains the same under ambient and high CO2 concentrations, as the accumulated levels of SPCH caused by the lack of CDK8 appear to override the negative regulation of increased CO2. Thus, our work provides novel mechanistic understanding of how plants alter critical leaf properties in response to increasing atmospheric CO2.},
	language = {en},
	number = {12},
	urldate = {2024-11-08},
	journal = {Plant, Cell \& Environment},
	author = {Hermida-Carrera, Carmen and Vergara, Alexander and Cervela-Cardona, Luis and Jin, Xu and Björklund, Stefan and Strand, Åsa},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.15102},
	keywords = {CO2 response, climate change, drought},
	pages = {5237--5251},
}

The components of the mediator kinase module are highly conserved across all eukaryotic lineages, and cyclin-dependent kinase 8 (CDK8) is essential for correct cell proliferation and differentiation in diverse eukaryotic systems. We show that CDK8 couples leaf development with the establishment of correct stomata patterning for prevailing CO2 conditions. In Arabidopsis, the basic helix-loop-helix (bHLH) transcription factor SPEECHLESS (SPCH) controls cellular entry into the stomatal cell lineage, and CDK8 interacts with and phosphorylates SPCH, controlling SPCH protein levels and thereby also expression of the SPCH target genes encoding key regulators of cell fate and asymmetric cell divisions. The lack of the CDK8-mediated control of SPCH results in an increased number of meristemoid and guard mother cells, and increased stomata index in the cdk8 mutants. Increasing atmospheric CO2 concentrations trigger a developmental programme controlling cell entry into stomatal lineage by limiting the asymmetric divisions. In cdk8, the number of meristemoids and guard mother cells remains the same under ambient and high CO2 concentrations, as the accumulated levels of SPCH caused by the lack of CDK8 appear to override the negative regulation of increased CO2. Thus, our work provides novel mechanistic understanding of how plants alter critical leaf properties in response to increasing atmospheric CO2.

@article{el_arbi_arabidopsis_2024,
	title = {The {Arabidopsis} splicing factor {PORCUPINE}/{SmE1} orchestrates temperature-dependent root development via auxin homeostasis maintenance},
	volume = {244},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20153},
	doi = {10.1111/nph.20153},
	abstract = {Appropriate abiotic stress response is pivotal for plant survival and makes use of multiple signaling molecules and phytohormones to achieve specific and fast molecular adjustments. A multitude of studies has highlighted the role of alternative splicing in response to abiotic stress, including temperature, emphasizing the role of transcriptional regulation for stress response. Here we investigated the role of the core-splicing factor PORCUPINE (PCP) on temperature-dependent root development. We used marker lines and transcriptomic analyses to study the expression profiles of meristematic regulators and mitotic markers, and chemical treatments, as well as root hormone profiling to assess the effect of auxin signaling. The loss of PCP significantly alters RAM architecture in a temperature-dependent manner. Our results indicate that PCP modulates the expression of central meristematic regulators and is required to maintain appropriate levels of auxin in the RAM. We conclude that alternative pre-mRNA splicing is sensitive to moderate temperature fluctuations and contributes to root meristem maintenance, possibly through the regulation of phytohormone homeostasis and meristematic activity.},
	language = {en},
	number = {4},
	urldate = {2024-10-25},
	journal = {New Phytologist},
	author = {El Arbi, Nabila and Nardeli, Sarah Muniz and Šimura, Jan and Ljung, Karin and Schmid, Markus},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20153},
	keywords = {Arabidopsis thaliana, SmE, alternative RNA splicing, auxin signaling, root apical meristem, root development, temperature signaling},
	pages = {1408--1421},
}

Appropriate abiotic stress response is pivotal for plant survival and makes use of multiple signaling molecules and phytohormones to achieve specific and fast molecular adjustments. A multitude of studies has highlighted the role of alternative splicing in response to abiotic stress, including temperature, emphasizing the role of transcriptional regulation for stress response. Here we investigated the role of the core-splicing factor PORCUPINE (PCP) on temperature-dependent root development. We used marker lines and transcriptomic analyses to study the expression profiles of meristematic regulators and mitotic markers, and chemical treatments, as well as root hormone profiling to assess the effect of auxin signaling. The loss of PCP significantly alters RAM architecture in a temperature-dependent manner. Our results indicate that PCP modulates the expression of central meristematic regulators and is required to maintain appropriate levels of auxin in the RAM. We conclude that alternative pre-mRNA splicing is sensitive to moderate temperature fluctuations and contributes to root meristem maintenance, possibly through the regulation of phytohormone homeostasis and meristematic activity.

@article{ding_molecular_2024,
	title = {Molecular advances in bud dormancy in trees},
	volume = {75},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erae183},
	doi = {10.1093/jxb/erae183},
	abstract = {Seasonal bud dormancy in perennial woody plants is a crucial and intricate process that is vital for the survival and development of plants. Over the past few decades, significant advancements have been made in understanding many features of bud dormancy, particularly in model species, where certain molecular mechanisms underlying this process have been elucidated. We provide an overview of recent molecular progress in understanding bud dormancy in trees, with a specific emphasis on the integration of common signaling and molecular mechanisms identified across different tree species. Additionally, we address some challenges that have emerged from our current understanding of bud dormancy and offer insights for future studies.},
	number = {19},
	urldate = {2024-10-18},
	journal = {Journal of Experimental Botany},
	author = {Ding, Jihua and Wang, Kejing and Pandey, Shashank and Perales, Mariano and Allona, Isabel and Khan, Md Rezaul Islam and Busov, Victor B and Bhalerao, Rishikesh P},
	month = oct,
	year = {2024},
	pages = {6063--6075},
}

Seasonal bud dormancy in perennial woody plants is a crucial and intricate process that is vital for the survival and development of plants. Over the past few decades, significant advancements have been made in understanding many features of bud dormancy, particularly in model species, where certain molecular mechanisms underlying this process have been elucidated. We provide an overview of recent molecular progress in understanding bud dormancy in trees, with a specific emphasis on the integration of common signaling and molecular mechanisms identified across different tree species. Additionally, we address some challenges that have emerged from our current understanding of bud dormancy and offer insights for future studies.

@article{hussein_cryoelectron_2024,
	title = {Cryo–electron microscopy reveals hydrogen positions and water networks in photosystem {II}},
	volume = {384},
	url = {https://www.science.org/doi/10.1126/science.adn6541},
	doi = {10.1126/science.adn6541},
	abstract = {Photosystem II starts the photosynthetic electron transport chain that converts solar energy into chemical energy and thus sustains life on Earth. It catalyzes two chemical reactions: water oxidation to molecular oxygen and plastoquinone reduction. Coupling of electron and proton transfer is crucial for efficiency; however, the molecular basis of these processes remains speculative owing to uncertain water binding sites and the lack of experimentally determined hydrogen positions. We thus collected high-resolution cryo–electron microscopy data of fully hydrated photosystem II from the thermophilic cyanobacterium Thermosynechococcus vestitus to a final resolution of 1.71 angstroms. The structure reveals several previously undetected partially occupied water binding sites and more than half of the hydrogen and proton positions. This clarifies the pathways of substrate water binding and plastoquinone B protonation.},
	number = {6702},
	urldate = {2024-06-26},
	journal = {Science},
	publisher = {American Association for the Advancement of Science},
	author = {Hussein, Rana and Graça, André and Forsman, Jack and Aydin, A. Orkun and Hall, Michael and Gaetcke, Julia and Chernev, Petko and Wendler, Petra and Dobbek, Holger and Messinger, Johannes and Zouni, Athina and Schröder, Wolfgang P.},
	month = jun,
	year = {2024},
	pages = {1349--1355},
}

Photosystem II starts the photosynthetic electron transport chain that converts solar energy into chemical energy and thus sustains life on Earth. It catalyzes two chemical reactions: water oxidation to molecular oxygen and plastoquinone reduction. Coupling of electron and proton transfer is crucial for efficiency; however, the molecular basis of these processes remains speculative owing to uncertain water binding sites and the lack of experimentally determined hydrogen positions. We thus collected high-resolution cryo–electron microscopy data of fully hydrated photosystem II from the thermophilic cyanobacterium Thermosynechococcus vestitus to a final resolution of 1.71 angstroms. The structure reveals several previously undetected partially occupied water binding sites and more than half of the hydrogen and proton positions. This clarifies the pathways of substrate water binding and plastoquinone B protonation.

@article{guo_closing_2024,
	title = {Closing {Kok}’s cycle of nature’s water oxidation catalysis},
	volume = {15},
	copyright = {2024 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-024-50210-6},
	doi = {10.1038/s41467-024-50210-6},
	abstract = {The Mn4CaO5(6) cluster in photosystem II catalyzes water splitting through the Si state cycle (i = 0–4). Molecular O2 is formed and the natural catalyst is reset during the final S3 → (S4) → S0 transition. Only recently experimental breakthroughs have emerged for this transition but without explicit information on the S0-state reconstitution, thus the progression after O2 release remains elusive. In this report, our molecular dynamics simulations combined with density functional calculations suggest a likely missing link for closing the cycle, i.e., restoring the first catalytic state. Specifically, the formation of closed-cubane intermediates with all hexa-coordinate Mn is observed, which would undergo proton release, water dissociation, and ligand transfer to produce the open-cubane structure of the S0 state. Thereby, we theoretically identify the previously unknown structural isomerism in the S0 state that acts as the origin of the proposed structural flexibility prevailing in the cycle, which may be functionally important for nature’s water oxidation catalysis.},
	language = {en},
	number = {1},
	urldate = {2024-07-19},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Guo, Yu and He, Lanlan and Ding, Yunxuan and Kloo, Lars and Pantazis, Dimitrios A. and Messinger, Johannes and Sun, Licheng},
	month = jul,
	year = {2024},
	keywords = {Bioinorganic chemistry, Catalytic mechanisms, Reaction mechanisms},
	pages = {5982},
}

The Mn4CaO5(6) cluster in photosystem II catalyzes water splitting through the Si state cycle (i = 0–4). Molecular O2 is formed and the natural catalyst is reset during the final S3 → (S4) → S0 transition. Only recently experimental breakthroughs have emerged for this transition but without explicit information on the S0-state reconstitution, thus the progression after O2 release remains elusive. In this report, our molecular dynamics simulations combined with density functional calculations suggest a likely missing link for closing the cycle, i.e., restoring the first catalytic state. Specifically, the formation of closed-cubane intermediates with all hexa-coordinate Mn is observed, which would undergo proton release, water dissociation, and ligand transfer to produce the open-cubane structure of the S0 state. Thereby, we theoretically identify the previously unknown structural isomerism in the S0 state that acts as the origin of the proposed structural flexibility prevailing in the cycle, which may be functionally important for nature’s water oxidation catalysis.

@incollection{shevela_measurements_2024,
	address = {New York, NY},
	title = {Measurements of {Oxygen} {Evolution} in {Photosynthesis}},
	isbn = {978-1-0716-3790-6},
	url = {https://doi.org/10.1007/978-1-0716-3790-6_8},
	doi = {10.1007/978-1-0716-3790-6_8},
	abstract = {This chapter compares two different techniques for monitoring photosynthetic O2 production; the wide-spread Clark-type O2 electrode and the more sophisticated membrane inlet mass spectrometry (MIMS) technique. We describe how a simple membrane inlet for MIMS can be made out of a commercial Clark-type cell and outline the advantages and drawbacks of the two techniques to guide researchers in deciding which method to use. Protocols and examples are given for measuring O2 evolution rates and for determining the number of chlorophyll molecules per active photosystem II reaction center.},
	language = {en},
	urldate = {2024-10-16},
	booktitle = {Photosynthesis : {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Shevela, Dmitry and Schröder, Wolfgang P. and Messinger, Johannes},
	editor = {Covshoff, Sarah},
	year = {2024},
	keywords = {Clark-type electrode, Membrane-inlet mass spectrometry, O2 evolution, Oxygenic photosynthesis, Photosynthetic water oxidation, Photosynthetic water splitting, Photosystem II},
	pages = {133--148},
}

This chapter compares two different techniques for monitoring photosynthetic O2 production; the wide-spread Clark-type O2 electrode and the more sophisticated membrane inlet mass spectrometry (MIMS) technique. We describe how a simple membrane inlet for MIMS can be made out of a commercial Clark-type cell and outline the advantages and drawbacks of the two techniques to guide researchers in deciding which method to use. Protocols and examples are given for measuring O2 evolution rates and for determining the number of chlorophyll molecules per active photosystem II reaction center.

@article{chernev_simulation_2024,
	title = {On the simulation and interpretation of substrate-water exchange experiments in photosynthetic water oxidation},
	issn = {1573-5079},
	url = {https://doi.org/10.1007/s11120-024-01084-8},
	doi = {10.1007/s11120-024-01084-8},
	abstract = {Water oxidation by photosystem II (PSII) sustains most life on Earth, but the molecular mechanism of this unique process remains controversial. The ongoing identification of the binding sites and modes of the two water-derived substrate oxygens (‘substrate waters’) in the various intermediates (Si states, i = 0, 1, 2, 3, 4) that the water-splitting tetra-manganese calcium penta-oxygen (Mn4CaO5) cluster attains during the reaction cycle provides central information towards resolving the unique chemistry of biological water oxidation. Mass spectrometric measurements of single- and double-labeled dioxygen species after various incubation times of PSII with H218O provide insight into the substrate binding modes and sites via determination of exchange rates. Such experiments have revealed that the two substrate waters exchange with different rates that vary independently with the Si state and are hence referred to as the fast (Wf) and the slow (WS) substrate waters. New insight for the molecular interpretation of these rates arises from our recent finding that in the S2 state, under special experimental conditions, two different rates of WS exchange are observed that appear to correlate with the high spin and low spin conformations of the Mn4CaO5 cluster. Here, we reexamine and unite various proposed methods for extracting and assigning rate constants from this recent data set. The analysis results in a molecular model for substrate-water binding and exchange that reconciles the expected non-exchangeability of the central oxo bridge O5 when located between two Mn(IV) ions with the experimental and theoretical assignment of O5 as WS in all S states. The analysis also excludes other published proposals for explaining the water exchange kinetics.},
	language = {en},
	urldate = {2024-10-16},
	journal = {Photosynthesis Research},
	author = {Chernev, Petko and Aydin, A. Orkun and Messinger, Johannes},
	month = mar,
	year = {2024},
	keywords = {Mechanism of water oxidation, Membrane inlet mass spectrometry (MIMS), Oxygen-evolving complex, Photosystem II, Substrate-water exchange},
}

Water oxidation by photosystem II (PSII) sustains most life on Earth, but the molecular mechanism of this unique process remains controversial. The ongoing identification of the binding sites and modes of the two water-derived substrate oxygens (‘substrate waters’) in the various intermediates (Si states, i = 0, 1, 2, 3, 4) that the water-splitting tetra-manganese calcium penta-oxygen (Mn4CaO5) cluster attains during the reaction cycle provides central information towards resolving the unique chemistry of biological water oxidation. Mass spectrometric measurements of single- and double-labeled dioxygen species after various incubation times of PSII with H218O provide insight into the substrate binding modes and sites via determination of exchange rates. Such experiments have revealed that the two substrate waters exchange with different rates that vary independently with the Si state and are hence referred to as the fast (Wf) and the slow (WS) substrate waters. New insight for the molecular interpretation of these rates arises from our recent finding that in the S2 state, under special experimental conditions, two different rates of WS exchange are observed that appear to correlate with the high spin and low spin conformations of the Mn4CaO5 cluster. Here, we reexamine and unite various proposed methods for extracting and assigning rate constants from this recent data set. The analysis results in a molecular model for substrate-water binding and exchange that reconciles the expected non-exchangeability of the central oxo bridge O5 when located between two Mn(IV) ions with the experimental and theoretical assignment of O5 as WS in all S states. The analysis also excludes other published proposals for explaining the water exchange kinetics.

@article{de_lichtenberg_assignment_2024,
	title = {Assignment of the slowly exchanging substrate water of nature’s water-splitting cofactor},
	volume = {121},
	url = {https://www.pnas.org/doi/full/10.1073/pnas.2319374121},
	doi = {10.1073/pnas.2319374121},
	abstract = {Identifying the two substrate water sites of nature’s water-splitting cofactor (Mn4CaO5 cluster) provides important information toward resolving the mechanism of O-O bond formation in Photosystem II (PSII). To this end, we have performed parallel substrate water exchange experiments in the S1 state of native Ca-PSII and biosynthetically substituted Sr-PSII employing Time-Resolved Membrane Inlet Mass Spectrometry (TR-MIMS) and a Time-Resolved 17O-Electron-electron Double resonance detected NMR (TR-17O-EDNMR) approach. TR-MIMS resolves the kinetics for incorporation of the oxygen-isotope label into the substrate sites after addition of H218O to the medium, while the magnetic resonance technique allows, in principle, the characterization of all exchangeable oxygen ligands of the Mn4CaO5 cofactor after mixing with H217O. This unique combination shows i) that the central oxygen bridge (O5) of Ca-PSII core complexes isolated from Thermosynechococcus vestitus has, within experimental conditions, the same rate of exchange as the slowly exchanging substrate water (WS) in the TR-MIMS experiments and ii) that the exchange rates of O5 and WS are both enhanced by Ca2+→Sr2+ substitution in a similar manner. In the context of previous TR-MIMS results, this shows that only O5 fulfills all criteria for being WS. This strongly restricts options for the mechanism of water oxidation.},
	number = {11},
	urldate = {2024-10-16},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {de Lichtenberg, Casper and Rapatskiy, Leonid and Reus, Michael and Heyno, Eiri and Schnegg, Alexander and Nowaczyk, Marc M. and Lubitz, Wolfgang and Messinger, Johannes and Cox, Nicholas},
	month = mar,
	year = {2024},
	pages = {e2319374121},
}

Identifying the two substrate water sites of nature’s water-splitting cofactor (Mn4CaO5 cluster) provides important information toward resolving the mechanism of O-O bond formation in Photosystem II (PSII). To this end, we have performed parallel substrate water exchange experiments in the S1 state of native Ca-PSII and biosynthetically substituted Sr-PSII employing Time-Resolved Membrane Inlet Mass Spectrometry (TR-MIMS) and a Time-Resolved 17O-Electron-electron Double resonance detected NMR (TR-17O-EDNMR) approach. TR-MIMS resolves the kinetics for incorporation of the oxygen-isotope label into the substrate sites after addition of H218O to the medium, while the magnetic resonance technique allows, in principle, the characterization of all exchangeable oxygen ligands of the Mn4CaO5 cofactor after mixing with H217O. This unique combination shows i) that the central oxygen bridge (O5) of Ca-PSII core complexes isolated from Thermosynechococcus vestitus has, within experimental conditions, the same rate of exchange as the slowly exchanging substrate water (WS) in the TR-MIMS experiments and ii) that the exchange rates of O5 and WS are both enhanced by Ca2+→Sr2+ substitution in a similar manner. In the context of previous TR-MIMS results, this shows that only O5 fulfills all criteria for being WS. This strongly restricts options for the mechanism of water oxidation.

@article{lin_tree-ring_2024,
	title = {A tree-ring cellulose extraction device adapted to radiocarbon analysis},
	issn = {0033-8222, 1945-5755},
	url = {https://www.cambridge.org/core/journals/radiocarbon/article/treering-cellulose-extraction-device-adapted-to-radiocarbon-analysis/7B981240F489EAC06325D1CA83798579},
	doi = {10.1017/RDC.2024.83},
	abstract = {Tree-ring cellulose is a commonly used material for radiocarbon analysis. Extracting cellulose is labor-consuming and several devices that enable batchwise extraction have been developed. However, these devices bear the risk of sample contamination. The present study describes a new device which improves upon two aspects of currently available devices. First, to prevent cross-sample-contamination, we redesigned the drainage module to enable independent removal of chemical waste from each individual sample funnel. Second, we added covers to the sample funnels to reduce the risk of external contamination. Cellulose purity (i.e., holocellulose) was confirmed by Fourier Transform Infrared (FTIR) Spectroscopy. Furthermore, accuracy of the radiocarbon analysis was confirmed by results of 14C-blank samples and samples of known age. In conclusion, while maintaining labor-saving, our modified device significantly reduces the risk of sample contamination during extraction of tree-ring cellulose.},
	language = {en},
	urldate = {2024-10-11},
	journal = {Radiocarbon},
	author = {Lin, Pengyu and Zhao, Yesi and Zhang, Hongyan and Wieloch, Thomas and Gu, Yao and Liang, Chenghong and Chen, Feng and Lu, Huayu},
	month = sep,
	year = {2024},
	keywords = {cellulose extraction, dendrochronology, radiocarbon analysis, tree-ring analysis},
	pages = {1--10},
}

Tree-ring cellulose is a commonly used material for radiocarbon analysis. Extracting cellulose is labor-consuming and several devices that enable batchwise extraction have been developed. However, these devices bear the risk of sample contamination. The present study describes a new device which improves upon two aspects of currently available devices. First, to prevent cross-sample-contamination, we redesigned the drainage module to enable independent removal of chemical waste from each individual sample funnel. Second, we added covers to the sample funnels to reduce the risk of external contamination. Cellulose purity (i.e., holocellulose) was confirmed by Fourier Transform Infrared (FTIR) Spectroscopy. Furthermore, accuracy of the radiocarbon analysis was confirmed by results of 14C-blank samples and samples of known age. In conclusion, while maintaining labor-saving, our modified device significantly reduces the risk of sample contamination during extraction of tree-ring cellulose.

@article{vishwakarma_pisolithus_2024,
	title = {\textit{{Pisolithus} microcarpus} isolates with contrasting abilities to colonise \textit{{Eucalyptus} grandis} exhibit significant differences in metabolic signalling},
	volume = {128},
	issn = {1878-6146},
	url = {https://www.sciencedirect.com/science/article/pii/S1878614624001247},
	doi = {10.1016/j.funbio.2024.09.001},
	abstract = {Biotic factors in fungal exudates impact plant-fungal symbioses establishment. Mutualistic ectomycorrhizal fungi play various ecological roles in forest soils by interacting with trees. Despite progress in understanding secreted fungal signals, dynamics of signal production in situ before or during direct host root contact remain unclear. We need to better understand how variability in intra-species fungal signaling at these stages impacts symbiosis with host tissues. Using the ECM model Pisolithus microcarpus, we selected two isolates (Si9 and Si14) with different abilities to colonize Eucalyptus grandis roots. Hypothesizing that distinct early signalling and metabolite profiles between these isolates would influence colonization and symbiosis, we used microdialysis to non-destructively collect secreted metabolites from either the fungus, host, or both, capturing the dynamic interplay of pre-symbiotic signalling over 48 hours. Our findings revealed significant differences in metabolite profiles between Si9 and Si14, grown alone or with a host root. Si9, with lower colonization efficiency than Si14, secreted a more diverse range of compounds, including lipids, oligopeptides, and carboxylic acids. In contrast, Si14's secretions, similar to the host's, included more aminoglycosides. This study emphasizes the importance of intra-specific metabolomic diversity in ectomycorrhizal fungi, suggesting that early metabolite secretion is crucial for establishing successful mutualistic relationships.},
	number = {7},
	urldate = {2024-10-11},
	journal = {Fungal Biology},
	author = {Vishwakarma, Kanchan and Buckley, Scott and Plett, Jonathan M. and Lundberg-Felten, Judith and Jämtgård, Sandra and Plett, Krista L.},
	month = nov,
	year = {2024},
	keywords = {Ectomycorrhizal fungi, Eucalyptus, Indirect contact, Isolates, Metabolites, Microdialysis system},
	pages = {2157--2166},
}

Biotic factors in fungal exudates impact plant-fungal symbioses establishment. Mutualistic ectomycorrhizal fungi play various ecological roles in forest soils by interacting with trees. Despite progress in understanding secreted fungal signals, dynamics of signal production in situ before or during direct host root contact remain unclear. We need to better understand how variability in intra-species fungal signaling at these stages impacts symbiosis with host tissues. Using the ECM model Pisolithus microcarpus, we selected two isolates (Si9 and Si14) with different abilities to colonize Eucalyptus grandis roots. Hypothesizing that distinct early signalling and metabolite profiles between these isolates would influence colonization and symbiosis, we used microdialysis to non-destructively collect secreted metabolites from either the fungus, host, or both, capturing the dynamic interplay of pre-symbiotic signalling over 48 hours. Our findings revealed significant differences in metabolite profiles between Si9 and Si14, grown alone or with a host root. Si9, with lower colonization efficiency than Si14, secreted a more diverse range of compounds, including lipids, oligopeptides, and carboxylic acids. In contrast, Si14's secretions, similar to the host's, included more aminoglycosides. This study emphasizes the importance of intra-specific metabolomic diversity in ectomycorrhizal fungi, suggesting that early metabolite secretion is crucial for establishing successful mutualistic relationships.

@article{baba_cell_2024,
	title = {Cell adhesion maintenance and controlled separation in plants},
	volume = {2},
	issn = {2813-821X},
	url = {https://www.frontiersin.org/journals/plant-physiology/articles/10.3389/fphgy.2024.1369575/full},
	doi = {10.3389/fphgy.2024.1369575},
	abstract = {{\textless}p{\textgreater}Cell-cell adhesion is a fundamental aspect of maintaining multicellular integrity while ensuring controlled cell and organ shedding, intercellular space formation and intrusive growth. Understanding of the precise mechanisms governing regulated cell separation, such as abscission, considerably progressed in recent decades. However, our comprehension of how plants maintain adhesion within tissues in which it is essential remains limited. Here we review some of the well-established knowledge along with latest discoveries that lead us to rethink the way developmentally controlled cell separation and adhesion maintenance may work. We also specifically explore the relationship between growth and adhesion, highlighting their similarities and coupling, and propose a plausible framework in which growth and adhesion are tightly co-regulated.{\textless}/p{\textgreater}},
	language = {English},
	urldate = {2024-10-09},
	journal = {Frontiers in Plant Physiology},
	publisher = {Frontiers},
	author = {Baba, Abu Imran and Verger, Stéphane},
	month = feb,
	year = {2024},
	keywords = {Abscission, Adhesion, Cell Wall, Growth, SEPARATION},
}

\textlessp\textgreaterCell-cell adhesion is a fundamental aspect of maintaining multicellular integrity while ensuring controlled cell and organ shedding, intercellular space formation and intrusive growth. Understanding of the precise mechanisms governing regulated cell separation, such as abscission, considerably progressed in recent decades. However, our comprehension of how plants maintain adhesion within tissues in which it is essential remains limited. Here we review some of the well-established knowledge along with latest discoveries that lead us to rethink the way developmentally controlled cell separation and adhesion maintenance may work. We also specifically explore the relationship between growth and adhesion, highlighting their similarities and coupling, and propose a plausible framework in which growth and adhesion are tightly co-regulated.\textless/p\textgreater

@incollection{mishra_adventitious_2024,
	edition = {5},
	title = {Adventitious {Root} {Development} in {Dicotyledons}},
	isbn = {978-1-00-332494-2},
	abstract = {The plant's root system is comprised of primary, lateral, and adventitious roots (ARs). Lateral roots emerge exclusively from existing roots, whereas ARs originate from stem- or leaf-derived cells. The progression of adventitious root development is a natural part of a plant's growth, commonly observed in most monocotyledonous species where they establish the primary root system or in various dicotyledonous plants that reproduce vegetatively. Adventitious rooting holds particular significance in the propagation of economically valuable horticultural and woody species, enabling the cloning of plants and swift establishment of superior genotypes before integrating them into production or breeding schemes. The process of AR development is intricate and influenced by numerous intrinsic and environmental factors, encompassing phytohormones, light exposure, nutritional state, stress responses like injury, and genetic traits. This chapter provides an overview of the latest advancements in research concerning adventitious root formation, with a specific focus on the interplay of key hormones and their interactions, as well as the influence of light, a significant environmental factor.},
	booktitle = {Plant {Roots}},
	publisher = {CRC Press},
	author = {Mishra, Priyanka and Kidwai, Maria and Lakehal, Abdellah and Bellini, Catherine},
	year = {2024},
	note = {Num Pages: 13},
}

The plant's root system is comprised of primary, lateral, and adventitious roots (ARs). Lateral roots emerge exclusively from existing roots, whereas ARs originate from stem- or leaf-derived cells. The progression of adventitious root development is a natural part of a plant's growth, commonly observed in most monocotyledonous species where they establish the primary root system or in various dicotyledonous plants that reproduce vegetatively. Adventitious rooting holds particular significance in the propagation of economically valuable horticultural and woody species, enabling the cloning of plants and swift establishment of superior genotypes before integrating them into production or breeding schemes. The process of AR development is intricate and influenced by numerous intrinsic and environmental factors, encompassing phytohormones, light exposure, nutritional state, stress responses like injury, and genetic traits. This chapter provides an overview of the latest advancements in research concerning adventitious root formation, with a specific focus on the interplay of key hormones and their interactions, as well as the influence of light, a significant environmental factor.

@article{bellini_synthetic_2024,
	title = {A synthetic auxin for cloning mature trees},
	copyright = {2024 Springer Nature America, Inc.},
	issn = {1546-1696},
	url = {https://www.nature.com/articles/s41587-024-02132-3},
	doi = {10.1038/s41587-024-02132-3},
	abstract = {A synthetic auxin improves the growth of adventitious roots in various plant species.},
	language = {en},
	urldate = {2024-10-07},
	journal = {Nature Biotechnology},
	publisher = {Nature Publishing Group},
	author = {Bellini, Catherine},
	month = jan,
	year = {2024},
	keywords = {Auxin, Plant regeneration},
	pages = {1--2},
}

A synthetic auxin improves the growth of adventitious roots in various plant species.

@article{nanda_chlorospec_2024,
	title = {{ChloroSpec}: {A} new in vivo chlorophyll fluorescence spectrometer for simultaneous wavelength- and time-resolved detection},
	volume = {176},
	copyright = {© 2024 The Authors. Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.14306},
	doi = {10.1111/ppl.14306},
	abstract = {Chlorophyll fluorescence is a ubiquitous tool in basic and applied plant science research. Various standard commercial instruments are available for characterization of photosynthetic material like leaves or microalgae, most of which integrate the overall fluorescence signals above a certain cut-off wavelength. However, wavelength-resolved (fluorescence signals appearing at different wavelengths having different time dependent decay) signals contain vast information required to decompose complex signals and processes into their underlying components that can untangle the photo-physiological process of photosynthesis. Hence, to address this we describe an advanced chlorophyll fluorescence spectrometer - ChloroSpec - allowing three-dimensional simultaneous detection of fluorescence intensities at different wavelengths in a time-resolved manner. We demonstrate for a variety of typical examples that most of the generally used fluorescence parameters are strongly wavelength dependent. This indicates a pronounced heterogeneity and a highly dynamic nature of the thylakoid and the photosynthetic apparatus under actinic illumination. Furthermore, we provide examples of advanced global analysis procedures integrating this three-dimensional signal and relevant information extracted from them that relate to the physiological properties of the organism. This conveniently obtained broad range of data can make ChloroSpec a new standard tool in photosynthesis research.},
	language = {en},
	number = {2},
	urldate = {2024-09-04},
	journal = {Physiologia Plantarum},
	author = {Nanda, Sanchali and Shutova, Tatyana and Cainzos, Maximiliano and Hu, Chen and Sasbrink, Bart and Bag, Pushan and Blanken, Tristian den and Buijs, Ronald and Gracht, Lex van der and Hendriks, Frans and Lambrev, Petar and Limburg, Rob and Mascoli, Vincenzo and Nawrocki, Wojciech J and Reus, Michael and Parmessar, Ramon and Singerling, Björn and Stokkum, Ivo H M and Jansson, Stefan and Holzwarth, Alfred R.},
	month = aug,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14306},
	pages = {e14306},
}

Chlorophyll fluorescence is a ubiquitous tool in basic and applied plant science research. Various standard commercial instruments are available for characterization of photosynthetic material like leaves or microalgae, most of which integrate the overall fluorescence signals above a certain cut-off wavelength. However, wavelength-resolved (fluorescence signals appearing at different wavelengths having different time dependent decay) signals contain vast information required to decompose complex signals and processes into their underlying components that can untangle the photo-physiological process of photosynthesis. Hence, to address this we describe an advanced chlorophyll fluorescence spectrometer - ChloroSpec - allowing three-dimensional simultaneous detection of fluorescence intensities at different wavelengths in a time-resolved manner. We demonstrate for a variety of typical examples that most of the generally used fluorescence parameters are strongly wavelength dependent. This indicates a pronounced heterogeneity and a highly dynamic nature of the thylakoid and the photosynthetic apparatus under actinic illumination. Furthermore, we provide examples of advanced global analysis procedures integrating this three-dimensional signal and relevant information extracted from them that relate to the physiological properties of the organism. This conveniently obtained broad range of data can make ChloroSpec a new standard tool in photosynthesis research.

@article{lorrai_cell_2024,
	title = {Cell wall integrity modulates {HOOKLESS1} and {PHYTOCHROME} {INTERACTING} {FACTOR4} expression controlling apical hook formation},
	volume = {196},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiae370},
	doi = {10.1093/plphys/kiae370},
	abstract = {Formation of the apical hook in etiolated dicot seedlings results from differential growth in the hypocotyl apex and is tightly controlled by environmental cues and hormones, among which auxin and gibberellins (GAs) play an important role. Cell expansion is tightly regulated by the cell wall, but whether and how feedback from this structure contributes to hook development are still unclear. Here, we show that etiolated seedlings of the Arabidopsis (Arabidopsis thaliana) quasimodo2-1 (qua2) mutant, defective in pectin biosynthesis, display severe defects in apical hook formation and maintenance, accompanied by loss of asymmetric auxin maxima and differential cell expansion. Moreover, qua2 seedlings show reduced expression of HOOKLESS1 (HLS1) and PHYTOCHROME INTERACTING FACTOR4 (PIF4), which are positive regulators of hook formation. Treatment of wild-type seedlings with the cellulose inhibitor isoxaben (isx) also prevents hook development and represses HLS1 and PIF4 expression. Exogenous GAs, loss of DELLA proteins, or HLS1 overexpression partially restore hook development in qua2 and isx-treated seedlings. Interestingly, increased agar concentration in the medium restores, both in qua2 and isx-treated seedlings, hook formation, asymmetric auxin maxima, and PIF4 and HLS1 expression. Analyses of plants expressing a Förster resonance energy transfer-based GA sensor indicate that isx reduces accumulation of GAs in the apical hook region in a turgor-dependent manner. Lack of the cell wall integrity sensor THESEUS 1, which modulates turgor loss point, restores hook formation in qua2 and isx-treated seedlings. We propose that turgor-dependent signals link changes in cell wall integrity to the PIF4-HLS1 signaling module to control differential cell elongation during hook formation.},
	number = {2},
	urldate = {2024-10-04},
	journal = {Plant Physiology},
	author = {Lorrai, Riccardo and Erguvan, Özer and Raggi, Sara and Jonsson, Kristoffer and Široká, Jitka and Tarkowská, Danuše and Novák, Ondřej and Griffiths, Jayne and Jones, Alexander M and Verger, Stéphane and Robert, Stéphanie and Ferrari, Simone},
	month = oct,
	year = {2024},
	pages = {1562--1578},
}

Formation of the apical hook in etiolated dicot seedlings results from differential growth in the hypocotyl apex and is tightly controlled by environmental cues and hormones, among which auxin and gibberellins (GAs) play an important role. Cell expansion is tightly regulated by the cell wall, but whether and how feedback from this structure contributes to hook development are still unclear. Here, we show that etiolated seedlings of the Arabidopsis (Arabidopsis thaliana) quasimodo2-1 (qua2) mutant, defective in pectin biosynthesis, display severe defects in apical hook formation and maintenance, accompanied by loss of asymmetric auxin maxima and differential cell expansion. Moreover, qua2 seedlings show reduced expression of HOOKLESS1 (HLS1) and PHYTOCHROME INTERACTING FACTOR4 (PIF4), which are positive regulators of hook formation. Treatment of wild-type seedlings with the cellulose inhibitor isoxaben (isx) also prevents hook development and represses HLS1 and PIF4 expression. Exogenous GAs, loss of DELLA proteins, or HLS1 overexpression partially restore hook development in qua2 and isx-treated seedlings. Interestingly, increased agar concentration in the medium restores, both in qua2 and isx-treated seedlings, hook formation, asymmetric auxin maxima, and PIF4 and HLS1 expression. Analyses of plants expressing a Förster resonance energy transfer-based GA sensor indicate that isx reduces accumulation of GAs in the apical hook region in a turgor-dependent manner. Lack of the cell wall integrity sensor THESEUS 1, which modulates turgor loss point, restores hook formation in qua2 and isx-treated seedlings. We propose that turgor-dependent signals link changes in cell wall integrity to the PIF4-HLS1 signaling module to control differential cell elongation during hook formation.

@article{kankaanpaa_extracellular_2024,
	title = {Extracellular vesicles of {Norway} spruce contain precursors and enzymes for lignin formation and salicylic acid},
	volume = {196},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiae287},
	doi = {10.1093/plphys/kiae287},
	abstract = {Lignin is a phenolic polymer in plants that rigidifies the cell walls of water-conducting tracheary elements and support-providing fibers and stone cells. Different mechanisms have been suggested for the transport of lignin precursors to the site of lignification in the cell wall. Extracellular vesicle (EV)-enriched samples isolated from a lignin-forming cell suspension culture of Norway spruce (Picea abies L. Karst.) contained both phenolic metabolites and enzymes related to lignin biosynthesis. Metabolomic analysis revealed mono-, di-, and oligolignols in the EV isolates, as well as carbohydrates and amino acids. In addition, salicylic acid (SA) and some proteins involved in SA signaling were detected in the EV-enriched samples. A proteomic analysis detected several laccases, peroxidases, β-glucosidases, putative dirigent proteins, and cell wall-modifying enzymes, such as glycosyl hydrolases, transglucosylase/hydrolases, and expansins in EVs. Our findings suggest that EVs are involved in transporting enzymes required for lignin polymerization in Norway spruce, and radical coupling of monolignols can occur in these vesicles.},
	number = {2},
	urldate = {2024-10-04},
	journal = {Plant Physiology},
	author = {Kankaanpää, Santeri and Väisänen, Enni and Goeminne, Geert and Soliymani, Rabah and Desmet, Sandrien and Samoylenko, Anatoliy and Vainio, Seppo and Wingsle, Gunnar and Boerjan, Wout and Vanholme, Ruben and Kärkönen, Anna},
	month = oct,
	year = {2024},
	pages = {788--809},
}

Lignin is a phenolic polymer in plants that rigidifies the cell walls of water-conducting tracheary elements and support-providing fibers and stone cells. Different mechanisms have been suggested for the transport of lignin precursors to the site of lignification in the cell wall. Extracellular vesicle (EV)-enriched samples isolated from a lignin-forming cell suspension culture of Norway spruce (Picea abies L. Karst.) contained both phenolic metabolites and enzymes related to lignin biosynthesis. Metabolomic analysis revealed mono-, di-, and oligolignols in the EV isolates, as well as carbohydrates and amino acids. In addition, salicylic acid (SA) and some proteins involved in SA signaling were detected in the EV-enriched samples. A proteomic analysis detected several laccases, peroxidases, β-glucosidases, putative dirigent proteins, and cell wall-modifying enzymes, such as glycosyl hydrolases, transglucosylase/hydrolases, and expansins in EVs. Our findings suggest that EVs are involved in transporting enzymes required for lignin polymerization in Norway spruce, and radical coupling of monolignols can occur in these vesicles.

@article{aliaga_fandino_ectopic_2024,
	title = {Ectopic assembly of an auxin efflux control machinery shifts developmental trajectories},
	volume = {36},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koae023},
	doi = {10.1093/plcell/koae023},
	abstract = {Polar auxin transport in the Arabidopsis (Arabidopsis thaliana) root tip maintains high auxin levels around the stem cell niche that gradually decrease in dividing cells but increase again once they transition toward differentiation. Protophloem differentiates earlier than other proximal tissues and employs a unique auxin “canalization” machinery that is thought to balance auxin efflux with retention. It consists of a proposed activator of PIN-FORMED (PIN) auxin efflux carriers, the cAMP-, cGMP- and Calcium-dependent (AGC) kinase PROTEIN KINASE ASSOCIATED WITH BRX (PAX); its inhibitor, BREVIS RADIX (BRX); and PHOSPHATIDYLINOSITOL-4-PHOSPHATE-5-KINASE (PIP5K) enzymes, which promote polar PAX and BRX localization. Because of a dynamic PAX–BRX–PIP5K interplay, the net cellular output of this machinery remains unclear. In this study, we deciphered the dosage-sensitive regulatory interactions among PAX, BRX, and PIP5K by their ectopic expression in developing xylem vessels. The data suggest that the dominant collective output of the PAX–BRX–PIP5K module is a localized reduction in PIN abundance. This requires PAX-stimulated clathrin-mediated PIN endocytosis upon site-specific phosphorylation, which distinguishes PAX from other AGC kinases. An ectopic assembly of the PAX–BRX–PIP5K module is sufficient to cause cellular auxin retention and affects root growth vigor by accelerating the trajectory of xylem vessel development. Our data thus provide direct evidence that local manipulation of auxin efflux alters the timing of cellular differentiation in the root.},
	number = {5},
	urldate = {2024-10-02},
	journal = {The Plant Cell},
	author = {Aliaga Fandino, Ana Cecilia and Jelínková, Adriana and Marhava, Petra and Petrášek, Jan and Hardtke, Christian S},
	month = may,
	year = {2024},
	pages = {1791--1805},
}

Polar auxin transport in the Arabidopsis (Arabidopsis thaliana) root tip maintains high auxin levels around the stem cell niche that gradually decrease in dividing cells but increase again once they transition toward differentiation. Protophloem differentiates earlier than other proximal tissues and employs a unique auxin “canalization” machinery that is thought to balance auxin efflux with retention. It consists of a proposed activator of PIN-FORMED (PIN) auxin efflux carriers, the cAMP-, cGMP- and Calcium-dependent (AGC) kinase PROTEIN KINASE ASSOCIATED WITH BRX (PAX); its inhibitor, BREVIS RADIX (BRX); and PHOSPHATIDYLINOSITOL-4-PHOSPHATE-5-KINASE (PIP5K) enzymes, which promote polar PAX and BRX localization. Because of a dynamic PAX–BRX–PIP5K interplay, the net cellular output of this machinery remains unclear. In this study, we deciphered the dosage-sensitive regulatory interactions among PAX, BRX, and PIP5K by their ectopic expression in developing xylem vessels. The data suggest that the dominant collective output of the PAX–BRX–PIP5K module is a localized reduction in PIN abundance. This requires PAX-stimulated clathrin-mediated PIN endocytosis upon site-specific phosphorylation, which distinguishes PAX from other AGC kinases. An ectopic assembly of the PAX–BRX–PIP5K module is sufficient to cause cellular auxin retention and affects root growth vigor by accelerating the trajectory of xylem vessel development. Our data thus provide direct evidence that local manipulation of auxin efflux alters the timing of cellular differentiation in the root.

@article{carrio-segui_weight-induced_2024,
	title = {Weight-induced radial growth in plant stems depends on {PIN3}},
	volume = {34},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982224010042},
	doi = {10.1016/j.cub.2024.07.065},
	abstract = {How multiple growth programs coordinate during development is a fundamental question in biology. During plant stem development, radial growth is continuously adjusted in response to longitudinal-growth-derived weight increase to guarantee stability.1,2,3 Here, we demonstrate that weight-stimulated stem radial growth depends on the auxin efflux carrier PIN3, which, upon weight increase, expands its cellular localization from the lower to the lateral sides of xylem parenchyma, phloem, procambium, and starch sheath cells, imposing a radial auxin flux that results in radial growth. Using the protein synthesis inhibitor cycloheximide (CHX) or the fluorescent endocytic tracer FM4-64, we reveal that this expansion of the PIN3 cellular localization domain occurs because weight increase breaks the balance between PIN3 biosynthesis and removal, favoring PIN3 biosynthesis. Experimentation using brefeldin A (BFA) treatments or arg1 and arl2 mutants further supports this conclusion. Analyses of CRISPR-Cas9 lines for Populus PIN3 orthologs reveals that PIN3 dependence of weight-induced radial growth is conserved at least in these woody species. Altogether, our work sheds new light on how longitudinal and radial growth coordinate during stem development.},
	number = {18},
	urldate = {2024-09-27},
	journal = {Current Biology},
	author = {Carrió-Seguí, Àngela and Brunot-Garau, Paula and Úrbez, Cristina and Miskolczi, Pál and Vera-Sirera, Francisco and Tuominen, Hannele and Agustí, Javier},
	month = sep,
	year = {2024},
	keywords = {Arabidopsis, PIN, Populus, auxin, cambium, meristem, plant development, proprioception, stem radial growth, wood development},
	pages = {4285--4293.e3},
}

How multiple growth programs coordinate during development is a fundamental question in biology. During plant stem development, radial growth is continuously adjusted in response to longitudinal-growth-derived weight increase to guarantee stability.1,2,3 Here, we demonstrate that weight-stimulated stem radial growth depends on the auxin efflux carrier PIN3, which, upon weight increase, expands its cellular localization from the lower to the lateral sides of xylem parenchyma, phloem, procambium, and starch sheath cells, imposing a radial auxin flux that results in radial growth. Using the protein synthesis inhibitor cycloheximide (CHX) or the fluorescent endocytic tracer FM4-64, we reveal that this expansion of the PIN3 cellular localization domain occurs because weight increase breaks the balance between PIN3 biosynthesis and removal, favoring PIN3 biosynthesis. Experimentation using brefeldin A (BFA) treatments or arg1 and arl2 mutants further supports this conclusion. Analyses of CRISPR-Cas9 lines for Populus PIN3 orthologs reveals that PIN3 dependence of weight-induced radial growth is conserved at least in these woody species. Altogether, our work sheds new light on how longitudinal and radial growth coordinate during stem development.

@article{ranade_lignin_2024,
	title = {Lignin biosynthesis pathway repressors in gymnosperms: differential repressor domains as compared to angiosperms},
	volume = {4},
	copyright = {2024 The Author(s)},
	issn = {2767-3812},
	shorttitle = {Lignin biosynthesis pathway repressors in gymnosperms},
	url = {https://www.maxapress.com/article/doi/10.48130/forres-0024-0029},
	doi = {10.48130/forres-0024-0029},
	abstract = {{\textless}p{\textgreater}Lignin is a polyphenolic polymer present in the cell walls of specialized plant cell types in vascular plants that provides structural support and plays a major role in plant protection. The lignin biosynthesis pathway is regulated by transcription factors from the MYB (myeloblastosis) family. While several MYB members positively regulate lignin synthesis, only a few negatively regulate lignin synthesis. These lignin suppressors are well characterized in model plant species; however, their role has not been fully explored in gymnosperms. Lignin forms one of the major hurdles for the forest-based industry e.g. paper, pulp, and biofuel production. Therefore, the detailed mechanisms involved in the regulation of lignin synthesis are valuable, especially in conifers that form the major source of softwood for timber and paper production. In this review, the potential and differential domains present in the MYB suppressors in gymnosperms are discussed, along with their phylogenetic analysis. Sequence analysis revealed that the N-terminal regions of the MYB suppressor members were found to be conserved among the gymnosperms and angiosperms containing the R2, R3, and bHLH domains, while the C-terminal regions were found to be highly variable. The typical repressor motifs like the LxLxL-type EAR motif and the TLLLFR motif were absent from the C-terminal regions of MYB suppressors from most gymnosperms. However, although the gymnosperms lacked the characteristic repressor domains, a R2R3-type MYB member from \textit{Ginkgo} was reported to repress the lignin biosynthetic pathway. It is proposed that gymnosperms possess unique kinds of repressors that need further functional validation.{\textless}/p{\textgreater}},
	language = {en},
	number = {1},
	urldate = {2024-09-27},
	journal = {Forestry Research},
	publisher = {Maximum Academic Press},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario and Ranade, Sonali Sachin and García-Gil, María Rosario},
	month = sep,
	year = {2024},
	note = {Bandiera\_abtest: a
Cc\_license\_type: cc\_by
Cg\_type: Maximum Academic Press
Number: forres-0024-0029
Primary\_atype: Forestry Research
Subject\_term: MINI REVIEW
Subject\_term\_id: MINI REVIEW},
}

\textlessp\textgreaterLignin is a polyphenolic polymer present in the cell walls of specialized plant cell types in vascular plants that provides structural support and plays a major role in plant protection. The lignin biosynthesis pathway is regulated by transcription factors from the MYB (myeloblastosis) family. While several MYB members positively regulate lignin synthesis, only a few negatively regulate lignin synthesis. These lignin suppressors are well characterized in model plant species; however, their role has not been fully explored in gymnosperms. Lignin forms one of the major hurdles for the forest-based industry e.g. paper, pulp, and biofuel production. Therefore, the detailed mechanisms involved in the regulation of lignin synthesis are valuable, especially in conifers that form the major source of softwood for timber and paper production. In this review, the potential and differential domains present in the MYB suppressors in gymnosperms are discussed, along with their phylogenetic analysis. Sequence analysis revealed that the N-terminal regions of the MYB suppressor members were found to be conserved among the gymnosperms and angiosperms containing the R2, R3, and bHLH domains, while the C-terminal regions were found to be highly variable. The typical repressor motifs like the LxLxL-type EAR motif and the TLLLFR motif were absent from the C-terminal regions of MYB suppressors from most gymnosperms. However, although the gymnosperms lacked the characteristic repressor domains, a R2R3-type MYB member from Ginkgo was reported to repress the lignin biosynthetic pathway. It is proposed that gymnosperms possess unique kinds of repressors that need further functional validation.\textless/p\textgreater

@article{canovi_resource_2024,
	title = {A resource of identified and annotated {lincRNAs} expressed during somatic embryogenesis development in {Norway} spruce},
	volume = {176},
	copyright = {© 2024 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.14537},
	doi = {10.1111/ppl.14537},
	abstract = {Long non-coding RNAs (lncRNAs) have emerged as important regulators of many biological processes, although their regulatory roles remain poorly characterized in woody plants, especially in gymnosperms. A major challenge of working with lncRNAs is to assign functional annotations, since they have a low coding potential and low cross-species conservation. We utilised an existing RNA-Sequencing resource and performed short RNA sequencing of somatic embryogenesis developmental stages in Norway spruce (Picea abies L. Karst). We implemented a pipeline to identify lncRNAs located within the intergenic space (lincRNAs) and generated a co-expression network including protein coding, lincRNA and miRNA genes. To assign putative functional annotation, we employed a guilt-by-association approach using the co-expression network and integrated these results with annotation assigned using semantic similarity and co-expression. Moreover, we evaluated the relationship between lincRNAs and miRNAs, and identified which lincRNAs are conserved in other species. We identified lincRNAs with clear evidence of differential expression during somatic embryogenesis and used network connectivity to identify those with the greatest regulatory potential. This work provides the most comprehensive view of lincRNAs in Norway spruce and is the first study to perform global identification of lincRNAs during somatic embryogenesis in conifers. The data have been integrated into the expression visualisation tools at the PlantGenIE.org web resource to enable easy access to the community. This will facilitate the use of the data to address novel questions about the role of lincRNAs in the regulation of embryogenesis and facilitate future comparative genomics studies.},
	language = {en},
	number = {5},
	urldate = {2024-09-27},
	journal = {Physiologia Plantarum},
	author = {Canovi, Camilla and Stojkovič, Katja and Benítez, Aarón Ayllón and Delhomme, Nicolas and Egertsdotter, Ulrika and Street, Nathaniel R.},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14537},
	pages = {e14537},
}

Long non-coding RNAs (lncRNAs) have emerged as important regulators of many biological processes, although their regulatory roles remain poorly characterized in woody plants, especially in gymnosperms. A major challenge of working with lncRNAs is to assign functional annotations, since they have a low coding potential and low cross-species conservation. We utilised an existing RNA-Sequencing resource and performed short RNA sequencing of somatic embryogenesis developmental stages in Norway spruce (Picea abies L. Karst). We implemented a pipeline to identify lncRNAs located within the intergenic space (lincRNAs) and generated a co-expression network including protein coding, lincRNA and miRNA genes. To assign putative functional annotation, we employed a guilt-by-association approach using the co-expression network and integrated these results with annotation assigned using semantic similarity and co-expression. Moreover, we evaluated the relationship between lincRNAs and miRNAs, and identified which lincRNAs are conserved in other species. We identified lincRNAs with clear evidence of differential expression during somatic embryogenesis and used network connectivity to identify those with the greatest regulatory potential. This work provides the most comprehensive view of lincRNAs in Norway spruce and is the first study to perform global identification of lincRNAs during somatic embryogenesis in conifers. The data have been integrated into the expression visualisation tools at the PlantGenIE.org web resource to enable easy access to the community. This will facilitate the use of the data to address novel questions about the role of lincRNAs in the regulation of embryogenesis and facilitate future comparative genomics studies.

@article{gessler_marriage_2024,
	title = {The marriage between stable isotope ecology and plant metabolomics – new perspectives for metabolic flux analysis and the interpretation of ecological archives},
	volume = {244},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19973},
	doi = {10.1111/nph.19973},
	abstract = {Even though they share many thematical overlaps, plant metabolomics and stable isotope ecology have been rather separate fields mainly due to different mass spectrometry demands. New high-resolution bioanalytical mass spectrometers are now not only offering high-throughput metabolite identification but are also suitable for compound- and intramolecular position-specific isotope analysis in the natural isotope abundance range. In plant metabolomics, label-free metabolic pathway and metabolic flux analysis might become possible when applying this new technology. This is because changes in the commitment of substrates to particular metabolic pathways and the activation or deactivation of others alter enzyme-specific isotope effects. This leads to differences in intramolecular and compound-specific isotope compositions. In plant isotope ecology, position-specific isotope analysis in plant archives informed by metabolic pathway analysis could be used to reconstruct and separate environmental impacts on complex metabolic processes. A technology-driven linkage between the two disciplines could allow us to extract information on environment–metabolism interaction from plant archives such as tree rings but also within ecosystems. This would contribute to a holistic understanding of how plants react to environmental drivers, thus also providing helpful information on the trajectories of the vegetation under the conditions to come.},
	language = {en},
	number = {1},
	urldate = {2024-09-19},
	journal = {New Phytologist},
	author = {Gessler, Arthur and Wieloch, Thomas and Saurer, Matthias and Lehmann, Marco M. and Werner, Roland A. and Kammerer, Bernd},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19973},
	keywords = {MS/MS, compound-specific isotope analysis, intramolecular isotope distribution, isotope ratio mass spectrometer, metabolic fluxes, soft ionisation},
	pages = {21--31},
}

Even though they share many thematical overlaps, plant metabolomics and stable isotope ecology have been rather separate fields mainly due to different mass spectrometry demands. New high-resolution bioanalytical mass spectrometers are now not only offering high-throughput metabolite identification but are also suitable for compound- and intramolecular position-specific isotope analysis in the natural isotope abundance range. In plant metabolomics, label-free metabolic pathway and metabolic flux analysis might become possible when applying this new technology. This is because changes in the commitment of substrates to particular metabolic pathways and the activation or deactivation of others alter enzyme-specific isotope effects. This leads to differences in intramolecular and compound-specific isotope compositions. In plant isotope ecology, position-specific isotope analysis in plant archives informed by metabolic pathway analysis could be used to reconstruct and separate environmental impacts on complex metabolic processes. A technology-driven linkage between the two disciplines could allow us to extract information on environment–metabolism interaction from plant archives such as tree rings but also within ecosystems. This would contribute to a holistic understanding of how plants react to environmental drivers, thus also providing helpful information on the trajectories of the vegetation under the conditions to come.

@article{vittozzi_abi5_2024,
	title = {{ABI5} binding proteins: key players in coordinating plant growth and development},
	volume = {29},
	issn = {1360-1385},
	shorttitle = {{ABI5} binding proteins},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138524000657},
	doi = {10.1016/j.tplants.2024.03.009},
	abstract = {During the course of terrestrial evolution, plants have developed complex networks that involve the coordination of phytohormone signalling pathways in order to adapt to an ever-changing environment. Transcription factors coordinate these responses by engaging in different protein complexes and exerting both positive and negative effects. ABA INSENSITIVE 5 (ABI5) binding proteins (AFPs), which are closely related to NOVEL INTERACTOR OF JAZ (NINJA)-like proteins, are known for their fundamental role in plants’ morphological and physiological growth. Recent studies have shown that AFPs regulate several hormone-signalling pathways, including abscisic acid (ABA) and gibberellic acid (GA). Here, we review the genetic control of AFPs and their crosstalk with plant hormone signalling, and discuss the contributions of AFPs to plants’ growth and development.},
	number = {9},
	urldate = {2024-09-20},
	journal = {Trends in Plant Science},
	author = {Vittozzi, Ylenia and Krüger, Thorben and Majee, Adity and Née, Guillaume and Wenkel, Stephan},
	month = sep,
	year = {2024},
	keywords = {AFP (ABI5 binding protein), abscisic acid, flowering regulation, microprotein, seed germination},
	pages = {1006--1017},
}

During the course of terrestrial evolution, plants have developed complex networks that involve the coordination of phytohormone signalling pathways in order to adapt to an ever-changing environment. Transcription factors coordinate these responses by engaging in different protein complexes and exerting both positive and negative effects. ABA INSENSITIVE 5 (ABI5) binding proteins (AFPs), which are closely related to NOVEL INTERACTOR OF JAZ (NINJA)-like proteins, are known for their fundamental role in plants’ morphological and physiological growth. Recent studies have shown that AFPs regulate several hormone-signalling pathways, including abscisic acid (ABA) and gibberellic acid (GA). Here, we review the genetic control of AFPs and their crosstalk with plant hormone signalling, and discuss the contributions of AFPs to plants’ growth and development.

@article{robinson_improved_2024,
	title = {An {Improved} {Chromosome}-scale {Genome} {Assembly} and {Population} {Genetics} resource for {Populus} tremula.},
	volume = {176},
	copyright = {© 2024 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.14511},
	doi = {10.1111/ppl.14511},
	abstract = {Aspen (Populus tremula L.) is a keystone species and a model system for forest tree genomics. We present an updated resource comprising a chromosome-scale assembly, population genetics and genomics data. Using the resource, we explore the genetic basis of natural variation in leaf size and shape, traits with complex genetic architecture. We generated the genome assembly using long-read sequencing, optical and high-density genetic maps. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection. Using the assembly and re-sequencing data from the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections we performed genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for 26 leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq), identified genomic regions of accessible chromatin, and subset SNPs to these regions, improving the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples, quantified their expression in an updated co-expression network, and used this to explore the functions of candidate genes identified from the GWAS. A GWAS found SNP associations for seven traits. The associated SNPs were in or near genes annotated with developmental functions, which represent candidates for further study. Of particular interest was a 177-kbp region harbouring associations with several leaf phenotypes in ScotAsp. We have incorporated the assembly, population genetics, genomics, and GWAS data into the PlantGenIE.org web resource, including updating existing genomics data to the new genome version, to enable easy exploration and visualisation. We provide all raw and processed data to facilitate reuse in future studies.},
	language = {en},
	number = {5},
	urldate = {2024-09-19},
	journal = {Physiologia Plantarum},
	author = {Robinson, Kathryn M. and Schiffthaler, Bastian and Liu, Hui and Rydman, Sara M. and Rendón-Anaya, Martha and Kalman, Teitur Ahlgren and Kumar, Vikash and Canovi, Camilla and Bernhardsson, Carolina and Delhomme, Nicolas and Jenkins, Jerry and Wang, Jing and Mähler, Niklas and Richau, Kerstin H. and Stokes, Victoria and A'Hara, Stuart and Cottrell, Joan and Coeck, Kizi and Diels, Tim and Vandepoele, Klaas and Mannapperuma, Chanaka and Park, Eung-Jun and Plaisance, Stephane and Jansson, Stefan and Ingvarsson, Pär K. and Street, Nathaniel R.},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14511},
	keywords = {ATAC-Seq, GWAS, Populus, aspen, co-expression, genetic architecture, genome assembly, leaf physiognomy, leaf shape, leaf size, lncRNA, natural selection, population genetics},
	pages = {e14511},
}

Aspen (Populus tremula L.) is a keystone species and a model system for forest tree genomics. We present an updated resource comprising a chromosome-scale assembly, population genetics and genomics data. Using the resource, we explore the genetic basis of natural variation in leaf size and shape, traits with complex genetic architecture. We generated the genome assembly using long-read sequencing, optical and high-density genetic maps. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection. Using the assembly and re-sequencing data from the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections we performed genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for 26 leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq), identified genomic regions of accessible chromatin, and subset SNPs to these regions, improving the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples, quantified their expression in an updated co-expression network, and used this to explore the functions of candidate genes identified from the GWAS. A GWAS found SNP associations for seven traits. The associated SNPs were in or near genes annotated with developmental functions, which represent candidates for further study. Of particular interest was a 177-kbp region harbouring associations with several leaf phenotypes in ScotAsp. We have incorporated the assembly, population genetics, genomics, and GWAS data into the PlantGenIE.org web resource, including updating existing genomics data to the new genome version, to enable easy exploration and visualisation. We provide all raw and processed data to facilitate reuse in future studies.

@article{meena_antisense_2024,
	title = {Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in {Arabidopsis}},
	volume = {36},
	issn = {1532-298X},
	doi = {10.1093/plcell/koae160},
	abstract = {Transcription of antisense long noncoding RNAs (lncRNAs) occurs pervasively across eukaryotic genomes. Only a few antisense lncRNAs have been characterized and shown to control biological processes, albeit with idiosyncratic regulatory mechanisms. Thus, we largely lack knowledge about the general role of antisense transcription in eukaryotic organisms. Here, we characterized genes with antisense transcription initiating close to the poly(A) signal of genes (PAS genes) in Arabidopsis (Arabidopsis thaliana). We compared plant native elongation transcript sequencing (plaNET-seq) with RNA sequencing during short-term cold exposure and detected massive differences between the response in active transcription and steady-state levels of PAS gene-derived mRNAs. The cold-induced expression of transcription factors B-BOX DOMAIN PROTEIN28 (BBX28) and C2H2-TYPE ZINC FINGER FAMILY PROTEIN5 (ZAT5) was detected by plaNET-seq, while their steady-state level was only slightly altered due to high mRNA turnover. Knockdown of BBX28 and ZAT5 or of their respective antisense transcripts severely compromised plant freezing tolerance. Decreased antisense transcript expression levels resulted in a reduced cold response of BBX28 and ZAT5, revealing a positive regulatory role of both antisense transcripts. This study expands the known repertoire of noncoding transcripts. It highlights that native transcription approaches can complement steady-state RNA techniques to identify biologically relevant players in stress responses.},
	language = {eng},
	number = {9},
	journal = {The Plant Cell},
	author = {Meena, Shiv Kumar and Quevedo, Marti and Nardeli, Sarah Muniz and Verez, Clément and Bhat, Susheel Sagar and Zacharaki, Vasiliki and Kindgren, Peter},
	month = sep,
	year = {2024},
	keywords = {Arabidopsis, Arabidopsis Proteins, Cold Temperature, Cold-Shock Response, Gene Expression Regulation, Plant, RNA, Antisense, RNA, Messenger, Stress, Physiological, Transcription Factors, Transcription, Genetic},
	pages = {3467--3482},
}

Transcription of antisense long noncoding RNAs (lncRNAs) occurs pervasively across eukaryotic genomes. Only a few antisense lncRNAs have been characterized and shown to control biological processes, albeit with idiosyncratic regulatory mechanisms. Thus, we largely lack knowledge about the general role of antisense transcription in eukaryotic organisms. Here, we characterized genes with antisense transcription initiating close to the poly(A) signal of genes (PAS genes) in Arabidopsis (Arabidopsis thaliana). We compared plant native elongation transcript sequencing (plaNET-seq) with RNA sequencing during short-term cold exposure and detected massive differences between the response in active transcription and steady-state levels of PAS gene-derived mRNAs. The cold-induced expression of transcription factors B-BOX DOMAIN PROTEIN28 (BBX28) and C2H2-TYPE ZINC FINGER FAMILY PROTEIN5 (ZAT5) was detected by plaNET-seq, while their steady-state level was only slightly altered due to high mRNA turnover. Knockdown of BBX28 and ZAT5 or of their respective antisense transcripts severely compromised plant freezing tolerance. Decreased antisense transcript expression levels resulted in a reduced cold response of BBX28 and ZAT5, revealing a positive regulatory role of both antisense transcripts. This study expands the known repertoire of noncoding transcripts. It highlights that native transcription approaches can complement steady-state RNA techniques to identify biologically relevant players in stress responses.

@article{luomaranta_systems_2024,
	title = {Systems genetic analysis of lignin biosynthesis in \textit{{Populus} tremula}},
	volume = {243},
	issn = {0028-646X, 1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.19993},
	doi = {10.1111/nph.19993},
	abstract = {Summary
            
              
                
                  
                    The genetic control underlying natural variation in lignin content and composition in trees is not fully understood. We performed a systems genetic analysis to uncover the genetic regulation of lignin biosynthesis in a natural ‘SwAsp’ population of aspen (
                    Populus tremula
                    ) trees.
                  
                
                
                  We analyzed gene expression by RNA sequencing (RNA‐seq) in differentiating xylem tissues, and lignin content and composition using Pyrolysis‐GC‐MS in mature wood of 268 trees from 99 genotypes.
                
                
                  
                    Abundant variation was observed for lignin content and composition, and genome‐wide association study identified proteins in the pentose phosphate pathway and arabinogalactan protein glycosylation among the top‐ranked genes that are associated with these traits. Variation in gene expression and the associated genetic polymorphism was revealed through the identification of 312 705 local and 292 003 distant expression quantitative trait loci (eQTL). A co‐expression network analysis suggested modularization of lignin biosynthesis and novel functions for the lignin‐biosynthetic CINNAMYL ALCOHOL DEHYDROGENASE 2 and CAFFEOYL‐CoA O‐METHYLTRANSFERASE 3.
                    PHENYLALANINE AMMONIA LYASE 3
                    was co‐expressed with
                    HOMEOBOX PROTEIN 5
                    (HB5), and the role of HB5 in stimulating lignification was demonstrated in transgenic trees.
                  
                
                
                  The systems genetic approach allowed linking natural variation in lignin biosynthesis to trees´ responses to external cues such as mechanical stimulus and nutrient availability.},
	language = {en},
	number = {6},
	urldate = {2024-08-30},
	journal = {New Phytologist},
	author = {Luomaranta, Mikko and Grones, Carolin and Choudhary, Shruti and Milhinhos, Ana and Kalman, Teitur Ahlgren and Nilsson, Ove and Robinson, Kathryn M. and Street, Nathaniel R. and Tuominen, Hannele},
	month = sep,
	year = {2024},
	keywords = {GWAS, HD-Zip III, Populus, aspen, eQTL, lignin biosynthesis, wood formation},
	pages = {2157--2174},
}

Summary The genetic control underlying natural variation in lignin content and composition in trees is not fully understood. We performed a systems genetic analysis to uncover the genetic regulation of lignin biosynthesis in a natural ‘SwAsp’ population of aspen ( Populus tremula ) trees. We analyzed gene expression by RNA sequencing (RNA‐seq) in differentiating xylem tissues, and lignin content and composition using Pyrolysis‐GC‐MS in mature wood of 268 trees from 99 genotypes. Abundant variation was observed for lignin content and composition, and genome‐wide association study identified proteins in the pentose phosphate pathway and arabinogalactan protein glycosylation among the top‐ranked genes that are associated with these traits. Variation in gene expression and the associated genetic polymorphism was revealed through the identification of 312 705 local and 292 003 distant expression quantitative trait loci (eQTL). A co‐expression network analysis suggested modularization of lignin biosynthesis and novel functions for the lignin‐biosynthetic CINNAMYL ALCOHOL DEHYDROGENASE 2 and CAFFEOYL‐CoA O‐METHYLTRANSFERASE 3. PHENYLALANINE AMMONIA LYASE 3 was co‐expressed with HOMEOBOX PROTEIN 5 (HB5), and the role of HB5 in stimulating lignification was demonstrated in transgenic trees. The systems genetic approach allowed linking natural variation in lignin biosynthesis to trees´ responses to external cues such as mechanical stimulus and nutrient availability.

@article{sivan_unraveling_2024,
	title = {Unraveling the unique structural motifs of glucuronoxylan from hybrid aspen wood},
	volume = {343},
	issn = {01448617},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S014486172400660X},
	doi = {10.1016/j.carbpol.2024.122434},
	language = {en},
	urldate = {2024-08-30},
	journal = {Carbohydrate Polymers},
	author = {Sivan, Pramod and Heinonen, Emilia and Escudero, Louis and Gandla, Madhavi Latha and Jiménez-Quero, Amparo and Jönsson, Leif J. and Mellerowicz, Ewa J. and Vilaplana, Francisco},
	month = nov,
	year = {2024},
	pages = {122434},
}

@article{jaillais_guidelines_2024,
	title = {Guidelines for naming and studying plasma membrane domains in plants},
	volume = {10},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-024-01742-8},
	doi = {10.1038/s41477-024-01742-8},
	language = {en},
	number = {8},
	urldate = {2024-08-30},
	journal = {Nature Plants},
	author = {Jaillais, Yvon and Bayer, Emmanuelle and Bergmann, Dominique C. and Botella, Miguel A. and Boutté, Yohann and Bozkurt, Tolga O. and Caillaud, Marie-Cecile and Germain, Véronique and Grossmann, Guido and Heilmann, Ingo and Hemsley, Piers A. and Kirchhelle, Charlotte and Martinière, Alexandre and Miao, Yansong and Mongrand, Sebastien and Müller, Sabine and Noack, Lise C. and Oda, Yoshihisa and Ott, Thomas and Pan, Xue and Pleskot, Roman and Potocky, Martin and Robert, Stéphanie and Rodriguez, Clara Sanchez and Simon-Plas, Françoise and Russinova, Eugenia and Van Damme, Daniel and Van Norman, Jaimie M. and Weijers, Dolf and Yalovsky, Shaul and Yang, Zhenbiao and Zelazny, Enric and Gronnier, Julien},
	month = aug,
	year = {2024},
	pages = {1172--1183},
}

@article{qamar_segmentation_2024,
	title = {Segmentation and characterization of macerated fibers and vessels using deep learning},
	volume = {20},
	issn = {1746-4811},
	url = {https://plantmethods.biomedcentral.com/articles/10.1186/s13007-024-01244-w},
	doi = {10.1186/s13007-024-01244-w},
	abstract = {Abstract
            
              Purpose
              Wood comprises different cell types, such as fibers, tracheids and vessels, defining its properties. Studying cells’ shape, size, and arrangement in microscopy images is crucial for understanding wood characteristics. Typically, this involves macerating (soaking) samples in a solution to separate cells, then spreading them on slides for imaging with a microscope that covers a wide area, capturing thousands of cells. However, these cells often cluster and overlap in images, making the segmentation difficult and time-consuming using standard image-processing methods.
            
            
              Results
              
                In this work, we developed an automatic deep learning segmentation approach that utilizes the one-stage YOLOv8 model for fast and accurate segmentation and characterization of macerated fiber and vessel form aspen trees in microscopy images. The model can analyze 32,640 x 25,920 pixels images and demonstrate effective cell detection and segmentation, achieving a
                
                  
                    \$\${\textbackslash}hbox \{mAP\}\_\{0.5-0.95\}\$\$
                    
                      
                        mAP
                        
                          0.5
                          -
                          0.95
                        
                      
                    
                  
                
                of 78 \%. To assess the model’s robustness, we examined fibers from a genetically modified tree line known for longer fibers. The outcomes were comparable to previous manual measurements. Additionally, we created a user-friendly web application for image analysis and provided the code for use on Google Colab.
              
            
            
              Conclusion
              By leveraging YOLOv8’s advances, this work provides a deep learning solution to enable efficient quantification and analysis of wood cells suitable for practical applications.},
	language = {en},
	number = {1},
	urldate = {2024-08-30},
	journal = {Plant Methods},
	author = {Qamar, Saqib and Baba, Abu Imran and Verger, Stéphane and Andersson, Magnus},
	month = aug,
	year = {2024},
	pages = {126},
}

Abstract Purpose Wood comprises different cell types, such as fibers, tracheids and vessels, defining its properties. Studying cells’ shape, size, and arrangement in microscopy images is crucial for understanding wood characteristics. Typically, this involves macerating (soaking) samples in a solution to separate cells, then spreading them on slides for imaging with a microscope that covers a wide area, capturing thousands of cells. However, these cells often cluster and overlap in images, making the segmentation difficult and time-consuming using standard image-processing methods. Results In this work, we developed an automatic deep learning segmentation approach that utilizes the one-stage YOLOv8 model for fast and accurate segmentation and characterization of macerated fiber and vessel form aspen trees in microscopy images. The model can analyze 32,640 x 25,920 pixels images and demonstrate effective cell detection and segmentation, achieving a $$\hbox \mAP\_\0.5-0.95\$$ mAP 0.5 - 0.95 of 78 %. To assess the model’s robustness, we examined fibers from a genetically modified tree line known for longer fibers. The outcomes were comparable to previous manual measurements. Additionally, we created a user-friendly web application for image analysis and provided the code for use on Google Colab. Conclusion By leveraging YOLOv8’s advances, this work provides a deep learning solution to enable efficient quantification and analysis of wood cells suitable for practical applications.

@article{blomberg_pseudomonas_2024,
	title = {Pseudomonas syringae infectivity correlates to altered transcript and metabolite levels of {Arabidopsis} mediator mutants},
	volume = {14},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-024-57192-x},
	doi = {10.1038/s41598-024-57192-x},
	abstract = {Abstract
            
              Rapid metabolic responses to pathogens are essential for plant survival and depend on numerous transcription factors. Mediator is the major transcriptional co-regulator for integration and transmission of signals from transcriptional regulators to RNA polymerase II. Using four Arabidopsis Mediator mutants,
              med16
              ,
              med18
              ,
              med25
              and
              cdk8
              , we studied how differences in regulation of their transcript and metabolite levels correlate to their responses to
              Pseudomonas syringae
              infection. We found that
              med16
              and
              cdk8
              were susceptible, while
              med25
              showed increased resistance. Glucosinolate, phytoalexin and carbohydrate levels were reduced already before infection in
              med16
              and
              cdk8
              , but increased in
              med25
              , which also displayed increased benzenoids levels. Early after infection, wild type plants showed reduced glucosinolate and nucleoside levels, but increases in amino acids, benzenoids, oxylipins and the phytoalexin camalexin. The Mediator mutants showed altered levels of these metabolites and in regulation of genes encoding key enzymes for their metabolism. At later stage, mutants displayed defective levels of specific amino acids, carbohydrates, lipids and jasmonates which correlated to their infection response phenotypes. Our results reveal that
              MED16
              ,
              MED25
              and
              CDK8
              are required for a proper, coordinated transcriptional response of genes which encode enzymes involved in important metabolic pathways for Arabidopsis responses to
              Pseudomonas syringae
              infections.},
	language = {en},
	number = {1},
	urldate = {2024-08-30},
	journal = {Scientific Reports},
	author = {Blomberg, Jeanette and Tasselius, Viktor and Vergara, Alexander and Karamat, Fazeelat and Imran, Qari Muhammad and Strand, Åsa and Rosvall, Martin and Björklund, Stefan},
	month = mar,
	year = {2024},
	pages = {6771},
}

Abstract Rapid metabolic responses to pathogens are essential for plant survival and depend on numerous transcription factors. Mediator is the major transcriptional co-regulator for integration and transmission of signals from transcriptional regulators to RNA polymerase II. Using four Arabidopsis Mediator mutants, med16 , med18 , med25 and cdk8 , we studied how differences in regulation of their transcript and metabolite levels correlate to their responses to Pseudomonas syringae infection. We found that med16 and cdk8 were susceptible, while med25 showed increased resistance. Glucosinolate, phytoalexin and carbohydrate levels were reduced already before infection in med16 and cdk8 , but increased in med25 , which also displayed increased benzenoids levels. Early after infection, wild type plants showed reduced glucosinolate and nucleoside levels, but increases in amino acids, benzenoids, oxylipins and the phytoalexin camalexin. The Mediator mutants showed altered levels of these metabolites and in regulation of genes encoding key enzymes for their metabolism. At later stage, mutants displayed defective levels of specific amino acids, carbohydrates, lipids and jasmonates which correlated to their infection response phenotypes. Our results reveal that MED16 , MED25 and CDK8 are required for a proper, coordinated transcriptional response of genes which encode enzymes involved in important metabolic pathways for Arabidopsis responses to Pseudomonas syringae infections.

@article{fernandez-calvo_leucine_2024,
	title = {Leucine rich repeat-malectin receptor kinases {IGP1}/{CORK1}, {IGP3} and {IGP4} are required for arabidopsis immune responses triggered by β-1,4-{D}-{Xylo}-oligosaccharides from plant cell walls},
	volume = {11},
	issn = {2468-2330},
	url = {https://www.sciencedirect.com/science/article/pii/S2468233024000069},
	doi = {10.1016/j.tcsw.2024.100124},
	abstract = {Pattern-Triggered Immunity (PTI) in plants is activated upon recognition by Pattern Recognition Receptors (PRRs) of Damage- and Microbe-Associated Molecular Patterns (DAMPs and MAMPs) from plants or microorganisms, respectively. An increasing number of identified DAMPs/MAMPs are carbohydrates from plant cell walls and microbial extracellular layers, which are perceived by plant PRRs, such as LysM and Leucine Rich Repeat-Malectin (LRR-MAL) receptor kinases (RKs). LysM-RKs (e.g. CERK1, LYK4 and LYK5) are needed for recognition of fungal MAMP chitohexaose (β-1,4-D-(GlcNAc)6, CHI6), whereas IGP1/CORK1, IGP3 and IGP4 LRR-MAL RKs are required for perception of β-glucans, like cellotriose (β-1,4-D-(Glc)3, CEL3) and mixed-linked glucans. We have explored the diversity of carbohydrates perceived by Arabidopsis thaliana seedlings by determining PTI responses upon treatment with different oligosaccharides and polysaccharides. These analyses revealed that plant oligosaccharides from xylans [β-1,4-D-(xylose)4 (XYL4)], glucuronoxylans and α-1,4-glucans, and polysaccharides from plants and seaweeds activate PTI. Cross-elicitation experiments of XYL4 with other glycans showed that the mechanism of recognition of XYL4 and the DAMP 33-α-L-arabinofuranosyl-xylotetraose (XA3XX) shares some features with that of CEL3 but differs from that of CHI6. Notably, XYL4 and XA3XX perception is impaired in igp1/cork1, igp3 and igp4 mutants, and almost not affected in cerk1 lyk4 lyk5 triple mutant. XYL4 perception is conserved in different plant species since XYL4 pre-treatment triggers enhanced disease resistance in tomato to Pseudomonas syringae pv tomato DC3000 and PTI responses in wheat. These results expand the number of glycans triggering plant immunity and support IGP1/CORK1, IGP3 and IGP4 relevance in Arabidopsis thaliana glycans perception and PTI activation.
Significance Statement
The characterization of plant immune mechanisms involved in the perception of carbohydrate-based structures recognized as DAMPs/MAMPs is needed to further understand plant disease resistance modulation. We show here that IGP1/CORK1, IGP3 and IGP4 LRR-MAL RKs are required for the perception of carbohydrate-based DAMPs β-1,4-D-(xylose)4 (XYL4) and 33-α-L-arabinofuranosyl-xylotetraose (XA3XX), further expanding the function of these LRR-MAL RKs in plant glycan perception and immune activation.},
	urldate = {2024-08-09},
	journal = {The Cell Surface},
	author = {Fernández-Calvo, Patricia and López, Gemma and Martín-Dacal, Marina and Aitouguinane, Meriem and Carrasco-López, Cristian and González-Bodí, Sara and Bacete, Laura and Mélida, Hugo and Sánchez-Vallet, Andrea and Molina, Antonio},
	month = jun,
	year = {2024},
	keywords = {Cell wall, Disease resistance, Leucine rich repeat-malectin receptor kinases, Pattern triggered immunity, Xylans, Xylotetraose},
	pages = {100124},
}

Pattern-Triggered Immunity (PTI) in plants is activated upon recognition by Pattern Recognition Receptors (PRRs) of Damage- and Microbe-Associated Molecular Patterns (DAMPs and MAMPs) from plants or microorganisms, respectively. An increasing number of identified DAMPs/MAMPs are carbohydrates from plant cell walls and microbial extracellular layers, which are perceived by plant PRRs, such as LysM and Leucine Rich Repeat-Malectin (LRR-MAL) receptor kinases (RKs). LysM-RKs (e.g. CERK1, LYK4 and LYK5) are needed for recognition of fungal MAMP chitohexaose (β-1,4-D-(GlcNAc)6, CHI6), whereas IGP1/CORK1, IGP3 and IGP4 LRR-MAL RKs are required for perception of β-glucans, like cellotriose (β-1,4-D-(Glc)3, CEL3) and mixed-linked glucans. We have explored the diversity of carbohydrates perceived by Arabidopsis thaliana seedlings by determining PTI responses upon treatment with different oligosaccharides and polysaccharides. These analyses revealed that plant oligosaccharides from xylans [β-1,4-D-(xylose)4 (XYL4)], glucuronoxylans and α-1,4-glucans, and polysaccharides from plants and seaweeds activate PTI. Cross-elicitation experiments of XYL4 with other glycans showed that the mechanism of recognition of XYL4 and the DAMP 33-α-L-arabinofuranosyl-xylotetraose (XA3XX) shares some features with that of CEL3 but differs from that of CHI6. Notably, XYL4 and XA3XX perception is impaired in igp1/cork1, igp3 and igp4 mutants, and almost not affected in cerk1 lyk4 lyk5 triple mutant. XYL4 perception is conserved in different plant species since XYL4 pre-treatment triggers enhanced disease resistance in tomato to Pseudomonas syringae pv tomato DC3000 and PTI responses in wheat. These results expand the number of glycans triggering plant immunity and support IGP1/CORK1, IGP3 and IGP4 relevance in Arabidopsis thaliana glycans perception and PTI activation. Significance Statement The characterization of plant immune mechanisms involved in the perception of carbohydrate-based structures recognized as DAMPs/MAMPs is needed to further understand plant disease resistance modulation. We show here that IGP1/CORK1, IGP3 and IGP4 LRR-MAL RKs are required for the perception of carbohydrate-based DAMPs β-1,4-D-(xylose)4 (XYL4) and 33-α-L-arabinofuranosyl-xylotetraose (XA3XX), further expanding the function of these LRR-MAL RKs in plant glycan perception and immune activation.

@article{barbut_integrity_2024,
	title = {Integrity of xylan backbone affects plant responses to drought},
	volume = {15},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1422701/full},
	doi = {10.3389/fpls.2024.1422701},
	abstract = {{\textless}p{\textgreater}Drought is a major factor affecting crops, thus efforts are needed to increase plant resilience to this abiotic stress. The overlapping signaling pathways between drought and cell wall integrity maintenance responses create a possibility of increasing drought resistance by modifying cell walls. Here, using herbaceous and woody plant model species, {\textless}italic{\textgreater}Arabidopsis{\textless}/italic{\textgreater} and hybrid aspen, respectively, we investigated how the integrity of xylan in secondary walls affects the responses of plants to drought stress. Plants, in which secondary wall xylan integrity was reduced by expressing fungal GH10 and GH11 xylanases or by affecting genes involved in xylan backbone biosynthesis, were subjected to controlled drought while their physiological responses were continuously monitored by RGB, fluorescence, and/or hyperspectral cameras. For {\textless}italic{\textgreater}Arabidopsis{\textless}/italic{\textgreater}, this was supplemented with survival test after complete water withdrawal and analyses of stomatal function and stem conductivity. All {\textless}italic{\textgreater}Arabidopsis{\textless}/italic{\textgreater} xylan-impaired lines showed better survival upon complete watering withdrawal, increased stomatal density and delayed growth inhibition by moderate drought, indicating increased resilience to moderate drought associated with modified xylan integrity. Subtle differences were recorded between xylan biosynthesis mutants ({\textless}italic{\textgreater}irx9{\textless}/italic{\textgreater}, {\textless}italic{\textgreater}irx10{\textless}/italic{\textgreater} and {\textless}italic{\textgreater}irx14{\textless}/italic{\textgreater}) and xylanase-expressing lines. {\textless}italic{\textgreater}irx14{\textless}/italic{\textgreater} was the most drought resistant genotype, and the only genotype with increased lignin content and unaltered xylem conductivity despite its {\textless}italic{\textgreater}irx{\textless}/italic{\textgreater} phenotype. Rosette growth was more affected by drought in GH11- than in GH10-expressing plants. In aspen, mild downregulation of {\textless}italic{\textgreater}GT43B{\textless}/italic{\textgreater} and {\textless}italic{\textgreater}C{\textless}/italic{\textgreater} genes did not affect drought responses and the transgenic plants grew better than the wild-type in drought and well-watered conditions. Both GH10 and GH11 xylanases strongly inhibited stem elongation and root growth in well-watered conditions but growth was less inhibited by drought in GH11-expressing plants than in wild-type. Overall, plants with xylan integrity impairment in secondary walls were less affected than wild-type by moderately reduced water availability but their responses also varied among genotypes and species. Thus, modifying the secondary cell wall integrity can be considered as a potential strategy for developing crops better suited to withstand water scarcity, but more research is needed to address the underlying molecular causes of this variability.{\textless}/p{\textgreater}},
	language = {English},
	urldate = {2024-07-17},
	journal = {Frontiers in Plant Science},
	publisher = {Frontiers},
	author = {Barbut, Félix R. and Cavel, Emilie and Donev, Evgeniy N. and Gaboreanu, Ioana and Urbancsok, János and Pandey, Garima and Demailly, Hervé and Jiao, Dianyi and Yassin, Zakiya and Derba-Maceluch, Marta and Master, Emma R. and Scheepers, Gerhard and Gutierrez, Laurent and Mellerowicz, Ewa J.},
	month = jun,
	year = {2024},
	keywords = {Arabidopsis, Drought stress, Glucuronoxylan, Populus, cell wall integrity, high-throughput phenotyping, hyperspectral imaging, secondary cell wall},
}

\textlessp\textgreaterDrought is a major factor affecting crops, thus efforts are needed to increase plant resilience to this abiotic stress. The overlapping signaling pathways between drought and cell wall integrity maintenance responses create a possibility of increasing drought resistance by modifying cell walls. Here, using herbaceous and woody plant model species, \textlessitalic\textgreaterArabidopsis\textless/italic\textgreater and hybrid aspen, respectively, we investigated how the integrity of xylan in secondary walls affects the responses of plants to drought stress. Plants, in which secondary wall xylan integrity was reduced by expressing fungal GH10 and GH11 xylanases or by affecting genes involved in xylan backbone biosynthesis, were subjected to controlled drought while their physiological responses were continuously monitored by RGB, fluorescence, and/or hyperspectral cameras. For \textlessitalic\textgreaterArabidopsis\textless/italic\textgreater, this was supplemented with survival test after complete water withdrawal and analyses of stomatal function and stem conductivity. All \textlessitalic\textgreaterArabidopsis\textless/italic\textgreater xylan-impaired lines showed better survival upon complete watering withdrawal, increased stomatal density and delayed growth inhibition by moderate drought, indicating increased resilience to moderate drought associated with modified xylan integrity. Subtle differences were recorded between xylan biosynthesis mutants (\textlessitalic\textgreaterirx9\textless/italic\textgreater, \textlessitalic\textgreaterirx10\textless/italic\textgreater and \textlessitalic\textgreaterirx14\textless/italic\textgreater) and xylanase-expressing lines. \textlessitalic\textgreaterirx14\textless/italic\textgreater was the most drought resistant genotype, and the only genotype with increased lignin content and unaltered xylem conductivity despite its \textlessitalic\textgreaterirx\textless/italic\textgreater phenotype. Rosette growth was more affected by drought in GH11- than in GH10-expressing plants. In aspen, mild downregulation of \textlessitalic\textgreaterGT43B\textless/italic\textgreater and \textlessitalic\textgreaterC\textless/italic\textgreater genes did not affect drought responses and the transgenic plants grew better than the wild-type in drought and well-watered conditions. Both GH10 and GH11 xylanases strongly inhibited stem elongation and root growth in well-watered conditions but growth was less inhibited by drought in GH11-expressing plants than in wild-type. Overall, plants with xylan integrity impairment in secondary walls were less affected than wild-type by moderately reduced water availability but their responses also varied among genotypes and species. Thus, modifying the secondary cell wall integrity can be considered as a potential strategy for developing crops better suited to withstand water scarcity, but more research is needed to address the underlying molecular causes of this variability.\textless/p\textgreater

@article{lecoutre_reduced_2024,
	title = {Reduced adipocyte glutaminase activity promotes energy expenditure and metabolic health},
	volume = {6},
	copyright = {2024 The Author(s)},
	issn = {2522-5812},
	url = {https://www.nature.com/articles/s42255-024-01083-y},
	doi = {10.1038/s42255-024-01083-y},
	abstract = {Glutamine and glutamate are interconverted by several enzymes and alterations in this metabolic cycle are linked to cardiometabolic traits. Herein, we show that obesity-associated insulin resistance is characterized by decreased plasma and white adipose tissue glutamine-to-glutamate ratios. We couple these stoichiometric changes to perturbed fat cell glutaminase and glutamine synthase messenger RNA and protein abundance, which together promote glutaminolysis. In human white adipocytes, reductions in glutaminase activity promote aerobic glycolysis and mitochondrial oxidative capacity via increases in hypoxia-inducible factor 1α abundance, lactate levels and p38 mitogen-activated protein kinase signalling. Systemic glutaminase inhibition in male and female mice, or genetically in adipocytes of male mice, triggers the activation of thermogenic gene programs in inguinal adipocytes. Consequently, the knockout mice display higher energy expenditure and improved glucose tolerance compared to control littermates, even under high-fat diet conditions. Altogether, our findings highlight white adipocyte glutamine turnover as an important determinant of energy expenditure and metabolic health.},
	language = {en},
	number = {7},
	urldate = {2024-07-29},
	journal = {Nature Metabolism},
	publisher = {Nature Publishing Group},
	author = {Lecoutre, Simon and Maqdasy, Salwan and Rizo-Roca, David and Renzi, Gianluca and Vlassakev, Ivan and Alaeddine, Lynn M. and Higos, Romane and Jalkanen, Jutta and Zhong, Jiawei and Zareifi, Danae S. and Frendo-Cumbo, Scott and Massier, Lucas and Hodek, Ondrej and Juvany, Marta and Moritz, Thomas and de Castro Barbosa, Thais and Omar-Hmeadi, Muhmmad and López-Yus, Marta and Merabtene, Fatiha and Abatan, Jimon Boniface and Marcelin, Geneviève and El Hachem, Elie-Julien and Rouault, Christine and Bergo, Martin O. and Petrus, Paul and Zierath, Juleen R. and Clément, Karine and Krook, Anna and Mejhert, Niklas and Rydén, Mikael},
	month = jul,
	year = {2024},
	keywords = {Fat metabolism, Obesity},
	pages = {1329--1346},
}

Glutamine and glutamate are interconverted by several enzymes and alterations in this metabolic cycle are linked to cardiometabolic traits. Herein, we show that obesity-associated insulin resistance is characterized by decreased plasma and white adipose tissue glutamine-to-glutamate ratios. We couple these stoichiometric changes to perturbed fat cell glutaminase and glutamine synthase messenger RNA and protein abundance, which together promote glutaminolysis. In human white adipocytes, reductions in glutaminase activity promote aerobic glycolysis and mitochondrial oxidative capacity via increases in hypoxia-inducible factor 1α abundance, lactate levels and p38 mitogen-activated protein kinase signalling. Systemic glutaminase inhibition in male and female mice, or genetically in adipocytes of male mice, triggers the activation of thermogenic gene programs in inguinal adipocytes. Consequently, the knockout mice display higher energy expenditure and improved glucose tolerance compared to control littermates, even under high-fat diet conditions. Altogether, our findings highlight white adipocyte glutamine turnover as an important determinant of energy expenditure and metabolic health.

@article{foresi_tiny_2024,
	title = {The tiny giant of the sea, \textit{{Ostreococcus}'s} unique adaptations},
	volume = {211},
	issn = {0981-9428},
	url = {https://www.sciencedirect.com/science/article/pii/S0981942824003292},
	doi = {10.1016/j.plaphy.2024.108661},
	abstract = {Ostreococcus spp. are unicellular organisms with one of the simplest cellular organizations. The sequencing of the genomes of different Ostreococcus species has reinforced this status since Ostreococcus tauri has one most compact nuclear genomes among eukaryotic organisms. Despite this, it has retained a number of genes, setting it apart from other organisms with similar small genomes. Ostreococcus spp. feature a substantial number of selenocysteine-containing proteins, which, due to their higher catalytic activity compared to their selenium-lacking counterparts, may require a reduced quantity of proteins. Notably, O. tauri encodes several ammonium transporter genes, that may provide it with a competitive edge for acquiring nitrogen (N). This characteristic makes it an intriguing model for studying the efficient use of N in eukaryotes. Under conditions of low N availability, O. tauri utilizes N from abundant proteins or amino acids, such as L-arginine, similar to higher plants. However, the presence of a nitric oxide synthase (L-arg substrate) sheds light on a new metabolic pathway for L-arg in algae. The metabolic adaptations of O. tauri to day and night cycles offer valuable insights into carbon and iron metabolic configuration. O. tauri has evolved novel strategies to optimize iron uptake, lacking the classic components of the iron absorption mechanism. Overall, the cellular and genetic characteristics of Ostreococcus contribute to its evolutionary success, making it an excellent model for studying the physiological and genetic aspects of how green algae have adapted to the marine environment. Furthermore, given its potential for lipid accumulation and its marine habitat, it may represent a promising avenue for third-generation biofuels.},
	urldate = {2024-05-17},
	journal = {Plant Physiology and Biochemistry},
	author = {Foresi, Noelia and De Marco, María Agustina and Del Castello, Fiorella and Ramirez, Leonor and Nejamkin, Andres and Calo, Gonzalo and Grimsley, Nigel and Correa-Aragunde, Natalia and Martínez-Noël, Giselle M. A.},
	month = jun,
	year = {2024},
	keywords = {Alga, Iron, Lipids-starch, Mamiellales, Mamiellophyceae, Nitrogen, Picoeukaryote, Picophytoplankton},
	pages = {108661},
}

Ostreococcus spp. are unicellular organisms with one of the simplest cellular organizations. The sequencing of the genomes of different Ostreococcus species has reinforced this status since Ostreococcus tauri has one most compact nuclear genomes among eukaryotic organisms. Despite this, it has retained a number of genes, setting it apart from other organisms with similar small genomes. Ostreococcus spp. feature a substantial number of selenocysteine-containing proteins, which, due to their higher catalytic activity compared to their selenium-lacking counterparts, may require a reduced quantity of proteins. Notably, O. tauri encodes several ammonium transporter genes, that may provide it with a competitive edge for acquiring nitrogen (N). This characteristic makes it an intriguing model for studying the efficient use of N in eukaryotes. Under conditions of low N availability, O. tauri utilizes N from abundant proteins or amino acids, such as L-arginine, similar to higher plants. However, the presence of a nitric oxide synthase (L-arg substrate) sheds light on a new metabolic pathway for L-arg in algae. The metabolic adaptations of O. tauri to day and night cycles offer valuable insights into carbon and iron metabolic configuration. O. tauri has evolved novel strategies to optimize iron uptake, lacking the classic components of the iron absorption mechanism. Overall, the cellular and genetic characteristics of Ostreococcus contribute to its evolutionary success, making it an excellent model for studying the physiological and genetic aspects of how green algae have adapted to the marine environment. Furthermore, given its potential for lipid accumulation and its marine habitat, it may represent a promising avenue for third-generation biofuels.

@article{hasan_redox_2024,
	title = {Redox signalling in plant–nematode interactions: {Insights} into molecular crosstalk and defense mechanisms},
	volume = {47},
	copyright = {© 2024 John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	shorttitle = {Redox signalling in plant–nematode interactions},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14925},
	doi = {10.1111/pce.14925},
	abstract = {Plant–parasitic nematodes, specifically cyst nematodes (CNs) and root-knot nematodes (RKNs), pose significant threats to global agriculture, leading to substantial crop losses. Both CNs and RKNs induce permanent feeding sites in the root of their host plants, which then serve as their only source of nutrients throughout their lifecycle. Plants deploy reactive oxygen species (ROS) as a primary defense mechanism against nematode invasion. Notably, both CNs and RKNs have evolved sophisticated strategies to manipulate the host's redox environment to their advantage, with each employing distinct tactics to combat ROS. In this review, we have focused on the role of ROS and its scavenging network in interactions between host plants and CNs and RKNs. Overall, this review emphasizes the complex interplay between plant defense mechanism, redox signalling and nematode survival tactics, suggesting potential avenues for developing innovative nematode management strategies in agriculture.},
	language = {en},
	number = {8},
	urldate = {2024-07-19},
	journal = {Plant, Cell \& Environment},
	author = {Hasan, M. Shamim and Lin, Ching-Jung and Marhavy, Peter and Kyndt, Tina and Siddique, Shahid},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14925},
	keywords = {ROS, antioxidants, cyst nematodes, effectors, root-knot nematodes},
	pages = {2811--2820},
}

Plant–parasitic nematodes, specifically cyst nematodes (CNs) and root-knot nematodes (RKNs), pose significant threats to global agriculture, leading to substantial crop losses. Both CNs and RKNs induce permanent feeding sites in the root of their host plants, which then serve as their only source of nutrients throughout their lifecycle. Plants deploy reactive oxygen species (ROS) as a primary defense mechanism against nematode invasion. Notably, both CNs and RKNs have evolved sophisticated strategies to manipulate the host's redox environment to their advantage, with each employing distinct tactics to combat ROS. In this review, we have focused on the role of ROS and its scavenging network in interactions between host plants and CNs and RKNs. Overall, this review emphasizes the complex interplay between plant defense mechanism, redox signalling and nematode survival tactics, suggesting potential avenues for developing innovative nematode management strategies in agriculture.

@article{davis_toward_2024,
	title = {Toward uncovering an operating system in plant organs},
	volume = {29},
	issn = {1360-1385},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138523003655},
	doi = {10.1016/j.tplants.2023.11.006},
	abstract = {Molecular motifs can explain information processing within single cells, while how assemblies of cells collectively achieve this remains less well understood. Plant fitness and survival depend upon robust and accurate decision-making in their decentralised multicellular organ systems. Mobile agents, including hormones, metabolites, and RNAs, have a central role in coordinating multicellular collective decision-making, yet mechanisms describing how cell–cell communication scales to organ-level transitions is poorly understood. Here, we explore how unified outputs may emerge in plant organs by distributed information processing across different scales and using different modalities. Mathematical and computational representations of these events are also explored toward understanding how these events take place and are leveraged to manipulate plant development in response to the environment.},
	number = {7},
	urldate = {2024-07-17},
	journal = {Trends in Plant Science},
	author = {Davis, Gwendolyn V. and de Souza Moraes, Tatiana and Khanapurkar, Swanand and Dromiack, Hannah and Ahmad, Zaki and Bayer, Emmanuelle M. and Bhalerao, Rishikesh P. and Walker, Sara I. and Bassel, George W.},
	month = jul,
	year = {2024},
	keywords = {Cellular Automata, collective behaviour, decentralised information processing, decision-making, plant development},
	pages = {742--753},
}

Molecular motifs can explain information processing within single cells, while how assemblies of cells collectively achieve this remains less well understood. Plant fitness and survival depend upon robust and accurate decision-making in their decentralised multicellular organ systems. Mobile agents, including hormones, metabolites, and RNAs, have a central role in coordinating multicellular collective decision-making, yet mechanisms describing how cell–cell communication scales to organ-level transitions is poorly understood. Here, we explore how unified outputs may emerge in plant organs by distributed information processing across different scales and using different modalities. Mathematical and computational representations of these events are also explored toward understanding how these events take place and are leveraged to manipulate plant development in response to the environment.

@article{graca_obscurity_2024,
	title = {Obscurity of chlorophyll tails - {Is} chlorophyll with farnesyl tail incorporated into {PSII} complexes?},
	volume = {176},
	issn = {0031-9317},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ppl.14428},
	doi = {10.1111/ppl.14428},
	abstract = {Abstract Chlorophyll is essential in photosynthesis, converting sunlight into chemical energy in plants, algae, and certain bacteria. Its structure, featuring a porphyrin ring enclosing a central magnesium ion, varies in forms like chlorophyll a, b, c, d, and f, allowing light absorption at a broader spectrum. With a 20-carbon phytyl tail (except for chlorophyll c), chlorophyll is anchored to proteins. Previous findings suggested the presence of chlorophyll with a modified farnesyl tail in thermophilic cyanobacteria Thermosynechoccocus vestitus. In our Arabidopsis thaliana PSII cryo-EM map, specific chlorophylls showed incomplete phytyl tails, suggesting potential farnesyl modifications. However, further high-resolution mass spectrometry (HRMS) analysis in A. thaliana and T. vestitus did not confirm the presence of any farnesyl tails. Instead, we propose the truncated tails in PSII models may result from binding pocket flexibility rather than actual modifications.},
	number = {4},
	urldate = {2024-07-17},
	journal = {Physiologia Plantarum},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Graça, André T. and Lihavainen, Jenna and Hussein, Rana and Schröder, Wolfgang P.},
	month = jul,
	year = {2024},
	pages = {e14428},
}

Abstract Chlorophyll is essential in photosynthesis, converting sunlight into chemical energy in plants, algae, and certain bacteria. Its structure, featuring a porphyrin ring enclosing a central magnesium ion, varies in forms like chlorophyll a, b, c, d, and f, allowing light absorption at a broader spectrum. With a 20-carbon phytyl tail (except for chlorophyll c), chlorophyll is anchored to proteins. Previous findings suggested the presence of chlorophyll with a modified farnesyl tail in thermophilic cyanobacteria Thermosynechoccocus vestitus. In our Arabidopsis thaliana PSII cryo-EM map, specific chlorophylls showed incomplete phytyl tails, suggesting potential farnesyl modifications. However, further high-resolution mass spectrometry (HRMS) analysis in A. thaliana and T. vestitus did not confirm the presence of any farnesyl tails. Instead, we propose the truncated tails in PSII models may result from binding pocket flexibility rather than actual modifications.

@article{khalfallah_ectomycorrhizal_2024,
	title = {“{Ectomycorrhizal} exploration type” could be a functional trait explaining the spatial distribution of tree symbiotic fungi as a function of forest humus forms},
	issn = {1432-1890},
	url = {https://doi.org/10.1007/s00572-024-01146-8},
	doi = {10.1007/s00572-024-01146-8},
	abstract = {In European forests, most tree species form symbioses with ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) fungi. The EM fungi are classified into different morphological types based on the development and structure of their extraradical mycelium. These structures could be root extensions that help trees to acquire nutrients. However, the relationship between these morphological traits and functions involved in soil nutrient foraging is still under debate.},
	language = {en},
	urldate = {2024-05-10},
	journal = {Mycorrhiza},
	author = {Khalfallah, F and Bon, L and El Mazlouzi, M and Bakker, M.R and Fanin, N and Bellanger, R and Bernier, F and De Schrijver, A and Ducatillon, C and Fotelli, M.N and Gateble, G and Gundale, M.J and Larsson, M and Legout, A and Mason, W.L and Nordin, A and Smolander, A and Spyroglou, G and Vanguelova, E.I. and Vesterdal, L and Zeller, B and Augusto, L and Derrien, D and Buée, M},
	month = may,
	year = {2024},
}

In European forests, most tree species form symbioses with ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) fungi. The EM fungi are classified into different morphological types based on the development and structure of their extraradical mycelium. These structures could be root extensions that help trees to acquire nutrients. However, the relationship between these morphological traits and functions involved in soil nutrient foraging is still under debate.

@article{long_comparative_2024,
	title = {Comparative metabolomics combined with genome sequencing provides insights into novel wolfberry-specific metabolites and their formation mechanisms},
	volume = {15},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1392175/full},
	doi = {10.3389/fpls.2024.1392175},
	abstract = {Wolfberry (Lycium, of the family Solanaceae) has special nutritional benefits due to its valuable metabolites. Here, 16 wolfberry-specific metabolites were identified by comparing the metabolome of wolfberry with those of six species, including maize, rice, wheat, soybean, tomato and grape. The copy numbers of the riboflavin and phenyllactate degradation genes riboflavin kinase (RFK) and phenyllactate UDP-glycosyltransferase (UGT1) were lower in wolfberry than in other species, while the copy number of the phenyllactate synthesis gene hydroxyphenyl-pyruvate reductase (HPPR) was higher in wolfberry, suggesting that the copy number variation of these genes among species may be the main reason for the specific accumulation of riboflavin and phenyllactate in wolfberry. Moreover, the metabolome-based neighbor-joining tree revealed distinct clustering of monocots and dicots, suggesting that metabolites could reflect the evolutionary relationship among those species. Taken together, we identified 16 specific metabolites in wolfberry and provided new insight into the accumulation mechanism of species-specific metabolites at the genomic level.},
	language = {English},
	urldate = {2024-05-17},
	journal = {Frontiers in Plant Science},
	publisher = {Frontiers},
	author = {Long, Qiyuan and Zhang, Changjian and Zhu, Hui and Zhou, Yutong and Liu, Shuo and Liu, Yanchen and Ma, Xuemin and An, Wei and Zhou, Jun and Zhao, Jianhua and Zhang, Yuanyuan and Jin, Cheng},
	month = apr,
	year = {2024},
	keywords = {Metabolome, Riboflavin, copy number variation, nutrition, phenyllactate},
}

Wolfberry (Lycium, of the family Solanaceae) has special nutritional benefits due to its valuable metabolites. Here, 16 wolfberry-specific metabolites were identified by comparing the metabolome of wolfberry with those of six species, including maize, rice, wheat, soybean, tomato and grape. The copy numbers of the riboflavin and phenyllactate degradation genes riboflavin kinase (RFK) and phenyllactate UDP-glycosyltransferase (UGT1) were lower in wolfberry than in other species, while the copy number of the phenyllactate synthesis gene hydroxyphenyl-pyruvate reductase (HPPR) was higher in wolfberry, suggesting that the copy number variation of these genes among species may be the main reason for the specific accumulation of riboflavin and phenyllactate in wolfberry. Moreover, the metabolome-based neighbor-joining tree revealed distinct clustering of monocots and dicots, suggesting that metabolites could reflect the evolutionary relationship among those species. Taken together, we identified 16 specific metabolites in wolfberry and provided new insight into the accumulation mechanism of species-specific metabolites at the genomic level.

@article{bruxaux_scots_2024,
	title = {Scots pine – panmixia and the elusive signal of genetic adaptation},
	volume = {243},
	copyright = {© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19563},
	doi = {10.1111/nph.19563},
	abstract = {Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation. We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients. The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.},
	language = {en},
	number = {3},
	urldate = {2024-07-11},
	journal = {New Phytologist},
	author = {Bruxaux, Jade and Zhao, Wei and Hall, David and Curtu, Alexandru Lucian and Androsiuk, Piotr and Drouzas, Andreas D. and Gailing, Oliver and Konrad, Heino and Sullivan, Alexis R. and Semerikov, Vladimir and Wang, Xiao-Ru},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19563},
	keywords = {Pinus sylvestris, conifer, demography, gene flow, genetic diversity, genetic-environmental association, population structure},
	pages = {1231--1246},
}

Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation. We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients. The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.

@article{abdel-fattah_growth-regulated_2024,
	title = {Growth-regulated co-occupancy of {Mediator} and {Lsm3} at intronic ribosomal protein genes},
	volume = {52},
	issn = {0305-1048},
	url = {https://doi.org/10.1093/nar/gkae266},
	doi = {10.1093/nar/gkae266},
	abstract = {Mediator is a well-known transcriptional co-regulator and serves as an adaptor between gene-specific regulatory proteins and RNA polymerase II. Studies on the chromatin-bound form of Mediator revealed interactions with additional protein complexes involved in various transcription-related processes, such as the Lsm2–8 complex that is part of the spliceosomal U6 small nuclear ribonucleoprotein complex. Here, we employ Chromatin Immunoprecipitation sequencing (ChIP-seq) of chromatin associated with the Lsm3 protein and the Med1 or Med15 Mediator subunits. We identify 86 genes co-occupied by both Lsm3 and Mediator, of which 73 were intron-containing ribosomal protein genes. In logarithmically growing cells, Mediator primarily binds to their promoter regions but also shows a second, less pronounced occupancy at their 3′-exons. During the late exponential phase, we observe a near-complete transition of Mediator from these promoters to a position in their 3′-ends, overlapping the Lsm3 binding sites ∼250 bp downstream of their last intron–exon boundaries. Using an unbiased RNA sequencing approach, we show that transition of Mediator from promoters to the last exon of these genes correlates to reduction of both their messenger RNA levels and splicing ratios, indicating that the Mediator and Lsm complexes cooperate to control growth-regulated expression of intron-containing ribosomal protein genes at the levels of transcription and splicing.},
	number = {11},
	urldate = {2024-07-01},
	journal = {Nucleic Acids Research},
	author = {Abdel-Fattah, Wael R and Carlsson, Mattias and Hu, Guo-Zhen and Singh, Ajeet and Vergara, Alexander and Aslam, Rameen and Ronne, Hans and Björklund, Stefan},
	month = jun,
	year = {2024},
	pages = {6220--6233},
}

Mediator is a well-known transcriptional co-regulator and serves as an adaptor between gene-specific regulatory proteins and RNA polymerase II. Studies on the chromatin-bound form of Mediator revealed interactions with additional protein complexes involved in various transcription-related processes, such as the Lsm2–8 complex that is part of the spliceosomal U6 small nuclear ribonucleoprotein complex. Here, we employ Chromatin Immunoprecipitation sequencing (ChIP-seq) of chromatin associated with the Lsm3 protein and the Med1 or Med15 Mediator subunits. We identify 86 genes co-occupied by both Lsm3 and Mediator, of which 73 were intron-containing ribosomal protein genes. In logarithmically growing cells, Mediator primarily binds to their promoter regions but also shows a second, less pronounced occupancy at their 3′-exons. During the late exponential phase, we observe a near-complete transition of Mediator from these promoters to a position in their 3′-ends, overlapping the Lsm3 binding sites ∼250 bp downstream of their last intron–exon boundaries. Using an unbiased RNA sequencing approach, we show that transition of Mediator from promoters to the last exon of these genes correlates to reduction of both their messenger RNA levels and splicing ratios, indicating that the Mediator and Lsm complexes cooperate to control growth-regulated expression of intron-containing ribosomal protein genes at the levels of transcription and splicing.

@article{strom_metabolomic_2024,
	title = {The {Metabolomic} {Profile} of {Microscopic} {Colitis} {Is} {Affected} by {Smoking} but {Not} {Histopathological} {Diagnosis}, {Clinical} {Course}, {Symptoms}, or {Treatment}},
	volume = {14},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2218-1989},
	url = {https://www.mdpi.com/2218-1989/14/6/303},
	doi = {10.3390/metabo14060303},
	abstract = {Microscopic colitis (MC) is classified as collagenous colitis (CC) and lymphocytic colitis (LC). Genetic associations between CC and human leucocyte antigens (HLAs) have been found, with smoking being a predisposing external factor. Smoking has a great impact on metabolomics. The aim of this explorative study was to analyze global metabolomics in MC and to examine whether the metabolomic profile differed regarding the type and course of MC, the presence of IBS-like symptoms, treatment, and smoking habits. Of the 240 identified women with MC aged ≤73 years, 131 completed the study questionnaire; the Rome III questionnaire; and the Visual Analog Scale for Irritable Bowel Syndrome (VAS-IBS). Blood samples were analyzed by ultra-high-performance liquid chromatograph mass spectrometry (UHLC-MS/UHPLC-MSMS). The women, 63.1 (58.7–67.2) years old, were categorized based on CC (n = 76) and LC (n = 55); one episode or refractory MC; IBS-like symptoms or not; use of corticosteroids or not; and smoking habits. The only metabolomic differences found in the univariate model after adjustment for false discovery rate (FDR) were between smokers and non-smokers. Serotonin was markedly increased in smokers (p {\textless} 0.001). No clear patterns appeared when conducting a principal component analysis (PCA). No differences in the metabolomic profile were found depending on the type or clinical course of the disease, neither in the whole MC group nor in the subgroup analysis of CC.},
	language = {en},
	number = {6},
	urldate = {2024-07-01},
	journal = {Metabolites},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Ström, Axel and Stenlund, Hans and Ohlsson, Bodil},
	month = jun,
	year = {2024},
	note = {Number: 6},
	keywords = {collagenous colitis, lymphocytic colitis, metabolomics, microscopic colitis, smoking habits},
	pages = {303},
}

Microscopic colitis (MC) is classified as collagenous colitis (CC) and lymphocytic colitis (LC). Genetic associations between CC and human leucocyte antigens (HLAs) have been found, with smoking being a predisposing external factor. Smoking has a great impact on metabolomics. The aim of this explorative study was to analyze global metabolomics in MC and to examine whether the metabolomic profile differed regarding the type and course of MC, the presence of IBS-like symptoms, treatment, and smoking habits. Of the 240 identified women with MC aged ≤73 years, 131 completed the study questionnaire; the Rome III questionnaire; and the Visual Analog Scale for Irritable Bowel Syndrome (VAS-IBS). Blood samples were analyzed by ultra-high-performance liquid chromatograph mass spectrometry (UHLC-MS/UHPLC-MSMS). The women, 63.1 (58.7–67.2) years old, were categorized based on CC (n = 76) and LC (n = 55); one episode or refractory MC; IBS-like symptoms or not; use of corticosteroids or not; and smoking habits. The only metabolomic differences found in the univariate model after adjustment for false discovery rate (FDR) were between smokers and non-smokers. Serotonin was markedly increased in smokers (p \textless 0.001). No clear patterns appeared when conducting a principal component analysis (PCA). No differences in the metabolomic profile were found depending on the type or clinical course of the disease, neither in the whole MC group nor in the subgroup analysis of CC.

@article{hayatgheibi_implications_2024,
	title = {Implications of accounting for marker-based population structure in the quantitative genetic evaluation of genetic parameters related to growth and wood properties in {Norway} spruce},
	volume = {25},
	issn = {2730-6844},
	url = {https://doi.org/10.1186/s12863-024-01241-x},
	doi = {10.1186/s12863-024-01241-x},
	abstract = {Forest geneticists typically use provenances to account for population differences in their improvement schemes; however, the historical records of the imported materials might not be very precise or well-aligned with the genetic clusters derived from advanced molecular techniques. The main objective of this study was to assess the impact of marker-based population structure on genetic parameter estimates related to growth and wood properties and their trade-offs in Norway spruce, by either incorporating it as a fixed effect (model-A) or excluding it entirely from the analysis (model-B).},
	number = {1},
	urldate = {2024-07-01},
	journal = {BMC Genomic Data},
	author = {Hayatgheibi, Haleh and Hallingbäck, Henrik R. and Lundqvist, Sven-Olof and Grahn, Thomas and Scheepers, Gerhard and Nordström, Peter and Chen, Zhi-Qiang and Kärkkäinen, Katri and Wu, Harry X. and García-Gil, M. Rosario},
	month = jun,
	year = {2024},
	keywords = {Cross-validation, Norway spruce, Population structure, Prediction accuracy, Wood properties},
	pages = {60},
}

Forest geneticists typically use provenances to account for population differences in their improvement schemes; however, the historical records of the imported materials might not be very precise or well-aligned with the genetic clusters derived from advanced molecular techniques. The main objective of this study was to assess the impact of marker-based population structure on genetic parameter estimates related to growth and wood properties and their trade-offs in Norway spruce, by either incorporating it as a fixed effect (model-A) or excluding it entirely from the analysis (model-B).

@article{dusi_involvement_2024,
	title = {Involvement of the tomato {BBX16} and {BBX17} {microProteins} in reproductive development},
	volume = {213},
	issn = {0981-9428},
	url = {https://www.sciencedirect.com/science/article/pii/S0981942824005412},
	doi = {10.1016/j.plaphy.2024.108873},
	abstract = {BBXs are B-Box zinc finger proteins that can act as transcription factors and regulators of protein complexes. Several BBX proteins play important roles in plant development. Two Arabidopsis thaliana microProteins belonging to the BBX family, named miP1a and miP1b, homotypically interact with and modulate the activity of other BBX proteins, including CONSTANS, which transcriptionally activates the florigen, FLOWERING LOCUS T. Arabidopsis plants overexpressing miP1a and miP1b showed delayed flowering. In tomato, the closest homologs of miP1a and miP1b are the microProteins SlBBX16 and SlBBX17. This study was aimed at investigating whether the constitutive expression of SlBBX16/17 in Arabidopsis and tomato impacted reproductive development. The heterologous expression of the two tomato microProteins in Arabidopsis caused a delay in the flowering transition; however, the effect was weaker than that observed when the native miP1a/b were overexpressed. In tomato, overexpression of SlBBX17 prolonged the flowering period; this effect was accompanied by downregulation of the flowering inhibitors Self Pruning (SP) and SP5G. SlBBX16 and SlBBX17 can hetero-oligomerize with TCMP-2, a cystine-knot peptide involved in flowering pattern regulation and early fruit development in tomato. The increased expression of both microProteins also caused alterations in tomato fruit development: we observed in the case of SlBBX17 a decrease in the number and size of ripe fruits as compared to WT plants, while for SlBBX16, a delay in fruit production up to the breaker stage. These effects were associated with changes in the expression of GA-responsive genes.},
	urldate = {2024-07-01},
	journal = {Plant Physiology and Biochemistry},
	author = {Dusi, Valentina and Pennisi, Federica and Fortini, Daniela and Atarés, Alejandro and Wenkel, Stephan and Molesini, Barbara and Pandolfini, Tiziana},
	month = aug,
	year = {2024},
	keywords = {BBX, Flowering time, Fruit development, Gibberellins, MicroProteins},
	pages = {108873},
}

BBXs are B-Box zinc finger proteins that can act as transcription factors and regulators of protein complexes. Several BBX proteins play important roles in plant development. Two Arabidopsis thaliana microProteins belonging to the BBX family, named miP1a and miP1b, homotypically interact with and modulate the activity of other BBX proteins, including CONSTANS, which transcriptionally activates the florigen, FLOWERING LOCUS T. Arabidopsis plants overexpressing miP1a and miP1b showed delayed flowering. In tomato, the closest homologs of miP1a and miP1b are the microProteins SlBBX16 and SlBBX17. This study was aimed at investigating whether the constitutive expression of SlBBX16/17 in Arabidopsis and tomato impacted reproductive development. The heterologous expression of the two tomato microProteins in Arabidopsis caused a delay in the flowering transition; however, the effect was weaker than that observed when the native miP1a/b were overexpressed. In tomato, overexpression of SlBBX17 prolonged the flowering period; this effect was accompanied by downregulation of the flowering inhibitors Self Pruning (SP) and SP5G. SlBBX16 and SlBBX17 can hetero-oligomerize with TCMP-2, a cystine-knot peptide involved in flowering pattern regulation and early fruit development in tomato. The increased expression of both microProteins also caused alterations in tomato fruit development: we observed in the case of SlBBX17 a decrease in the number and size of ripe fruits as compared to WT plants, while for SlBBX16, a delay in fruit production up to the breaker stage. These effects were associated with changes in the expression of GA-responsive genes.

@article{blaschek_functional_2024,
	title = {Functional {Complexity} on a {Cellular} {Scale}: {Why} {In} {Situ} {Analyses} {Are} {Indispensable} for {Our} {Understanding} of {Lignified} {Tissues}},
	volume = {72},
	issn = {0021-8561},
	shorttitle = {Functional {Complexity} on a {Cellular} {Scale}},
	url = {https://doi.org/10.1021/acs.jafc.4c01999},
	doi = {10.1021/acs.jafc.4c01999},
	abstract = {Lignins are a key adaptation that enables vascular plants to thrive in terrestrial habitats. Lignin is heterogeneous, containing upward of 30 different monomers, and its function is multifarious: It provides structural support, predetermined breaking points, ultraviolet protection, diffusion barriers, pathogen resistance, and drought resilience. Recent studies, carefully characterizing lignin in situ, have started to identify specific lignin compositions and ultrastructures with distinct cellular functions, but our understanding remains fractional. We summarize recent works and highlight where further in situ lignin analysis could provide valuable insights into plant growth and adaptation. We also summarize strengths and weaknesses of lignin in situ analysis methods.},
	number = {24},
	urldate = {2024-07-01},
	journal = {Journal of Agricultural and Food Chemistry},
	publisher = {American Chemical Society},
	author = {Blaschek, Leonard and Serk, Henrik and Pesquet, Edouard},
	month = jun,
	year = {2024},
	pages = {13552--13560},
}

Lignins are a key adaptation that enables vascular plants to thrive in terrestrial habitats. Lignin is heterogeneous, containing upward of 30 different monomers, and its function is multifarious: It provides structural support, predetermined breaking points, ultraviolet protection, diffusion barriers, pathogen resistance, and drought resilience. Recent studies, carefully characterizing lignin in situ, have started to identify specific lignin compositions and ultrastructures with distinct cellular functions, but our understanding remains fractional. We summarize recent works and highlight where further in situ lignin analysis could provide valuable insights into plant growth and adaptation. We also summarize strengths and weaknesses of lignin in situ analysis methods.

@article{mishra_overexpression_2024,
	title = {Overexpression of the plastidial pseudo-protease {AtFtsHi3} enhances drought tolerance while sustaining plant growth},
	volume = {176},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.14370},
	doi = {10.1111/ppl.14370},
	abstract = {With climate change, droughts are expected to be more frequent and severe, severely impacting plant biomass and quality. Here, we show that overexpressing the Arabidopsis gene AtFtsHi3 (FtsHi3OE) enhances drought-tolerant phenotypes without compromising plant growth. AtFtsHi3 encodes a chloroplast envelope pseudo-protease; knock-down mutants (ftshi3-1) are found to be drought tolerant but exhibit stunted growth. Altered AtFtsHi3 expression therefore leads to drought tolerance, while only diminished expression of this gene leads to growth retardation. To understand the underlying mechanisms of the enhanced drought tolerance, we compared the proteomes of ftshi3-1 and pFtsHi3-FtsHi3OE (pFtsHi3-OE) to wild-type plants under well-watered and drought conditions. Drought-related processes like osmotic stress, water transport, and abscisic acid response were enriched in pFtsHi3-OE and ftshi3-1 mutants following their enhanced drought response compared to wild-type. The knock-down mutant ftshi3-1 showed an increased abundance of HSP90, HSP93, and TIC110 proteins, hinting at a potential downstream role of AtFtsHi3 in chloroplast pre-protein import. Mathematical modeling was performed to understand how variation in the transcript abundance of AtFtsHi3 can, on the one hand, lead to drought tolerance in both overexpression and knock-down lines, yet, on the other hand, affect plant growth so differently. The results led us to hypothesize that AtFtsHi3 may form complexes with at least two other protease subunits, either as homo- or heteromeric structures. Enriched amounts of AtFtsH7/9, AtFtsH11, AtFtsH12, and AtFtsHi4 in ftshi3-1 suggest a possible compensation mechanism for these proteases in the hexamer.},
	language = {en},
	number = {3},
	urldate = {2024-06-10},
	journal = {Physiologia Plantarum},
	author = {Mishra, Laxmi S. and Cook, Sam D. and Kushwah, Sunita and Isaksson, Hanna and Straub, Isabella R. and Abele, Miriam and Mishra, Sanatkumar and Ludwig, Christina and Libby, Eric and Funk, Christiane},
	month = may,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14370},
	pages = {e14370},
}

With climate change, droughts are expected to be more frequent and severe, severely impacting plant biomass and quality. Here, we show that overexpressing the Arabidopsis gene AtFtsHi3 (FtsHi3OE) enhances drought-tolerant phenotypes without compromising plant growth. AtFtsHi3 encodes a chloroplast envelope pseudo-protease; knock-down mutants (ftshi3-1) are found to be drought tolerant but exhibit stunted growth. Altered AtFtsHi3 expression therefore leads to drought tolerance, while only diminished expression of this gene leads to growth retardation. To understand the underlying mechanisms of the enhanced drought tolerance, we compared the proteomes of ftshi3-1 and pFtsHi3-FtsHi3OE (pFtsHi3-OE) to wild-type plants under well-watered and drought conditions. Drought-related processes like osmotic stress, water transport, and abscisic acid response were enriched in pFtsHi3-OE and ftshi3-1 mutants following their enhanced drought response compared to wild-type. The knock-down mutant ftshi3-1 showed an increased abundance of HSP90, HSP93, and TIC110 proteins, hinting at a potential downstream role of AtFtsHi3 in chloroplast pre-protein import. Mathematical modeling was performed to understand how variation in the transcript abundance of AtFtsHi3 can, on the one hand, lead to drought tolerance in both overexpression and knock-down lines, yet, on the other hand, affect plant growth so differently. The results led us to hypothesize that AtFtsHi3 may form complexes with at least two other protease subunits, either as homo- or heteromeric structures. Enriched amounts of AtFtsH7/9, AtFtsH11, AtFtsH12, and AtFtsHi4 in ftshi3-1 suggest a possible compensation mechanism for these proteases in the hexamer.

@article{prasad_quantitative_2024,
	chapter = {Minireview},
	title = {Quantitative {Proteomics} for {Translational} {Pharmacology} and {Precision} {Medicine}: {State} of {The} {Art} and {Future} {Outlook}},
	copyright = {Copyright © 2024 American Society for Pharmacology and Experimental Therapeutics},
	issn = {0090-9556, 1521-009X},
	shorttitle = {Quantitative {Proteomics} for {Translational} {Pharmacology} and {Precision} {Medicine}},
	url = {https://dmd.aspetjournals.org/content/early/2024/05/31/dmd.124.001600},
	doi = {10.1124/dmd.124.001600},
	abstract = {Over the past 20 years, quantitative proteomics has contributed a wealth of protein expression data, which are currently used for a variety of systems pharmacology applications, as a complement or a surrogate for activity of the corresponding proteins. A symposium at the 25th North American ISSX meeting, in Boston, in September 2023, was held to explore current and emerging applications of quantitative proteomics in translational pharmacology and strategies for improved integration into model-informed drug development based on practical experience of each of the presenters. A summary of the talks and discussions is presented in this perspective alongside future outlooks that were outlined for future meetings.
Significance Statement This perspective explores current and emerging applications of quantitative proteomics in translational pharmacology and precision medicine, and outlines outlooks for improved integration into model-informed drug development.},
	language = {en},
	urldate = {2024-06-10},
	journal = {Drug Metabolism and Disposition},
	publisher = {American Society for Pharmacology and Experimental Therapeutics},
	author = {Prasad, Bhagwat and Al-Majdoub, Zubida M. and Wegler, Christine and Rostami-Hodjegan, Amin and Achour, Brahim},
	month = jan,
	year = {2024},
	keywords = {physiologically-based pharmacokinetic modeling/PBPK, proteomics, systems pharmacology},
}

Over the past 20 years, quantitative proteomics has contributed a wealth of protein expression data, which are currently used for a variety of systems pharmacology applications, as a complement or a surrogate for activity of the corresponding proteins. A symposium at the 25th North American ISSX meeting, in Boston, in September 2023, was held to explore current and emerging applications of quantitative proteomics in translational pharmacology and strategies for improved integration into model-informed drug development based on practical experience of each of the presenters. A summary of the talks and discussions is presented in this perspective alongside future outlooks that were outlined for future meetings. Significance Statement This perspective explores current and emerging applications of quantitative proteomics in translational pharmacology and precision medicine, and outlines outlooks for improved integration into model-informed drug development.

@article{chaudhari_modifying_2024,
	title = {Modifying lignin composition and xylan {O}-acetylation induces changes in cell wall composition, extractability, and digestibility},
	volume = {17},
	issn = {2731-3654},
	url = {https://doi.org/10.1186/s13068-024-02513-5},
	doi = {10.1186/s13068-024-02513-5},
	abstract = {Lignin and xylan are important determinants of cell wall structure and lignocellulosic biomass digestibility. Genetic manipulations that individually modify either lignin or xylan structure improve polysaccharide digestibility. However, the effects of their simultaneous modifications have not been explored in a similar context. Here, both individual and combinatorial modification in xylan and lignin was studied by analysing the effect on plant cell wall properties, biotic stress responses and integrity sensing.},
	number = {1},
	urldate = {2024-06-10},
	journal = {Biotechnology for Biofuels and Bioproducts},
	author = {Chaudhari, Aniket Anant and Sharma, Anant Mohan and Rastogi, Lavi and Dewangan, Bhagwat Prasad and Sharma, Raunak and Singh, Deepika and Sah, Rajan Kumar and Das, Shouvik and Bhattacharjee, Saikat and Mellerowicz, Ewa J. and Pawar, Prashant Anupama-Mohan},
	month = may,
	year = {2024},
	keywords = {Acetyl Xylan Esterase (AXE), G Lignin, Saccharification, Xylose release},
	pages = {73},
}

Lignin and xylan are important determinants of cell wall structure and lignocellulosic biomass digestibility. Genetic manipulations that individually modify either lignin or xylan structure improve polysaccharide digestibility. However, the effects of their simultaneous modifications have not been explored in a similar context. Here, both individual and combinatorial modification in xylan and lignin was studied by analysing the effect on plant cell wall properties, biotic stress responses and integrity sensing.

@article{schneider_effects_2024,
	title = {Effects of small-scale outplanting fertilization on conifer seedling growth and fungal community establishment},
	volume = {16},
	issn = {2666-7193},
	url = {https://www.sciencedirect.com/science/article/pii/S266671932400075X},
	doi = {10.1016/j.tfp.2024.100568},
	abstract = {Forestry in Sweden largely relies on planting genetically improved seedlings after clear-cutting, and high survival and early growth of planted seedlings is vital for stand establishment, economic viability, and carbon sequestration. Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) are the two most important tree species in Swedish forest stands and both are associated with a variety of ectomycorrhizal fungi. While seedlings are generally not fertilized at outplanting, previous results have shown that fertilization with arginine phosphate can increase root growth and seedling survival. However, it is not clear how this affects fungal community composition on the roots of growing seedlings. In a planting experiment sampled after one and two growing seasons, we found that planting position had the largest effects both on seedling performance and on fungal community composition and provide insight into the early stages of fungal community succession on planted Norway spruce and Scots pine seedlings. Fungal taxa present on seedlings before planting persisted on seedling roots, while some degree of novel colonization by site indigenous taxa was observed. Fertilization modified the relative abundance of some fungal taxa but did not lead to significant changes in overall community composition. In terms of seedling performance, ammonium nitrate led to increased mortality while arginine phosphate improved root growth.},
	urldate = {2024-06-10},
	journal = {Trees, Forests and People},
	author = {Schneider, Andreas N. and Castro, David and Holmlund, Mattias and Näsholm, Torgny and Hurry, Vaughan and Street, Nathaniel R.},
	month = jun,
	year = {2024},
	keywords = {Ectomycorrhiza, Fertilization, Norway spruce, Rotation forestry, Scots pine, Seedling establishment},
	pages = {100568},
}

Forestry in Sweden largely relies on planting genetically improved seedlings after clear-cutting, and high survival and early growth of planted seedlings is vital for stand establishment, economic viability, and carbon sequestration. Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) are the two most important tree species in Swedish forest stands and both are associated with a variety of ectomycorrhizal fungi. While seedlings are generally not fertilized at outplanting, previous results have shown that fertilization with arginine phosphate can increase root growth and seedling survival. However, it is not clear how this affects fungal community composition on the roots of growing seedlings. In a planting experiment sampled after one and two growing seasons, we found that planting position had the largest effects both on seedling performance and on fungal community composition and provide insight into the early stages of fungal community succession on planted Norway spruce and Scots pine seedlings. Fungal taxa present on seedlings before planting persisted on seedling roots, while some degree of novel colonization by site indigenous taxa was observed. Fertilization modified the relative abundance of some fungal taxa but did not lead to significant changes in overall community composition. In terms of seedling performance, ammonium nitrate led to increased mortality while arginine phosphate improved root growth.

@article{diao_development_2024,
	title = {Development of 51 {K} liquid-phased probe array for {Loblolly} and {Slash} pines and its application to {GWAS} of {Slash} pine breeding population},
	volume = {216},
	issn = {0926-6690},
	doi = {10.1016/j.indcrop.2024.118777},
	abstract = {Loblolly pine (Pinus taeda) and Slash pine (Pinus elliottii) are important economically and ecologically tree species worldwide. To implement genomic based breeding strategy, genotyping large number of samples is needed. However, huge and complex pines genome make it difficult to obtain abundant and cost-effectively markers. In this study, we designed a SNP array containing 51 K liquid-phased probes based on the published SNPs and probes of the two species, novel Slash pine-specific long-read transcript, and SNPs obtained from a double digest Restriction-Site Associated DNA sequencing (ddRADseq). We performed targeted capture sequencing using the developed SNP array on three pine species of Loblolly, Slash, and Caribbean pine (Pinus caribaea). The probe capture had an efficiency of 68.26\% on average. Principal Component Analysis (PCA), phylogenetic analysis, and genetic structure analysis of 28,670 SNPs genotyped for the three pine species demonstrated the transferability of the SNP array for the three pines. Furthermore, we genotyped 221 range-wide Slash pine genotypes, analyzed their genetic diversity and performed a genome-wide association study (GWAS). We identified 95 SNPs significantly associated with growth and wood quality traits of Slash pine. We have identified potential roles of the MYB2 and MYB46 transcription factors in regulating cell cycle and differentiation in Slash pine, while also suggesting that AP2/ERF and Glycosyl hydrolase may play significant roles in wood formation processes. This new SNP array can be widely applied in future molecular breeding research of conifers. © 2024 Elsevier B.V.},
	language = {English},
	journal = {Industrial Crops and Products},
	author = {Diao, S. and Ding, X. and Luan, Q. and Chen, Z.-Q. and Wu, H.X. and Li, X. and Zhang, Y. and Sun, J. and Wu, Y. and Zou, L.-H. and Jiang, J.},
	month = sep,
	year = {2024},
	keywords = {Candidate gene, Genetic variation, Genotyping by target sequencing, In-solution probe, SNPs},
}

Loblolly pine (Pinus taeda) and Slash pine (Pinus elliottii) are important economically and ecologically tree species worldwide. To implement genomic based breeding strategy, genotyping large number of samples is needed. However, huge and complex pines genome make it difficult to obtain abundant and cost-effectively markers. In this study, we designed a SNP array containing 51 K liquid-phased probes based on the published SNPs and probes of the two species, novel Slash pine-specific long-read transcript, and SNPs obtained from a double digest Restriction-Site Associated DNA sequencing (ddRADseq). We performed targeted capture sequencing using the developed SNP array on three pine species of Loblolly, Slash, and Caribbean pine (Pinus caribaea). The probe capture had an efficiency of 68.26% on average. Principal Component Analysis (PCA), phylogenetic analysis, and genetic structure analysis of 28,670 SNPs genotyped for the three pine species demonstrated the transferability of the SNP array for the three pines. Furthermore, we genotyped 221 range-wide Slash pine genotypes, analyzed their genetic diversity and performed a genome-wide association study (GWAS). We identified 95 SNPs significantly associated with growth and wood quality traits of Slash pine. We have identified potential roles of the MYB2 and MYB46 transcription factors in regulating cell cycle and differentiation in Slash pine, while also suggesting that AP2/ERF and Glycosyl hydrolase may play significant roles in wood formation processes. This new SNP array can be widely applied in future molecular breeding research of conifers. © 2024 Elsevier B.V.

@article{yang_genomic_2024,
	title = {Genomic basis of the distinct biosynthesis of β-glucogallin, a biochemical marker for hydrolyzable tannin production, in three oak species},
	volume = {242},
	copyright = {© 2024 The Authors New Phytologist © 2024 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19711},
	doi = {10.1111/nph.19711},
	abstract = {Hydrolyzable tannins (HTs), predominant polyphenols in oaks, are widely used in grape wine aging, feed additives, and human healthcare. However, the limited availability of a high-quality reference genome of oaks greatly hampered the recognition of the mechanism of HT biosynthesis. Here, high-quality reference genomes of three Asian oak species (Quercus variabilis, Quercus aliena, and Quercus dentata) that have different HT contents were generated. Multi-omics studies were carried out to identify key genes regulating HT biosynthesis. In vitro enzyme activity assay was also conducted. Dual-luciferase and yeast one-hybrid assays were used to reveal the transcriptional regulation. Our results revealed that β-glucogallin was a biochemical marker for HT production in the cupules of the three Asian oaks. UGT84A13 was confirmed as the key enzyme for β-glucogallin biosynthesis. The differential expression of UGT84A13, rather than enzyme activity, was the main reason for different β-glucogallin and HT accumulation. Notably, sequence variations in UGT84A13 promoters led to different trans-activating activities of WRKY32/59, explaining the different expression patterns of UGT84A13 among the three species. Our findings provide three high-quality new reference genomes for oak trees and give new insights into different transcriptional regulation for understanding β-glucogallin and HT biosynthesis in closely related oak species.},
	language = {en},
	number = {6},
	urldate = {2024-05-24},
	journal = {New Phytologist},
	author = {Yang, Qinsong and Li, Jinjin and Wang, Yan and Wang, Zefu and Pei, Ziqi and Street, Nathaniel R. and Bhalerao, Rishikesh P. and Yu, Zhaowei and Gao, Yuhao and Ni, Junbei and Jiao, Yang and Sun, Minghui and Yang, Xiong and Chen, Yixin and Liu, Puyuan and Wang, Jiaxi and Liu, Yong and Li, Guolei},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19711},
	keywords = {UGT84A13, hydrolyzable tannin, oak, whole-genome sequencing, β-glucogallin},
	pages = {2702--2718},
}

Hydrolyzable tannins (HTs), predominant polyphenols in oaks, are widely used in grape wine aging, feed additives, and human healthcare. However, the limited availability of a high-quality reference genome of oaks greatly hampered the recognition of the mechanism of HT biosynthesis. Here, high-quality reference genomes of three Asian oak species (Quercus variabilis, Quercus aliena, and Quercus dentata) that have different HT contents were generated. Multi-omics studies were carried out to identify key genes regulating HT biosynthesis. In vitro enzyme activity assay was also conducted. Dual-luciferase and yeast one-hybrid assays were used to reveal the transcriptional regulation. Our results revealed that β-glucogallin was a biochemical marker for HT production in the cupules of the three Asian oaks. UGT84A13 was confirmed as the key enzyme for β-glucogallin biosynthesis. The differential expression of UGT84A13, rather than enzyme activity, was the main reason for different β-glucogallin and HT accumulation. Notably, sequence variations in UGT84A13 promoters led to different trans-activating activities of WRKY32/59, explaining the different expression patterns of UGT84A13 among the three species. Our findings provide three high-quality new reference genomes for oak trees and give new insights into different transcriptional regulation for understanding β-glucogallin and HT biosynthesis in closely related oak species.

@article{hoermayer_mechanical_2024,
	title = {Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization},
	volume = {59},
	issn = {1534-5807},
	url = {https://www.sciencedirect.com/science/article/pii/S1534580724001771},
	doi = {10.1016/j.devcel.2024.03.009},
	abstract = {Plant morphogenesis relies exclusively on oriented cell expansion and division. Nonetheless, the mechanism(s) determining division plane orientation remain elusive. Here, we studied tissue healing after laser-assisted wounding in roots of Arabidopsis thaliana and uncovered how mechanical forces stabilize and reorient the microtubule cytoskeleton for the orientation of cell division. We identified that root tissue functions as an interconnected cell matrix, with a radial gradient of tissue extendibility causing predictable tissue deformation after wounding. This deformation causes instant redirection of expansion in the surrounding cells and reorientation of microtubule arrays, ultimately predicting cell division orientation. Microtubules are destabilized under low tension, whereas stretching of cells, either through wounding or external aspiration, immediately induces their polymerization. The higher microtubule abundance in the stretched cell parts leads to the reorientation of microtubule arrays and, ultimately, informs cell division planes. This provides a long-sought mechanism for flexible re-arrangement of cell divisions by mechanical forces for tissue reconstruction and plant architecture.},
	number = {10},
	urldate = {2024-05-24},
	journal = {Developmental Cell},
	author = {Hoermayer, Lukas and Montesinos, Juan Carlos and Trozzi, Nicola and Spona, Leonhard and Yoshida, Saiko and Marhava, Petra and Caballero-Mancebo, Silvia and Benková, Eva and Heisenberg, Carl-Philip and Dagdas, Yasin and Majda, Mateusz and Friml, Jiří},
	month = may,
	year = {2024},
	keywords = {ablation, cell division, cell division plane, cell expansion, mechanical forces, microscopy, microtubules, plant development},
	pages = {1333--1344.e4},
}

Plant morphogenesis relies exclusively on oriented cell expansion and division. Nonetheless, the mechanism(s) determining division plane orientation remain elusive. Here, we studied tissue healing after laser-assisted wounding in roots of Arabidopsis thaliana and uncovered how mechanical forces stabilize and reorient the microtubule cytoskeleton for the orientation of cell division. We identified that root tissue functions as an interconnected cell matrix, with a radial gradient of tissue extendibility causing predictable tissue deformation after wounding. This deformation causes instant redirection of expansion in the surrounding cells and reorientation of microtubule arrays, ultimately predicting cell division orientation. Microtubules are destabilized under low tension, whereas stretching of cells, either through wounding or external aspiration, immediately induces their polymerization. The higher microtubule abundance in the stretched cell parts leads to the reorientation of microtubule arrays and, ultimately, informs cell division planes. This provides a long-sought mechanism for flexible re-arrangement of cell divisions by mechanical forces for tissue reconstruction and plant architecture.

@article{larsson_diminishing_2024,
	title = {Diminishing legacy effects from forest fertilization on stand structure, vegetation community, and soil function},
	volume = {563},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112724002792},
	doi = {10.1016/j.foreco.2024.121967},
	abstract = {While there is consensus that fertilization with nitrogen (N) is a cost-effective way of increasing both forest biomass yield and timber harvest profitability, the strength and longevity of legacy effects are debated. To quantify legacy effects of past fertilization, we analysed 21 mixed Pinus sylvesteris and Picea abies stands. The stands, on average 23 years old at the time of this study, were either unfertilized (n=7), fertilized with 150 kg N ha−1 once 36 years ago (n=7), or twice, 45 and 36 years ago, respectively (n=7), during the previous stand rotation. We performed measurements on soil N mineralisation and N availability, forest growth, ground vegetation community composition, soil and vegetation C/N ratios and soil C and N stocks, many of which responded to legacy N fertilization earlier in stand development. Our results show that the legacy effects of fertilization during the previous stand rotation have diminished through time, indicating an eventual convergence of stand properties. Specifically, all significant effects present in the previous measurement period (over a decade ago), were weaker or completely absent in the current study (i.e. 36 years after fertilization and 23 years after initiation of the new stands). None-the-less, this indicates a longer legacy effect of N fertilization than what is normally considered and suggests that care should be taken to mitigate unwanted, long-term effects when utilizing N addition to promote tree growth in boreal forests.},
	urldate = {2024-05-15},
	journal = {Forest Ecology and Management},
	author = {Larsson, Marcus and Strengbom, Joachim and Gundale, Michael J. and Nordin, Annika},
	month = jul,
	year = {2024},
	keywords = {Forest fertilization, Forest growth, Ion-exchange resin, Mineralization, Soil organic carbon, Vegetation community composition},
	pages = {121967},
}

While there is consensus that fertilization with nitrogen (N) is a cost-effective way of increasing both forest biomass yield and timber harvest profitability, the strength and longevity of legacy effects are debated. To quantify legacy effects of past fertilization, we analysed 21 mixed Pinus sylvesteris and Picea abies stands. The stands, on average 23 years old at the time of this study, were either unfertilized (n=7), fertilized with 150 kg N ha−1 once 36 years ago (n=7), or twice, 45 and 36 years ago, respectively (n=7), during the previous stand rotation. We performed measurements on soil N mineralisation and N availability, forest growth, ground vegetation community composition, soil and vegetation C/N ratios and soil C and N stocks, many of which responded to legacy N fertilization earlier in stand development. Our results show that the legacy effects of fertilization during the previous stand rotation have diminished through time, indicating an eventual convergence of stand properties. Specifically, all significant effects present in the previous measurement period (over a decade ago), were weaker or completely absent in the current study (i.e. 36 years after fertilization and 23 years after initiation of the new stands). None-the-less, this indicates a longer legacy effect of N fertilization than what is normally considered and suggests that care should be taken to mitigate unwanted, long-term effects when utilizing N addition to promote tree growth in boreal forests.

@article{haggstrom_effects_2024,
	title = {Effects of {Planting} {Position}, {Seedling} {Size}, and {Organic} {Nitrogen} {Fertilization} on the {Establishment} of {Scots} {Pine} ({Pinus} sylvestris {L}.) and {Norway} {Spruce} ({Picea} abies ({L}.) {Karst}) {Seedlings}},
	volume = {15},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/15/4/703},
	doi = {10.3390/f15040703},
	abstract = {The forest regeneration phase in Sweden commonly involves mechanical soil preparation followed by the planting of Scots pine (Pinus sylvestris L.) or Norway spruce (Picea abies (L.) Karst) seedlings. The prepared soil offers planting positions with different properties, including reduced damage by pine weevils (Hylobius abietis L.). Nitrogen fertilization can be applied at the time of planting to aid establishment of the seedlings. In this study, we compared the effects of different planting positions, organic nitrogen fertilization, and different seedling sizes on the early survival and growth of Scots pine and Norway spruce seedlings. The main planting positions were capped mound, hinge, and mineral soil. Seedlings planted close to organic material were categorized as being in “low-quality positions”, since proximity to organic material increases pine weevil attraction. Higher mortality rates related to pine weevil damage were recorded for the seedlings planted in the low-quality positions, regardless of seedling size or N fertilization. Pine weevil attack rates increased with increasing seedling size. Growth was, in general, lowest in the mineral soil positions. The effect of organic N fertilization on growth was positive for the spruce regardless of the planting position or seedling size, while it depended on the planting position and seedling size for the pine, indicating that the effects of organic N fertilization depend on the seedling species, seedling size, and planting position.},
	language = {en},
	number = {4},
	urldate = {2024-05-10},
	journal = {Forests},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Häggström, Bodil and Hajek, Jörgen and Nordin, Annika and Öhlund, Jonas},
	month = apr,
	year = {2024},
	note = {Number: 4},
	keywords = {Norway spruce, Scots pine, forest regeneration, organic N fertilization, pine weevil, planting position, seedling size},
	pages = {703},
}

The forest regeneration phase in Sweden commonly involves mechanical soil preparation followed by the planting of Scots pine (Pinus sylvestris L.) or Norway spruce (Picea abies (L.) Karst) seedlings. The prepared soil offers planting positions with different properties, including reduced damage by pine weevils (Hylobius abietis L.). Nitrogen fertilization can be applied at the time of planting to aid establishment of the seedlings. In this study, we compared the effects of different planting positions, organic nitrogen fertilization, and different seedling sizes on the early survival and growth of Scots pine and Norway spruce seedlings. The main planting positions were capped mound, hinge, and mineral soil. Seedlings planted close to organic material were categorized as being in “low-quality positions”, since proximity to organic material increases pine weevil attraction. Higher mortality rates related to pine weevil damage were recorded for the seedlings planted in the low-quality positions, regardless of seedling size or N fertilization. Pine weevil attack rates increased with increasing seedling size. Growth was, in general, lowest in the mineral soil positions. The effect of organic N fertilization on growth was positive for the spruce regardless of the planting position or seedling size, while it depended on the planting position and seedling size for the pine, indicating that the effects of organic N fertilization depend on the seedling species, seedling size, and planting position.

@article{raebild_polyploidy_2024,
	title = {Polyploidy – {A} tool in adapting trees to future climate changes? {A} review of polyploidy in trees},
	volume = {560},
	issn = {0378-1127},
	shorttitle = {Polyploidy – {A} tool in adapting trees to future climate changes?},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112724000793},
	doi = {10.1016/j.foreco.2024.121767},
	abstract = {Polyploidy, or genome doubling, has occurred repeatedly through plant evolution. While polyploid plants are used extensively in agriculture and horticulture, they have so far found limited use in forestry. Here we review the potentials of polyploid trees under climate change, and investigate if there is support for increased use. We find that polyploid trees like other plants have consistent increases in cell sizes compared to diploids, and that leaf-area based rates of photosynthesis tend to increase with increasing levels of ploidy. While no particular trend could be discerned in terms of biomass between trees of different ploidy levels, physiology is affected by polyploidization and several studies point towards a high potential for polyploid trees to adapt to drought stress. The ploidy level of most tree species is unknown, and analysis of geographical patterns in frequencies of polyploid trees are inconclusive. Artificial polyploid trees are often created by colchicine and in a few cases these have been successfully applied in forestry, but the effects of induced polyploidization in many economically important tree species remains untested. Polyploids would also be increasingly useful in tree breeding programs, to create synthetic hybrids or sterile triploids that could control unwanted spreading of germplasm in nature. In conclusion, this review suggests that polyploid trees may be superior under climate change in some cases, but that the potential of polyploids is not yet fully known and should be evaluated on a case-to-case basis for different tree species.},
	urldate = {2024-05-10},
	journal = {Forest Ecology and Management},
	author = {Ræbild, Anders and Anamthawat-Jónsson, Kesara and Egertsdotter, Ulrika and Immanen, Juha and Jensen, Anna Monrad and Koutouleas, Athina and Martens, Helle Jakobe and Nieminen, Kaisa and Olofsson, Jill Katharina and Röper, Anna-Catharina and Salojärvi, Jarkko and Strömvik, Martina and Vatanparast, Mohammad and Vivian-Smith, Adam},
	month = may,
	year = {2024},
	keywords = {Adaptation, Ecophysiology, Fitness, Forestry, Tree breeding, Whole genome duplication (WGD)},
	pages = {121767},
}

Polyploidy, or genome doubling, has occurred repeatedly through plant evolution. While polyploid plants are used extensively in agriculture and horticulture, they have so far found limited use in forestry. Here we review the potentials of polyploid trees under climate change, and investigate if there is support for increased use. We find that polyploid trees like other plants have consistent increases in cell sizes compared to diploids, and that leaf-area based rates of photosynthesis tend to increase with increasing levels of ploidy. While no particular trend could be discerned in terms of biomass between trees of different ploidy levels, physiology is affected by polyploidization and several studies point towards a high potential for polyploid trees to adapt to drought stress. The ploidy level of most tree species is unknown, and analysis of geographical patterns in frequencies of polyploid trees are inconclusive. Artificial polyploid trees are often created by colchicine and in a few cases these have been successfully applied in forestry, but the effects of induced polyploidization in many economically important tree species remains untested. Polyploids would also be increasingly useful in tree breeding programs, to create synthetic hybrids or sterile triploids that could control unwanted spreading of germplasm in nature. In conclusion, this review suggests that polyploid trees may be superior under climate change in some cases, but that the potential of polyploids is not yet fully known and should be evaluated on a case-to-case basis for different tree species.

@article{shi_super-pangenome_2024,
	title = {The super-pangenome of {Populus} unveils genomic facets for its adaptation and diversification in widespread forest trees},
	volume = {17},
	issn = {1674-2052},
	url = {https://www.cell.com/molecular-plant/abstract/S1674-2052(24)00082-0},
	doi = {10.1016/j.molp.2024.03.009},
	abstract = {{\textless}h2{\textgreater}Abstract{\textless}/h2{\textgreater}{\textless}p{\textgreater}Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 \textit{Populus} genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the \textit{CUC2} gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the \textit{Populus} super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.{\textless}/p{\textgreater}},
	language = {English},
	number = {5},
	urldate = {2024-05-10},
	journal = {Molecular Plant},
	publisher = {Elsevier},
	author = {Shi, Tingting and Zhang, Xinxin and Hou, Yukang and Jia, Changfu and Dan, Xuming and Zhang, Yulin and Jiang, Yuanzhong and Lai, Qiang and Feng, Jiajun and Feng, Jianju and Ma, Tao and Wu, Jiali and Liu, Shuyu and Zhang, Lei and Long, Zhiqin and Chen, Liyang and Street, Nathaniel R. and Ingvarsson, Pär K. and Liu, Jianquan and Yin, Tongming and Wang, Jing},
	month = may,
	year = {2024},
	keywords = {genome evolution, pan-genomes, structural variation, whole genome duplication},
	pages = {725--746},
}

\textlessh2\textgreaterAbstract\textless/h2\textgreater\textlessp\textgreaterUnderstanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.\textless/p\textgreater

@article{zhao_evolutionary_2024,
	title = {Evolutionary radiation of the {Eurasian} {Pinus} species under pervasive gene flow},
	volume = {242},
	copyright = {© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19694},
	doi = {10.1111/nph.19694},
	abstract = {Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers with c. 90\% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.},
	language = {en},
	number = {5},
	urldate = {2024-05-10},
	journal = {New Phytologist},
	author = {Zhao, Wei and Gao, Jie and Hall, David and Andersson, Bea Angelica and Bruxaux, Jade and Tomlinson, Kyle W. and Drouzas, Andreas D. and Suyama, Yoshihisa and Wang, Xiao-Ru},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19694},
	keywords = {Pinus evolution, demographic history, divergent adaptation, ecological gradients, introgression, phylogeny, selection},
	pages = {2353--2368},
}

Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers with c. 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.

@article{bekele_methane_2024,
	title = {Methane production from locally available ruminant feedstuffs in {Ethiopia} – {An} \textit{in vitro} study},
	volume = {312},
	issn = {0377-8401},
	url = {https://www.sciencedirect.com/science/article/pii/S0377840124001056},
	doi = {10.1016/j.anifeedsci.2024.115977},
	abstract = {Achieving optimal nutrient composition in locally sourced ruminant feeds is important, but can be challenging in resource-limited production systems. For example, improving the composition of available local feed resources is a key obstacle to efficiently mitigating enteric methane (CH4) emissions in ruminants. This study characterized the nutritional content and in vitro methane (CH4) yield of ruminant feedstuffs accessible in Ethiopia. A survey of 60 experienced farmers in two representative districts in Amhara region, Ethiopia, provided 33 feed samples, which were classified into four ruminant feed categories: Grasses (n=10); indigenous plants (trees, shrubs, herbaceous plants) (n=13); crop residues (n=5); and agro-industrial by-products (n=5). Nutritional composition was assessed by proximate and detergent methods. Methane yield (g CH4/kg feed dry matter (DM)) and total gas yield (L/kg DM) were evaluated using a fully automated in vitro gas production system. A colorimetric assay was conducted to measure condensed tannin content (CT, mg/g) in relevant feeds. Lower crude protein (CP) values were observed for the grass (mean 65.2 g/kg DM) and crop residues (mean 54.5 g/kg DM) categories. Agro-industrial by-products had the highest CP (mean 260 g/kg DM), while indigenous plants exhibited intermediate levels (163 g/kg DM). There was significant variation in CH4 yield (P{\textless}0.01) between grasses (12.4–24.7 g/kg DM) indigenous plants (1.8–19.3 g/kg DM), and agro-industrial by-products (8.1–26.9 g/kg DM). The indigenous plant Trifolium acaule gave the lowest in vitro CH4 yield (1.8 g/kg DM). A positive relationship was observed between in vitro dry matter digestibility (IVDMD), CH4, and total gas yield. Percentage of CH4 in total gas production varied with feed category (grasses 14.5–19.6\%; indigenous plants 3.1–16.9\%; crop residues 15.8–20.6\%; agro-industrial by-products 12.8–18.7\%), and within category, e.g., Trifolium acaule (3.1\%), Acacia nilotica L. (7.1\%), Ziziphus spina-christi (9.9\%), brewer’s spent grains (BSG) (12.8\%), local liquor (areki) residues (14.1\%), and local beer (tella) residues (15.1\%). A negative relationship was observed between CT content and in vitro CH4 yield, with a stronger (P{\textless}0.05) correlation for soluble CTs (R2 = 0.46) than cell-bound CTs (R2 = 0.25) and total CTs (R2 = 0.29). Based on methanogenic properties and effects of CTs on in vitro CH4 yield, indigenous plants should be prioritized in ruminant rations in Ethiopia. Making nutritional composition and CH4 data publicly available could help develop environmentally sound, cost-effective rations for ruminant livestock, benefiting local farmers and leading to more sustainable and efficient livestock production in Ethiopia.},
	urldate = {2024-05-06},
	journal = {Animal Feed Science and Technology},
	author = {Bekele, Wondimagegne and Huhtanen, Pekka and Zegeye, Abiy and Simachew, Addis and Siddique, Abu Bakar and Albrectsen, Benedicte Riber and Ramin, Mohammad},
	month = jun,
	year = {2024},
	keywords = {CH, CH gas percentage, Local feeds, condensed tannins, dry matter digestibility},
	pages = {115977},
}

Achieving optimal nutrient composition in locally sourced ruminant feeds is important, but can be challenging in resource-limited production systems. For example, improving the composition of available local feed resources is a key obstacle to efficiently mitigating enteric methane (CH4) emissions in ruminants. This study characterized the nutritional content and in vitro methane (CH4) yield of ruminant feedstuffs accessible in Ethiopia. A survey of 60 experienced farmers in two representative districts in Amhara region, Ethiopia, provided 33 feed samples, which were classified into four ruminant feed categories: Grasses (n=10); indigenous plants (trees, shrubs, herbaceous plants) (n=13); crop residues (n=5); and agro-industrial by-products (n=5). Nutritional composition was assessed by proximate and detergent methods. Methane yield (g CH4/kg feed dry matter (DM)) and total gas yield (L/kg DM) were evaluated using a fully automated in vitro gas production system. A colorimetric assay was conducted to measure condensed tannin content (CT, mg/g) in relevant feeds. Lower crude protein (CP) values were observed for the grass (mean 65.2 g/kg DM) and crop residues (mean 54.5 g/kg DM) categories. Agro-industrial by-products had the highest CP (mean 260 g/kg DM), while indigenous plants exhibited intermediate levels (163 g/kg DM). There was significant variation in CH4 yield (P\textless0.01) between grasses (12.4–24.7 g/kg DM) indigenous plants (1.8–19.3 g/kg DM), and agro-industrial by-products (8.1–26.9 g/kg DM). The indigenous plant Trifolium acaule gave the lowest in vitro CH4 yield (1.8 g/kg DM). A positive relationship was observed between in vitro dry matter digestibility (IVDMD), CH4, and total gas yield. Percentage of CH4 in total gas production varied with feed category (grasses 14.5–19.6%; indigenous plants 3.1–16.9%; crop residues 15.8–20.6%; agro-industrial by-products 12.8–18.7%), and within category, e.g., Trifolium acaule (3.1%), Acacia nilotica L. (7.1%), Ziziphus spina-christi (9.9%), brewer’s spent grains (BSG) (12.8%), local liquor (areki) residues (14.1%), and local beer (tella) residues (15.1%). A negative relationship was observed between CT content and in vitro CH4 yield, with a stronger (P\textless0.05) correlation for soluble CTs (R2 = 0.46) than cell-bound CTs (R2 = 0.25) and total CTs (R2 = 0.29). Based on methanogenic properties and effects of CTs on in vitro CH4 yield, indigenous plants should be prioritized in ruminant rations in Ethiopia. Making nutritional composition and CH4 data publicly available could help develop environmentally sound, cost-effective rations for ruminant livestock, benefiting local farmers and leading to more sustainable and efficient livestock production in Ethiopia.

@article{shi_high-quality_2024,
	title = {High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar},
	volume = {195},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiae078},
	doi = {10.1093/plphys/kiae078},
	abstract = {Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid “84K” (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77\% accuracy on the training set and 74\% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.},
	number = {1},
	urldate = {2024-05-03},
	journal = {Plant Physiology},
	author = {Shi, Tian-Le and Jia, Kai-Hua and Bao, Yu-Tao and Nie, Shuai and Tian, Xue-Chan and Yan, Xue-Mei and Chen, Zhao-Yang and Li, Zhi-Chao and Zhao, Shi-Wei and Ma, Hai-Yao and Zhao, Ye and Li, Xiang and Zhang, Ren-Gang and Guo, Jing and Zhao, Wei and El-Kassaby, Yousry Aly and Müller, Niels and Van de Peer, Yves and Wang, Xiao-Ru and Street, Nathaniel Robert and Porth, Ilga and An, Xinmin and Mao, Jian-Feng},
	month = may,
	year = {2024},
	pages = {652--670},
}

Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid “84K” (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.

@article{wang_slnac3_2024,
	title = {{SlNAC3} suppresses cold tolerance in tomatoes by enhancing ethylene biosynthesis},
	copyright = {© 2024 John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14933},
	doi = {10.1111/pce.14933},
	abstract = {Low temperature stress poses a significant challenge to the productivity of horticultural crops. The dynamic expression of cold-responsive genes plays a crucial role in plant cold tolerance. While NAC transcription factors have been extensively studied in plant growth and development, their involvement in regulating plant cold tolerance remains poorly understood. In this study, we focused on the identification and characterisation of SlNAC3 as the most rapid and robust responsive gene in tomato under low temperature conditions. Manipulating SlNAC3 through overexpression or silencing resulted in reduced or enhanced cold tolerance, respectively. Surprisingly, we discovered a negative correlation between the expression of CBF and cold tolerance in the SlNAC3 transgenic lines. These findings suggest that SlNAC3 regulates tomato cold tolerance likely through a CBF-independent pathway. Furthermore, we conducted additional investigations to identify the molecular mechanisms underlying SINAC3-mediated cold tolerance in tomatoes. Our results revealed that SlNAC3 controls the transcription of ethylene biosynthetic genes, thereby bursting ethylene release in response to cold stress. Indeed, the silencing of these genes led to an augmentation in cold tolerance. This discovery provides valuable insights into the regulatory pathways involved in ethylene-mediated cold tolerance in tomatoes, offering potential strategies for developing innovative approaches to enhance cold stress resilience in this economically important crop species.},
	language = {en},
	urldate = {2024-05-03},
	journal = {Plant, Cell \& Environment},
	author = {Wang, Tao and Ma, Xuemin and Chen, Ying and Wang, Cuicui and Xia, Zhenxiao and Liu, Zixi and Gao, Lihong and Zhang, Wenna},
	month = may,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14933},
	keywords = {NAC transcription factor, cold response},
}

Low temperature stress poses a significant challenge to the productivity of horticultural crops. The dynamic expression of cold-responsive genes plays a crucial role in plant cold tolerance. While NAC transcription factors have been extensively studied in plant growth and development, their involvement in regulating plant cold tolerance remains poorly understood. In this study, we focused on the identification and characterisation of SlNAC3 as the most rapid and robust responsive gene in tomato under low temperature conditions. Manipulating SlNAC3 through overexpression or silencing resulted in reduced or enhanced cold tolerance, respectively. Surprisingly, we discovered a negative correlation between the expression of CBF and cold tolerance in the SlNAC3 transgenic lines. These findings suggest that SlNAC3 regulates tomato cold tolerance likely through a CBF-independent pathway. Furthermore, we conducted additional investigations to identify the molecular mechanisms underlying SINAC3-mediated cold tolerance in tomatoes. Our results revealed that SlNAC3 controls the transcription of ethylene biosynthetic genes, thereby bursting ethylene release in response to cold stress. Indeed, the silencing of these genes led to an augmentation in cold tolerance. This discovery provides valuable insights into the regulatory pathways involved in ethylene-mediated cold tolerance in tomatoes, offering potential strategies for developing innovative approaches to enhance cold stress resilience in this economically important crop species.

@article{mishra_adventitious_2024,
	title = {Adventitious rooting in response to long-term cold: a possible mechanism of clonal growth in alpine perennials},
	volume = {15},
	issn = {1664-462X},
	shorttitle = {Adventitious rooting in response to long-term cold},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1352830/full},
	doi = {10.3389/fpls.2024.1352830},
	abstract = {{\textless}p{\textgreater}Arctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximize fitness and ensure reproductive success. We used the arctic alpine perennial {\textless}italic{\textgreater}Arabis alpina{\textless}/italic{\textgreater} to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4°C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4°C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developing in specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in {\textless}italic{\textgreater}A. alpina{\textless}/italic{\textgreater} stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of {\textless}italic{\textgreater}DR5{\textless}/italic{\textgreater} auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.{\textless}/p{\textgreater}},
	language = {English},
	urldate = {2024-05-03},
	journal = {Frontiers in Plant Science},
	publisher = {Frontiers},
	author = {Mishra, Priyanka and Roggen, Adrian and Ljung, Karin and Albani, Maria C. and Vayssières, Alice},
	month = apr,
	year = {2024},
	keywords = {Adventitious root, Arabis alpina, Clonal propagation, Transcriptome, alpine, extended cold exposure, phytohormones},
}

\textlessp\textgreaterArctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximize fitness and ensure reproductive success. We used the arctic alpine perennial \textlessitalic\textgreaterArabis alpina\textless/italic\textgreater to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4°C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4°C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developing in specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in \textlessitalic\textgreaterA. alpina\textless/italic\textgreater stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of \textlessitalic\textgreaterDR5\textless/italic\textgreater auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.\textless/p\textgreater

@article{tian_plant-lncpipe_2024,
	title = {Plant-{LncPipe}: a computational pipeline providing significant improvement in plant {lncRNA} identification},
	volume = {11},
	issn = {2662-6810},
	shorttitle = {Plant-{LncPipe}},
	url = {https://doi.org/10.1093/hr/uhae041},
	doi = {10.1093/hr/uhae041},
	abstract = {Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.},
	number = {4},
	urldate = {2024-04-29},
	journal = {Horticulture Research},
	author = {Tian, Xue-Chan and Chen, Zhao-Yang and Nie, Shuai and Shi, Tian-Le and Yan, Xue-Mei and Bao, Yu-Tao and Li, Zhi-Chao and Ma, Hai-Yao and Jia, Kai-Hua and Zhao, Wei and Mao, Jian-Feng},
	month = apr,
	year = {2024},
	pages = {uhae041},
}

Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.

@article{sandell_genomic_2024,
	title = {Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting},
	volume = {22},
	copyright = {© 2023 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley \& Sons Ltd.},
	issn = {1467-7652},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.14267},
	doi = {10.1111/pbi.14267},
	abstract = {Quinoa is an agriculturally important crop species originally domesticated in the Andes of central South America. One of its most important phenotypic traits is seed colour. Seed colour variation is determined by contrasting abundance of betalains, a class of strong antioxidant and free radicals scavenging colour pigments only found in plants of the order Caryophyllales. However, the genetic basis for these pigments in seeds remains to be identified. Here we demonstrate the application of machine learning (extreme gradient boosting) to identify genetic variants predictive of seed colour. We show that extreme gradient boosting outperforms the classical genome-wide association approach. We provide re-sequencing and phenotypic data for 156 South American quinoa accessions and identify candidate genes potentially controlling betalain content in quinoa seeds. Genes identified include novel cytochrome P450 genes and known members of the betalain synthesis pathway, as well as genes annotated as being involved in seed development. Our work showcases the power of modern machine learning methods to extract biologically meaningful information from large sequencing data sets.},
	language = {en},
	number = {5},
	urldate = {2024-04-19},
	journal = {Plant Biotechnology Journal},
	author = {Sandell, Felix L. and Holzweber, Thomas and Street, Nathaniel R. and Dohm, Juliane C. and Himmelbauer, Heinz},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.14267},
	keywords = {betalain synthesis pathway, genome sequencing, genotype-phenotype relationships, machine learning, quinoa, seed colour},
	pages = {1312--1324},
}

Quinoa is an agriculturally important crop species originally domesticated in the Andes of central South America. One of its most important phenotypic traits is seed colour. Seed colour variation is determined by contrasting abundance of betalains, a class of strong antioxidant and free radicals scavenging colour pigments only found in plants of the order Caryophyllales. However, the genetic basis for these pigments in seeds remains to be identified. Here we demonstrate the application of machine learning (extreme gradient boosting) to identify genetic variants predictive of seed colour. We show that extreme gradient boosting outperforms the classical genome-wide association approach. We provide re-sequencing and phenotypic data for 156 South American quinoa accessions and identify candidate genes potentially controlling betalain content in quinoa seeds. Genes identified include novel cytochrome P450 genes and known members of the betalain synthesis pathway, as well as genes annotated as being involved in seed development. Our work showcases the power of modern machine learning methods to extract biologically meaningful information from large sequencing data sets.

@article{lathe_nks1elmo4_2024,
	title = {{NKS1}/{ELMO4} is an integral protein of a pectin synthesis protein complex and maintains {Golgi} morphology and cell adhesion in {Arabidopsis}},
	volume = {121},
	url = {https://www.pnas.org/doi/10.1073/pnas.2321759121},
	doi = {10.1073/pnas.2321759121},
	abstract = {Adjacent plant cells are connected by specialized cell wall regions, called middle lamellae, which influence critical agricultural characteristics, including fruit ripening and organ abscission. Middle lamellae are enriched in pectin polysaccharides, specifically homogalacturonan (HG). Here, we identify a plant-specific Arabidopsis DUF1068 protein, called NKS1/ELMO4, that is required for middle lamellae integrity and cell adhesion. NKS1 localizes to the Golgi apparatus and loss of NKS1 results in changes to Golgi structure and function. The nks1 mutants also display HG deficient phenotypes, including reduced seedling growth, changes to cell wall composition, and tissue integrity defects. These phenotypes are comparable to qua1 and qua2 mutants, which are defective in HG biosynthesis. Notably, genetic interactions indicate that NKS1 and the QUAs work in a common pathway. Protein interaction analyses and modeling corroborate that they work together in a stable protein complex with other pectin-related proteins. We propose that NKS1 is an integral part of a large pectin synthesis protein complex and that proper function of this complex is important to support Golgi structure and function.},
	number = {15},
	urldate = {2024-04-12},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {Lathe, Rahul S. and McFarlane, Heather E. and Kesten, Christopher and Wang, Liu and Khan, Ghazanfar Abbas and Ebert, Berit and Ramírez-Rodríguez, Eduardo Antonio and Zheng, Shuai and Noord, Niels and Frandsen, Kristian and Bhalerao, Rishikesh P. and Persson, Staffan},
	month = apr,
	year = {2024},
	pages = {e2321759121},
}

Adjacent plant cells are connected by specialized cell wall regions, called middle lamellae, which influence critical agricultural characteristics, including fruit ripening and organ abscission. Middle lamellae are enriched in pectin polysaccharides, specifically homogalacturonan (HG). Here, we identify a plant-specific Arabidopsis DUF1068 protein, called NKS1/ELMO4, that is required for middle lamellae integrity and cell adhesion. NKS1 localizes to the Golgi apparatus and loss of NKS1 results in changes to Golgi structure and function. The nks1 mutants also display HG deficient phenotypes, including reduced seedling growth, changes to cell wall composition, and tissue integrity defects. These phenotypes are comparable to qua1 and qua2 mutants, which are defective in HG biosynthesis. Notably, genetic interactions indicate that NKS1 and the QUAs work in a common pathway. Protein interaction analyses and modeling corroborate that they work together in a stable protein complex with other pectin-related proteins. We propose that NKS1 is an integral part of a large pectin synthesis protein complex and that proper function of this complex is important to support Golgi structure and function.

@article{ortiz_genomic_2024,
	title = {Genomic {Prediction} for {Inbred} and {Hybrid} {Polysomic} {Tetraploid} {Potato} {Offspring}},
	volume = {14},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2077-0472},
	url = {https://www.mdpi.com/2077-0472/14/3/455},
	doi = {10.3390/agriculture14030455},
	abstract = {Potato genetic improvement begins with crossing cultivars or breeding clones which often have complementary characteristics for producing heritable variation in segregating offspring, in which phenotypic selection is used thereafter across various vegetative generations (Ti). The aim of this research was to determine whether tetrasomic genomic best linear unbiased predictors (GBLUPs) may facilitate selecting for tuber yield across early Ti within and across breeding sites in inbred (S1) and hybrid (F1) tetraploid potato offspring. This research used 858 breeding clones for a T1 trial at Umeå (Norrland, 63°49′30″ N 20°15′50″ E) in 2021, as well as 829 and 671 clones from the breeding population for T2 trials during 2022 at Umeå and Helgegården (Skåne, 56°01′46″ N 14°09′24″ E), respectively, along with their parents (S0) and check cultivars. The S1 and F1 were derived from selfing and crossing four S0. The experimental layout was an augmented design of four-plant plots across testing sites, where breeding clones were non-replicated, and the parents and cultivars were placed in all blocks between the former. The genomic prediction abilities (r) for tuber weight per plant were 0.5944 and 0.6776 in T2 at Helgegården and Umeå, respectively, when T1 at Umeå was used as the training population. On average, r was larger in inbred than in hybrid offspring at both breeding sites. The r was also estimated using multi-environment data (involving at least one S1 and one F1) for T2 performance at both breeding sites. The r was strongly influenced by the genotype in both S1 and F1 offspring irrespective of the breeding site.},
	language = {en},
	number = {3},
	urldate = {2024-04-04},
	journal = {Agriculture},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Ortiz, Rodomiro and Reslow, Fredrik and Vetukuri, Ramesh and García-Gil, M. Rosario and Pérez-Rodríguez, Paulino and Crossa, José},
	month = mar,
	year = {2024},
	note = {Number: 3},
	keywords = {\textit{Solanum tuberosum}, Nordic latitude, crossing, genomic estimated breeding values, linear models, polyploidy, selfing, tetrasomic inheritance},
	pages = {455},
}

Potato genetic improvement begins with crossing cultivars or breeding clones which often have complementary characteristics for producing heritable variation in segregating offspring, in which phenotypic selection is used thereafter across various vegetative generations (Ti). The aim of this research was to determine whether tetrasomic genomic best linear unbiased predictors (GBLUPs) may facilitate selecting for tuber yield across early Ti within and across breeding sites in inbred (S1) and hybrid (F1) tetraploid potato offspring. This research used 858 breeding clones for a T1 trial at Umeå (Norrland, 63°49′30″ N 20°15′50″ E) in 2021, as well as 829 and 671 clones from the breeding population for T2 trials during 2022 at Umeå and Helgegården (Skåne, 56°01′46″ N 14°09′24″ E), respectively, along with their parents (S0) and check cultivars. The S1 and F1 were derived from selfing and crossing four S0. The experimental layout was an augmented design of four-plant plots across testing sites, where breeding clones were non-replicated, and the parents and cultivars were placed in all blocks between the former. The genomic prediction abilities (r) for tuber weight per plant were 0.5944 and 0.6776 in T2 at Helgegården and Umeå, respectively, when T1 at Umeå was used as the training population. On average, r was larger in inbred than in hybrid offspring at both breeding sites. The r was also estimated using multi-environment data (involving at least one S1 and one F1) for T2 performance at both breeding sites. The r was strongly influenced by the genotype in both S1 and F1 offspring irrespective of the breeding site.

@article{kleczkowski_multiple_2024,
	title = {Multiple {Roles} of {Glycerate} {Kinase}—{From} {Photorespiration} to {Gluconeogenesis}, {C4} {Metabolism}, and {Plant} {Immunity}},
	volume = {25},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1422-0067},
	url = {https://www.mdpi.com/1422-0067/25/6/3258},
	doi = {10.3390/ijms25063258},
	abstract = {Plant glycerate kinase (GK) was previously considered an exclusively chloroplastic enzyme of the glycolate pathway (photorespiration), and its sole predicted role was to return most of the glycolate-derived carbon (as glycerate) to the Calvin cycle. However, recent discovery of cytosolic GK revealed metabolic links for glycerate to other processes. Although GK was initially proposed as being solely regulated by substrate availability, subsequent discoveries of its redox regulation and the light involvement in the production of chloroplastic and cytosolic GK isoforms have indicated a more refined regulation of the pathways of glycerate conversion. Here, we re-evaluate the importance of GK and emphasize its multifaceted role in plants. Thus, GK can be a major player in several branches of primary metabolism, including the glycolate pathway, gluconeogenesis, glycolysis, and C4 metabolism. In addition, recently, the chloroplastic (but not cytosolic) GK isoform was implicated as part of a light-dependent plant immune response to pathogen attack. The origins of glycerate are also discussed here; it is produced in several cell compartments and undergoes huge fluctuations depending on light/dark conditions. The recent discovery of the vacuolar glycerate transporter adds yet another layer to our understanding of glycerate transport/metabolism and that of other two- and three-carbon metabolites.},
	language = {en},
	number = {6},
	urldate = {2024-04-02},
	journal = {International Journal of Molecular Sciences},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Kleczkowski, Leszek A. and Igamberdiev, Abir U.},
	month = mar,
	year = {2024},
	note = {Number: 6},
	keywords = {\textit{Phytophthora infestans}, C$_{\textrm{4}}$ photosynthesis, gluconeogenesis, glycerate metabolism, glycolate pathway, sucrose synthesis},
	pages = {3258},
}

Plant glycerate kinase (GK) was previously considered an exclusively chloroplastic enzyme of the glycolate pathway (photorespiration), and its sole predicted role was to return most of the glycolate-derived carbon (as glycerate) to the Calvin cycle. However, recent discovery of cytosolic GK revealed metabolic links for glycerate to other processes. Although GK was initially proposed as being solely regulated by substrate availability, subsequent discoveries of its redox regulation and the light involvement in the production of chloroplastic and cytosolic GK isoforms have indicated a more refined regulation of the pathways of glycerate conversion. Here, we re-evaluate the importance of GK and emphasize its multifaceted role in plants. Thus, GK can be a major player in several branches of primary metabolism, including the glycolate pathway, gluconeogenesis, glycolysis, and C4 metabolism. In addition, recently, the chloroplastic (but not cytosolic) GK isoform was implicated as part of a light-dependent plant immune response to pathogen attack. The origins of glycerate are also discussed here; it is produced in several cell compartments and undergoes huge fluctuations depending on light/dark conditions. The recent discovery of the vacuolar glycerate transporter adds yet another layer to our understanding of glycerate transport/metabolism and that of other two- and three-carbon metabolites.

@article{aguida_seeing_2024,
	title = {‘{Seeing}’ the electromagnetic spectrum: spotlight on the cryptochrome photocycle},
	volume = {15},
	issn = {1664-462X},
	shorttitle = {‘{Seeing}’ the electromagnetic spectrum},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1340304},
	doi = {10.3389/fpls.2024.1340304},
	abstract = {Cryptochromes are widely dispersed flavoprotein photoreceptors that regulate numerous developmental responses to light in plants, as well as to stress and entrainment of the circadian clock in animals and humans. All cryptochromes are closely related to an ancient family of light-absorbing flavoenzymes known as photolyases, which use light as an energy source for DNA repair but themselves have no light sensing role. Here we review the means by which plant cryptochromes acquired a light sensing function. This transition involved subtle changes within the flavin binding pocket which gave rise to a visual photocycle consisting of light-inducible and dark-reversible flavin redox state transitions. In this photocycle, light first triggers flavin reduction from an initial dark-adapted resting state (FADox). The reduced state is the biologically active or ‘lit’ state, correlating with biological activity. Subsequently, the photoreduced flavin reoxidises back to the dark adapted or ‘resting’ state. Because the rate of reoxidation determines the lifetime of the signaling state, it significantly modulates biological activity. As a consequence of this redox photocycle Crys respond to both the wavelength and the intensity of light, but are in addition regulated by factors such as temperature, oxygen concentration, and cellular metabolites that alter rates of flavin reoxidation even independently of light. Mechanistically, flavin reduction is correlated with conformational change in the protein, which is thought to mediate biological activity through interaction with biological signaling partners. In addition, a second, entirely independent signaling mechanism arises from the cryptochrome photocycle in the form of reactive oxygen species (ROS). These are synthesized during flavin reoxidation, are known mediators of biotic and abiotic stress responses, and have been linked to Cry biological activity in plants and animals. Additional special properties arising from the cryptochrome photocycle include responsivity to electromagnetic fields and their applications in optogenetics. Finally, innovations in methodology such as the use of Nitrogen Vacancy (NV) diamond centers to follow cryptochrome magnetic field sensitivity in vivo are discussed, as well as the potential for a whole new technology of ‘magneto-genetics’ for future applications in synthetic biology and medicine.},
	urldate = {2024-03-22},
	journal = {Frontiers in Plant Science},
	author = {Aguida, Blanche and Babo, Jonathan and Baouz, Soria and Jourdan, Nathalie and Procopio, Maria and El-Esawi, Mohamed A. and Engle, Dorothy and Mills, Stephen and Wenkel, Stephan and Huck, Alexander and Berg-Sørensen, Kirstine and Kampranis, Sotirios C. and Link, Justin and Ahmad, Margaret},
	month = mar,
	year = {2024},
	keywords = {⛔ No DOI found},
}

Cryptochromes are widely dispersed flavoprotein photoreceptors that regulate numerous developmental responses to light in plants, as well as to stress and entrainment of the circadian clock in animals and humans. All cryptochromes are closely related to an ancient family of light-absorbing flavoenzymes known as photolyases, which use light as an energy source for DNA repair but themselves have no light sensing role. Here we review the means by which plant cryptochromes acquired a light sensing function. This transition involved subtle changes within the flavin binding pocket which gave rise to a visual photocycle consisting of light-inducible and dark-reversible flavin redox state transitions. In this photocycle, light first triggers flavin reduction from an initial dark-adapted resting state (FADox). The reduced state is the biologically active or ‘lit’ state, correlating with biological activity. Subsequently, the photoreduced flavin reoxidises back to the dark adapted or ‘resting’ state. Because the rate of reoxidation determines the lifetime of the signaling state, it significantly modulates biological activity. As a consequence of this redox photocycle Crys respond to both the wavelength and the intensity of light, but are in addition regulated by factors such as temperature, oxygen concentration, and cellular metabolites that alter rates of flavin reoxidation even independently of light. Mechanistically, flavin reduction is correlated with conformational change in the protein, which is thought to mediate biological activity through interaction with biological signaling partners. In addition, a second, entirely independent signaling mechanism arises from the cryptochrome photocycle in the form of reactive oxygen species (ROS). These are synthesized during flavin reoxidation, are known mediators of biotic and abiotic stress responses, and have been linked to Cry biological activity in plants and animals. Additional special properties arising from the cryptochrome photocycle include responsivity to electromagnetic fields and their applications in optogenetics. Finally, innovations in methodology such as the use of Nitrogen Vacancy (NV) diamond centers to follow cryptochrome magnetic field sensitivity in vivo are discussed, as well as the potential for a whole new technology of ‘magneto-genetics’ for future applications in synthetic biology and medicine.

@article{climent_trade-offs_2024,
	title = {Trade-offs and {Trait} {Integration} in {Tree} {Phenotypes}: {Consequences} for the {Sustainable} {Use} of {Genetic} {Resources}},
	issn = {2198-6436},
	shorttitle = {Trade-offs and {Trait} {Integration} in {Tree} {Phenotypes}},
	url = {https://doi.org/10.1007/s40725-024-00217-5},
	doi = {10.1007/s40725-024-00217-5},
	abstract = {In this review, we synthesise current knowledge on trade-offs among traits in key fitness dimensions and identify major research gaps with the intention of laying the groundwork for a rapid advance in tree breeding for multiple objectives as a key contribution to the sustainability of planted forests in the future.},
	language = {en},
	urldate = {2024-04-02},
	journal = {Current Forestry Reports},
	author = {Climent, Jose and Alía, Ricardo and Karkkainen, Katri and Bastien, Catherine and Benito-Garzon, Marta and Bouffier, Laurent and De Dato, Giovanbattista and Delzon, Sylvain and Dowkiw, Arnaud and Elvira-Recuenco, Margarita and Grivet, Delphine and González-Martínez, Santiago C. and Hayatgheibi, Haleh and Kujala, Sonja and Leplé, Jean-Charles and Martín-Sanz, Ruth C. and de Miguel, Marina and Monteverdi, M. Cristina and Mutke, Sven and Plomion, Christophe and Ramírez-Valiente, José Alberto and Sanchez, Leopoldo and Solé-Medina, Aida and Soularue, Jean-Paul and Steffenrem, Arne and Teani, Angela and Westin, Johan and Whittet, Richard and Wu, Harry and Zas, Rafael and Cavers, Stephen},
	month = mar,
	year = {2024},
	keywords = {Breeding, Forest trees, Global change, Phenotypic integration, Resilience, Trade-offs},
}

In this review, we synthesise current knowledge on trade-offs among traits in key fitness dimensions and identify major research gaps with the intention of laying the groundwork for a rapid advance in tree breeding for multiple objectives as a key contribution to the sustainability of planted forests in the future.

@article{karady_profiling_2024,
	title = {Profiling of 1-aminocyclopropane-1-carboxylic acid and selected phytohormones in {Arabidopsis} using liquid chromatography-tandem mass spectrometry},
	volume = {20},
	issn = {1746-4811},
	url = {https://doi.org/10.1186/s13007-024-01165-8},
	doi = {10.1186/s13007-024-01165-8},
	abstract = {Gaseous phytohormone ethylene levels are directly influenced by the production of its immediate non-volatile precursor 1-aminocyclopropane-1-carboxylic acid (ACC). Owing to the strongly acidic character of the ACC molecule, its quantification has been difficult to perform. Here, we present a simple and straightforward validated method for accurate quantification of not only ACC levels, but also major members of other important phytohormonal classes – auxins, cytokinins, jasmonic acid, abscisic acid and salicylic acid from the same biological sample.},
	number = {1},
	urldate = {2024-03-22},
	journal = {Plant Methods},
	author = {Karady, Michal and Hladík, Pavel and Cermanová, Kateřina and Jiroutová, Petra and Antoniadi, Ioanna and Casanova-Sáez, Rubén and Ljung, Karin and Novák, Ondřej},
	month = mar,
	year = {2024},
	keywords = {1-aminocyclopropane-1-carboxylic acid, ACC, Abscisic acid, Arabidopsis, Auxin, Cytokinin, Ethylene, Jasmonic acid, Liquid chromatography, Mass spectrometry, Plant hormones, Salicylic acid},
	pages = {41},
}

Gaseous phytohormone ethylene levels are directly influenced by the production of its immediate non-volatile precursor 1-aminocyclopropane-1-carboxylic acid (ACC). Owing to the strongly acidic character of the ACC molecule, its quantification has been difficult to perform. Here, we present a simple and straightforward validated method for accurate quantification of not only ACC levels, but also major members of other important phytohormonal classes – auxins, cytokinins, jasmonic acid, abscisic acid and salicylic acid from the same biological sample.

@article{sharma_fungal-bacterial_2024,
	title = {Fungal-{Bacterial} {Combinations} in {Plant} {Health} under {Stress}: {Physiological} and {Biochemical} {Characteristics} of the {Filamentous} {Fungus} {Serendipita} indica and the {Actinobacterium} {Zhihengliuella} sp. {ISTPL4} under {In} {Vitro} {Arsenic} {Stress}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2076-2607},
	shorttitle = {Fungal-{Bacterial} {Combinations} in {Plant} {Health} under {Stress}},
	url = {https://www.mdpi.com/2076-2607/12/2/405},
	doi = {10.3390/microorganisms12020405},
	abstract = {Fungal-bacterial combinations have a significant role in increasing and improving plant health under various stress conditions. Metabolites secreted by fungi and bacteria play an important role in this process. Our study emphasizes the significance of secondary metabolites secreted by the fungus Serendipita indica alone and by an actinobacterium Zhihengliuella sp. ISTPL4 under normal growth conditions and arsenic (As) stress condition. Here, we evaluated the arsenic tolerance ability of S. indica alone and in combination with Z. sp. ISTPL4 under in vitro conditions. The growth of S. indica and Z. sp. ISTPL4 was measured in varying concentrations of arsenic and the effect of arsenic on spore size and morphology of S. indica was determined using confocal microscopy and scanning electron microscopy. The metabolomics study indicated that S. indica alone in normal growth conditions and under As stress released pentadecanoic acid, glycerol tricaprylate, L-proline and cyclo(L-prolyl-L-valine). Similarly, d-Ribose, 2-deoxy-bis(thioheptyl)-dithioacetal were secreted by a combination of S. indica and Z. sp. ISTPL4. Confocal studies revealed that spore size of S. indica decreased by 18\% at 1.9 mM and by 15\% when in combination with Z. sp. ISTPL4 at a 2.4 mM concentration of As. Arsenic above this concentration resulted in spore degeneration and hyphae fragmentation. Scanning electron microscopy (SEM) results indicated an increased spore size of S. indica in the presence of Z. sp. ISTPL4 (18 ± 0.75 µm) compared to S. indica alone (14 ± 0.24 µm) under normal growth conditions. Our study concluded that the suggested combination of microbial consortium can be used to increase sustainable agriculture by combating biotic as well as abiotic stress. This is because the metabolites released by the microbial combination display antifungal and antibacterial properties. The metabolites, besides evading stress, also confer other survival strategies. Therefore, the choice of consortia and combination partners is important and can help in developing strategies for coping with As stress.},
	language = {en},
	number = {2},
	urldate = {2024-03-18},
	journal = {Microorganisms},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Sharma, Neha and Koul, Monika and Joshi, Naveen Chandra and Dufossé, Laurent and Mishra, Arti},
	month = feb,
	year = {2024},
	note = {Number: 2},
	keywords = {\textit{Oryza sativa}, \textit{Serendipita indica}, arsenic, heavy metal stress, secondary metabolites},
	pages = {405},
}

Fungal-bacterial combinations have a significant role in increasing and improving plant health under various stress conditions. Metabolites secreted by fungi and bacteria play an important role in this process. Our study emphasizes the significance of secondary metabolites secreted by the fungus Serendipita indica alone and by an actinobacterium Zhihengliuella sp. ISTPL4 under normal growth conditions and arsenic (As) stress condition. Here, we evaluated the arsenic tolerance ability of S. indica alone and in combination with Z. sp. ISTPL4 under in vitro conditions. The growth of S. indica and Z. sp. ISTPL4 was measured in varying concentrations of arsenic and the effect of arsenic on spore size and morphology of S. indica was determined using confocal microscopy and scanning electron microscopy. The metabolomics study indicated that S. indica alone in normal growth conditions and under As stress released pentadecanoic acid, glycerol tricaprylate, L-proline and cyclo(L-prolyl-L-valine). Similarly, d-Ribose, 2-deoxy-bis(thioheptyl)-dithioacetal were secreted by a combination of S. indica and Z. sp. ISTPL4. Confocal studies revealed that spore size of S. indica decreased by 18% at 1.9 mM and by 15% when in combination with Z. sp. ISTPL4 at a 2.4 mM concentration of As. Arsenic above this concentration resulted in spore degeneration and hyphae fragmentation. Scanning electron microscopy (SEM) results indicated an increased spore size of S. indica in the presence of Z. sp. ISTPL4 (18 ± 0.75 µm) compared to S. indica alone (14 ± 0.24 µm) under normal growth conditions. Our study concluded that the suggested combination of microbial consortium can be used to increase sustainable agriculture by combating biotic as well as abiotic stress. This is because the metabolites released by the microbial combination display antifungal and antibacterial properties. The metabolites, besides evading stress, also confer other survival strategies. Therefore, the choice of consortia and combination partners is important and can help in developing strategies for coping with As stress.

@article{liu_proxitome-rna-capture_2024,
	title = {A proxitome-{RNA}-capture approach reveals that processing bodies repress coregulated hub genes},
	volume = {36},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koad288},
	doi = {10.1093/plcell/koad288},
	abstract = {Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate.},
	number = {3},
	urldate = {2024-03-01},
	journal = {The Plant Cell},
	author = {Liu, Chen and Mentzelopoulou, Andriani and Hatzianestis, Ioannis H and Tzagkarakis, Epameinondas and Skaltsogiannis, Vasileios and Ma, Xuemin and Michalopoulou, Vassiliki A and Romero-Campero, Francisco J and Romero-Losada, Ana B and Sarris, Panagiotis F and Marhavy, Peter and Bölter, Bettina and Kanterakis, Alexandros and Gutierrez-Beltran, Emilio and Moschou, Panagiotis N},
	month = mar,
	year = {2024},
	pages = {559--584},
}

Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate.

@article{dube_gene_2024,
	title = {Gene co-expression network analysis reveal core responsive genes in {Parascaris} univalens tissues following ivermectin exposure},
	volume = {19},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0298039},
	doi = {10.1371/journal.pone.0298039},
	abstract = {Anthelmintic resistance in equine parasite Parascaris univalens, compromises ivermectin (IVM) effectiveness and necessitates an in-depth understanding of its resistance mechanisms. Most research, primarily focused on holistic gene expression analyses, may overlook vital tissue-specific responses and often limit the scope of novel genes. This study leveraged gene co-expression network analysis to elucidate tissue-specific transcriptional responses and to identify core genes implicated in the IVM response in P. univalens. Adult worms (n = 28) were exposed to 10−11 M and 10−9 M IVM in vitro for 24 hours. RNA-sequencing examined transcriptional changes in the anterior end and intestine. Differential expression analysis revealed pronounced tissue differences, with the intestine exhibiting substantially more IVM-induced transcriptional activity. Gene co-expression network analysis identified seven modules significantly associated with the response to IVM. Within these, 219 core genes were detected, largely expressed in the intestinal tissue and spanning diverse biological processes with unspecific patterns. After 10−11 M IVM, intestinal tissue core genes showed transcriptional suppression, cell cycle inhibition, and ribosomal alterations. Interestingly, genes PgR028\_g047 (sorb-1), PgB01\_g200 (gmap-1) and PgR046\_g017 (col-37 \& col-102) switched from downregulation at 10−11 M to upregulation at 10−9 M IVM. The 10−9 M concentration induced expression of cuticle and membrane integrity core genes in the intestinal tissue. No clear core gene patterns were visible in the anterior end after 10−11 M IVM. However, after 10−9 M IVM, the anterior end mostly displayed downregulation, indicating disrupted transcriptional regulation. One interesting finding was the non-modular calcium-signaling gene, PgR047\_g066 (gegf-1), which uniquely connected 71 genes across four modules. These genes were enriched for transmembrane signaling activity, suggesting that PgR047\_g066 (gegf-1) could have a key signaling role. By unveiling tissue-specific expression patterns and highlighting biological processes through unbiased core gene detection, this study reveals intricate IVM responses in P. univalens. These findings suggest alternative drug uptake of IVM and can guide functional validations to further IVM resistance mechanism understanding.},
	language = {en},
	number = {2},
	urldate = {2024-02-23},
	journal = {PLOS ONE},
	publisher = {Public Library of Science},
	author = {Dube, Faruk and Delhomme, Nicolas and Martin, Frida and Hinas, Andrea and Åbrink, Magnus and Svärd, Staffan and Tydén, Eva},
	month = feb,
	year = {2024},
	keywords = {Cellular structures and organelles, Gastrointestinal tract, Gene expression, Gene ontologies, Gene regulatory networks, Genetic networks, Nematode infections, Signal transduction},
	pages = {e0298039},
}

Anthelmintic resistance in equine parasite Parascaris univalens, compromises ivermectin (IVM) effectiveness and necessitates an in-depth understanding of its resistance mechanisms. Most research, primarily focused on holistic gene expression analyses, may overlook vital tissue-specific responses and often limit the scope of novel genes. This study leveraged gene co-expression network analysis to elucidate tissue-specific transcriptional responses and to identify core genes implicated in the IVM response in P. univalens. Adult worms (n = 28) were exposed to 10−11 M and 10−9 M IVM in vitro for 24 hours. RNA-sequencing examined transcriptional changes in the anterior end and intestine. Differential expression analysis revealed pronounced tissue differences, with the intestine exhibiting substantially more IVM-induced transcriptional activity. Gene co-expression network analysis identified seven modules significantly associated with the response to IVM. Within these, 219 core genes were detected, largely expressed in the intestinal tissue and spanning diverse biological processes with unspecific patterns. After 10−11 M IVM, intestinal tissue core genes showed transcriptional suppression, cell cycle inhibition, and ribosomal alterations. Interestingly, genes PgR028_g047 (sorb-1), PgB01_g200 (gmap-1) and PgR046_g017 (col-37 & col-102) switched from downregulation at 10−11 M to upregulation at 10−9 M IVM. The 10−9 M concentration induced expression of cuticle and membrane integrity core genes in the intestinal tissue. No clear core gene patterns were visible in the anterior end after 10−11 M IVM. However, after 10−9 M IVM, the anterior end mostly displayed downregulation, indicating disrupted transcriptional regulation. One interesting finding was the non-modular calcium-signaling gene, PgR047_g066 (gegf-1), which uniquely connected 71 genes across four modules. These genes were enriched for transmembrane signaling activity, suggesting that PgR047_g066 (gegf-1) could have a key signaling role. By unveiling tissue-specific expression patterns and highlighting biological processes through unbiased core gene detection, this study reveals intricate IVM responses in P. univalens. These findings suggest alternative drug uptake of IVM and can guide functional validations to further IVM resistance mechanism understanding.

@article{blume-werry_situ_2024,
	title = {In situ seasonal patterns of root auxin concentrations and meristem length in an arctic sedge},
	copyright = {© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19616},
	doi = {10.1111/nph.19616},
	abstract = {Seasonal dynamics of root growth play an important role in large-scale ecosystem processes; they are largely governed by growth regulatory compounds and influenced by environmental conditions. Yet, our knowledge about physiological drivers of root growth is mostly limited to laboratory-based studies on model plant species. We sampled root tips of Eriophorum vaginatum and analyzed their auxin concentrations and meristem lengths biweekly over a growing season in situ in a subarctic peatland, both in surface soil and at the permafrost thawfront. Auxin concentrations were almost five times higher in surface than in thawfront soils and increased over the season, especially at the thawfront. Surprisingly, meristem length showed an opposite pattern and was almost double in thawfront compared with surface soils. Meristem length increased from peak to late season in the surface soils but decreased at the thawfront. Our study of in situ seasonal dynamics in root physiological parameters illustrates the potential for physiological methods to be applied in ecological studies and emphasizes the importance of in situ measurements. The strong effect of root location and the unexpected opposite patterns of meristem length and auxin concentrations likely show that auxin actively governs root growth to ensure a high potential for nutrient uptake at the thawfront.},
	language = {en},
	urldate = {2024-02-23},
	journal = {New Phytologist},
	author = {Blume-Werry, Gesche and Semenchuk, Philipp and Ljung, Karin and Milbau, Ann and Novak, Ondrej and Olofsson, Johan and Brunoni, Federica},
	month = feb,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19616},
	keywords = {Eriophorum vaginatum, auxin, meristem length, permafrost, root growth, root phenology},
}

Seasonal dynamics of root growth play an important role in large-scale ecosystem processes; they are largely governed by growth regulatory compounds and influenced by environmental conditions. Yet, our knowledge about physiological drivers of root growth is mostly limited to laboratory-based studies on model plant species. We sampled root tips of Eriophorum vaginatum and analyzed their auxin concentrations and meristem lengths biweekly over a growing season in situ in a subarctic peatland, both in surface soil and at the permafrost thawfront. Auxin concentrations were almost five times higher in surface than in thawfront soils and increased over the season, especially at the thawfront. Surprisingly, meristem length showed an opposite pattern and was almost double in thawfront compared with surface soils. Meristem length increased from peak to late season in the surface soils but decreased at the thawfront. Our study of in situ seasonal dynamics in root physiological parameters illustrates the potential for physiological methods to be applied in ecological studies and emphasizes the importance of in situ measurements. The strong effect of root location and the unexpected opposite patterns of meristem length and auxin concentrations likely show that auxin actively governs root growth to ensure a high potential for nutrient uptake at the thawfront.

@article{renstrom_effect_2024,
	title = {The effect of nitrogen source and levels on hybrid aspen tree physiology and wood formation},
	volume = {176},
	copyright = {© 2024 The Authors. Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.14219},
	doi = {10.1111/ppl.14219},
	abstract = {Nitrogen can be taken up by trees in the form of nitrate, ammonium and amino acids, but the influence of the different forms on tree growth and development is poorly understood in angiosperm species like Populus. We studied the effects of both organic and inorganic forms of nitrogen on growth and wood formation of hybrid aspen trees in experimental conditions that allowed growth under four distinct steady-state nitrogen levels. Increased nitrogen availability had a positive influence on biomass accumulation and the radial dimensions of both xylem vessels and fibers, and a negative influence on wood density. An optimal level of nitrogen availability was identified where increases in biomass accumulation outweighed decreases in wood density. None of these responses depended on the source of nitrogen except for shoot biomass accumulation, which was stimulated more by treatments complemented with nitrate than by ammonium alone or the organic source arginine. The most striking difference between the nitrogen sources was the effect on lignin composition, whereby the abundance of H-type lignin increased only in the presence of nitrate. The differential effect of nitrate is possibly related to the well-known role of nitrate as a signaling compound. RNA-sequencing revealed that while the lignin-biosynthetic genes did not significantly (FDR {\textless}0.01) respond to added NO3−, the expression of several laccases, catalysing lignin polymerization, was dependent on N-availability. These results reveal a unique role of nitrate in wood formation and contribute to the knowledge basis for decision-making in utilizing hybrid aspen as a bioresource.},
	language = {en},
	number = {1},
	urldate = {2024-02-23},
	journal = {Physiologia Plantarum},
	author = {Renström, Anna and Choudhary, Shruti and Gandla, Madhavi Latha and Jönsson, Leif J. and Hedenström, Mattias and Jämtgård, Sandra and Tuominen, Hannele},
	month = feb,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14219},
	keywords = {H-type lignin, N-nutrition, Populus tremula x P. tremuloides, Pyrolysis-GC/MS, lignin composition, organic vs. inorganic N, xylogenesis},
	pages = {e14219},
}

Nitrogen can be taken up by trees in the form of nitrate, ammonium and amino acids, but the influence of the different forms on tree growth and development is poorly understood in angiosperm species like Populus. We studied the effects of both organic and inorganic forms of nitrogen on growth and wood formation of hybrid aspen trees in experimental conditions that allowed growth under four distinct steady-state nitrogen levels. Increased nitrogen availability had a positive influence on biomass accumulation and the radial dimensions of both xylem vessels and fibers, and a negative influence on wood density. An optimal level of nitrogen availability was identified where increases in biomass accumulation outweighed decreases in wood density. None of these responses depended on the source of nitrogen except for shoot biomass accumulation, which was stimulated more by treatments complemented with nitrate than by ammonium alone or the organic source arginine. The most striking difference between the nitrogen sources was the effect on lignin composition, whereby the abundance of H-type lignin increased only in the presence of nitrate. The differential effect of nitrate is possibly related to the well-known role of nitrate as a signaling compound. RNA-sequencing revealed that while the lignin-biosynthetic genes did not significantly (FDR \textless0.01) respond to added NO3−, the expression of several laccases, catalysing lignin polymerization, was dependent on N-availability. These results reveal a unique role of nitrate in wood formation and contribute to the knowledge basis for decision-making in utilizing hybrid aspen as a bioresource.

@article{nie_progress_2024,
	title = {Progress in phylogenetics, multi-omics and flower coloration studies in \textit{{Rhododendron}}},
	volume = {4},
	copyright = {2024 The Author(s)},
	issn = {2769-2094},
	url = {https://www.maxapress.com/rticle/doi/10.48130/opr-0024-0001},
	doi = {10.48130/opr-0024-0001},
	abstract = {{\textless}p{\textgreater}The genus {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater} exhibits an immense diversity of flower colors and represents one of the largest groups of woody plants, which is of great importance for ornamental plant research. This review summarizes recent progress in deciphering the genetic basis for flower coloration in {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater}. We describe advances in phylogenetic reconstruction and genome sequencing of {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater} species. The metabolic pathways of flower color are outlined, focusing on key structural and regulatory genes involved in pigment synthesis. Gene duplications and losses associated with color diversification are discussed. In addition, the application of multi-omics approaches and analysis of gene co-expression networks to elucidate complex gene regulatory mechanisms is emphasized. This synthesis of current knowledge provides a foundation for future research on the evolution of flower color diversity within the {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater} lineage. Ultimately, these discoveries will support breeding endeavors aimed at harnessing the genetics of flower coloration and developing novel cultivars that exhibit desired floral traits.{\textless}/p{\textgreater}},
	language = {en},
	number = {1},
	urldate = {2024-02-23},
	journal = {Ornamental Plant Research},
	publisher = {Maximum Academic Press},
	author = {Nie, Shuai and Ma, Hai-Yao and Shi, Tian-Le and Tian, Xue-Chan and El-Kassaby, Yousry A. and Porth, Ilga and Yang, Fu-Sheng and Mao, Jian-Feng and Nie, Shuai and Ma, Hai-Yao and Shi, Tian-Le and Tian, Xue-Chan and El-Kassaby, Yousry A. and Porth, Ilga and Yang, Fu-Sheng and Mao, Jian-Feng},
	month = jan,
	year = {2024},
	note = {Bandiera\_abtest: a
Cc\_license\_type: cc\_by
Cg\_type: Maximum Academic Press
Number: opr-0024-0001
Primary\_atype: Ornamental Plant Research
Subject\_term: REVIEW
Subject\_term\_id: REVIEW},
}

\textlessp\textgreaterThe genus \textlessitalic\textgreaterRhododendron\textless/italic\textgreater exhibits an immense diversity of flower colors and represents one of the largest groups of woody plants, which is of great importance for ornamental plant research. This review summarizes recent progress in deciphering the genetic basis for flower coloration in \textlessitalic\textgreaterRhododendron\textless/italic\textgreater. We describe advances in phylogenetic reconstruction and genome sequencing of \textlessitalic\textgreaterRhododendron\textless/italic\textgreater species. The metabolic pathways of flower color are outlined, focusing on key structural and regulatory genes involved in pigment synthesis. Gene duplications and losses associated with color diversification are discussed. In addition, the application of multi-omics approaches and analysis of gene co-expression networks to elucidate complex gene regulatory mechanisms is emphasized. This synthesis of current knowledge provides a foundation for future research on the evolution of flower color diversity within the \textlessitalic\textgreaterRhododendron\textless/italic\textgreater lineage. Ultimately, these discoveries will support breeding endeavors aimed at harnessing the genetics of flower coloration and developing novel cultivars that exhibit desired floral traits.\textless/p\textgreater

@article{forsmark_shifts_2024,
	title = {Shifts in microbial community composition and metabolism correspond with rapid soil carbon accumulation in response to 20 years of simulated nitrogen deposition},
	volume = {918},
	issn = {0048-9697},
	doi = {10.1016/j.scitotenv.2024.170741},
	abstract = {Anthropogenic nitrogen (N) deposition and fertilization in boreal forests frequently reduces decomposition and soil respiration and enhances C storage in the topsoil. This enhancement of the C sink can be as strong as the aboveground biomass response to N additions and has implications for the global C cycle, but the mechanisms remain elusive. We hypothesized that this effect would be associated with a shift in the microbial community and its activity, and particularly by fungal taxa reported to be capable of lignin degradation and organic N acquisition. We sampled the organic layer below the intact litter of a Norway spruce (Picea abies (L.) Karst) forest in northern Sweden after 20 years of annual N additions at low (12.5 kg N ha−1 yr−1) and high (50 kg N ha−1 yr−1) rates. We measured microbial biomass using phospholipid fatty-acid analysis (PLFA) and ergosterol measurements and used ITS metagenomics to profile the fungal community of soil and fine-roots. We probed the metabolic activity of the soil community by measuring the activity of extracellular enzymes and evaluated its relationships with the most N responsive soil fungal species. Nitrogen addition decreased the abundance of fungal PLFA markers and changed the fungal community in humus and fine-roots. Specifically, the humus community changed in part due to a shift from Oidiodendron pilicola, Cenococcum geophilum, and Cortinarius caperatus to Tylospora fibrillosa and Russula griseascens. These microbial community changes were associated with decreased activity of Mn-peroxidase and peptidase, and an increase in the activity of C acquiring enzymes. Our results show that the rapid accumulation of C in the humus layer frequently observed in areas with high N deposition is consistent with a shift in microbial metabolism, where decomposition associated with organic N acquisition is downregulated when inorganic N forms are readily available. © 2024 The Authors},
	language = {English},
	number = {170741},
	journal = {Science of the Total Environment},
	author = {Forsmark, B. and Bizjak, T. and Nordin, A. and Rosenstock, N.P. and Wallander, H. and Gundale, M.J.},
	month = feb,
	year = {2024},
	keywords = {Boreal forest, Carbon sequestration, Ectomycorrhizal fungi, Extracellular enzymes, Microbial community, Nitrogen deposition},
}

Anthropogenic nitrogen (N) deposition and fertilization in boreal forests frequently reduces decomposition and soil respiration and enhances C storage in the topsoil. This enhancement of the C sink can be as strong as the aboveground biomass response to N additions and has implications for the global C cycle, but the mechanisms remain elusive. We hypothesized that this effect would be associated with a shift in the microbial community and its activity, and particularly by fungal taxa reported to be capable of lignin degradation and organic N acquisition. We sampled the organic layer below the intact litter of a Norway spruce (Picea abies (L.) Karst) forest in northern Sweden after 20 years of annual N additions at low (12.5 kg N ha−1 yr−1) and high (50 kg N ha−1 yr−1) rates. We measured microbial biomass using phospholipid fatty-acid analysis (PLFA) and ergosterol measurements and used ITS metagenomics to profile the fungal community of soil and fine-roots. We probed the metabolic activity of the soil community by measuring the activity of extracellular enzymes and evaluated its relationships with the most N responsive soil fungal species. Nitrogen addition decreased the abundance of fungal PLFA markers and changed the fungal community in humus and fine-roots. Specifically, the humus community changed in part due to a shift from Oidiodendron pilicola, Cenococcum geophilum, and Cortinarius caperatus to Tylospora fibrillosa and Russula griseascens. These microbial community changes were associated with decreased activity of Mn-peroxidase and peptidase, and an increase in the activity of C acquiring enzymes. Our results show that the rapid accumulation of C in the humus layer frequently observed in areas with high N deposition is consistent with a shift in microbial metabolism, where decomposition associated with organic N acquisition is downregulated when inorganic N forms are readily available. © 2024 The Authors

@article{shi_differential_2024,
	title = {Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn ({Xanthoceras} sorbifolium), an oil-producing tree with significant deployment values},
	volume = {14},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1297817},
	abstract = {Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.},
	urldate = {2024-02-16},
	journal = {Frontiers in Plant Science},
	author = {Shi, Tian-Le and Ma, Hai-Yao and Wang, Xinrui and Liu, Hui and Yan, Xue-Mei and Tian, Xue-Chan and Li, Zhi-Chao and Bao, Yu-Tao and Chen, Zhao-Yang and Zhao, Shi-Wei and Xiang, Qiuhong and Jia, Kai-Hua and Nie, Shuai and Guan, Wenbin and Mao, Jian-Feng},
	month = jan,
	year = {2024},
	keywords = {⛔ No DOI found},
}

Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.

@article{tognacca_unveiling_2024,
	title = {Unveiling {Molecular} {Signatures} in {Light}-{Induced} {Seed} {Germination}: {Insights} from {PIN3}, {PIN7}, and {AUX1} in {Arabidopsis} thaliana},
	volume = {13},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	shorttitle = {Unveiling {Molecular} {Signatures} in {Light}-{Induced} {Seed} {Germination}},
	url = {https://www.mdpi.com/2223-7747/13/3/408},
	doi = {10.3390/plants13030408},
	abstract = {Light provides seeds with information that is essential for the adjustment of their germination to the conditions that are most favorable for the successful establishment of the future seedling. The promotion of germination depends mainly on environmental factors, like temperature and light, as well as internal factors associated with the hormonal balance between gibberellins (GA) and abscisic acid (ABA), although other hormones such as auxins may act secondarily. While transcriptomic studies of light-germinating Arabidopsis thaliana seeds suggest that auxins and auxin transporters are necessary, there are still no functional studies connecting the activity of the auxin transporters in light-induced seed germination. In this study, we investigated the roles of two auxin efflux carrier (PIN3 and PIN7) proteins and one auxin influx (AUX1) carrier protein during Arabidopsis thaliana seed germination. By using next-generation sequencing (RNAseq), gene expression analyses, hormonal sensitivity assays, and the quantification of indole-3-acetic acid (IAA) levels, we assessed the functional roles of PIN3, PIN7, and AUX1 during light-induced seed germination. We showed that auxin levels are increased 24 h after a red-pulse (Rp). Additionally, we evaluated the germination responses of pin3, pin7, and aux1 mutant seeds and showed that PIN3, PIN7, and AUX1 auxin carriers are important players in the regulation of seed germination. By using gene expression analysis in water, fluridone (F), and ABA+F treated seeds, we confirmed that Rp-induced seed germination is associated with auxin transport, and ABA controls the function of PIN3, PIN7, and AUX1 during this process. Overall, our results highlight the relevant and positive role of auxin transporters in germinating the seeds of Arabidopsis thaliana.},
	language = {en},
	number = {3},
	urldate = {2024-02-16},
	journal = {Plants},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Tognacca, Rocío Soledad and Ljung, Karin and Botto, Javier Francisco},
	month = jan,
	year = {2024},
	note = {Number: 3},
	keywords = {\textit{Arabidopsis thaliana}, ABA, AUX1, PIN3, PIN7, auxin, hormonal crosstalk, molecular regulation, seed germination},
	pages = {408},
}

Light provides seeds with information that is essential for the adjustment of their germination to the conditions that are most favorable for the successful establishment of the future seedling. The promotion of germination depends mainly on environmental factors, like temperature and light, as well as internal factors associated with the hormonal balance between gibberellins (GA) and abscisic acid (ABA), although other hormones such as auxins may act secondarily. While transcriptomic studies of light-germinating Arabidopsis thaliana seeds suggest that auxins and auxin transporters are necessary, there are still no functional studies connecting the activity of the auxin transporters in light-induced seed germination. In this study, we investigated the roles of two auxin efflux carrier (PIN3 and PIN7) proteins and one auxin influx (AUX1) carrier protein during Arabidopsis thaliana seed germination. By using next-generation sequencing (RNAseq), gene expression analyses, hormonal sensitivity assays, and the quantification of indole-3-acetic acid (IAA) levels, we assessed the functional roles of PIN3, PIN7, and AUX1 during light-induced seed germination. We showed that auxin levels are increased 24 h after a red-pulse (Rp). Additionally, we evaluated the germination responses of pin3, pin7, and aux1 mutant seeds and showed that PIN3, PIN7, and AUX1 auxin carriers are important players in the regulation of seed germination. By using gene expression analysis in water, fluridone (F), and ABA+F treated seeds, we confirmed that Rp-induced seed germination is associated with auxin transport, and ABA controls the function of PIN3, PIN7, and AUX1 during this process. Overall, our results highlight the relevant and positive role of auxin transporters in germinating the seeds of Arabidopsis thaliana.

@article{kreisz_s1_2024,
	title = {S1 basic leucine zipper transcription factors shape plant architecture by controlling {C}/{N} partitioning to apical and lateral organs},
	volume = {121},
	url = {https://www.pnas.org/doi/10.1073/pnas.2313343121},
	doi = {10.1073/pnas.2313343121},
	abstract = {Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant’s nutritional status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S1-basic-leucine-zipper (S1-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S1-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III SWEET sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase GLUTAMINE AMIDO-TRANSFERASE 1\_2.1, involved in N homeostasis, as direct S1-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S1-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.},
	number = {7},
	urldate = {2024-02-09},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {Kreisz, Philipp and Hellens, Alicia M. and Fröschel, Christian and Krischke, Markus and Maag, Daniel and Feil, Regina and Wildenhain, Theresa and Draken, Jan and Braune, Gabriel and Erdelitsch, Leon and Cecchino, Laura and Wagner, Tobias C. and Ache, Peter and Mueller, Martin J. and Becker, Dirk and Lunn, John E. and Hanson, Johannes and Beveridge, Christine A. and Fichtner, Franziska and Barbier, Francois F. and Weiste, Christoph},
	month = feb,
	year = {2024},
	pages = {e2313343121},
}

Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant’s nutritional status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S1-basic-leucine-zipper (S1-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S1-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III SWEET sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase GLUTAMINE AMIDO-TRANSFERASE 1_2.1, involved in N homeostasis, as direct S1-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S1-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.

@article{fuchs_plant_2024,
	title = {{PLANT} {UNCOUPLING} {MITOCHONDRIAL} {PROTEIN} 2 localizes to the {Golgi}},
	volume = {194},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiad540},
	doi = {10.1093/plphys/kiad540},
	abstract = {Mitochondria act as cellular hubs of energy transformation and metabolite conversion in most eukaryotes. Plant mitochondrial electron transport chains are particularly flexible, featuring components that can bypass proton translocation steps, such as ALTERNATIVE NAD(P)H DEHYDROGENASES and ALTERNATIVE OXIDASES (AOXs). PLANT UNCOUPLING MITOCHONDRIAL PROTEINS (PUMPs or plant UNCOUPLING PROTEINS [UCPs]) have been identified in plants as homologs of mammalian UCPs, and their physiological roles have been investigated in the context of mitochondrial energy metabolism. To dissect UCP function in Arabidopsis (Arabidopsis thaliana), the 2 most conserved family members, UCP1 and UCP2, have been genetically ablated assuming that they both reside in the inner mitochondrial membrane. Yet, contradicting results have been reported on plant UCP2 localization. After UCP1 (Maia et al. 1998) and UCP2 (Watanabe et al. 1999) were identified as plant homologs of mammalian UCP1, 6 Arabidopsis isogenes were named PUMP1 to PUMP6 (Borecký et al. 2006). However, PUMP4 to PUMP6 exhibit properties typical of the phylogenetically related mitochondrial dicarboxylate carrier (DIC) proteins (Palmieri et al. 2008). Accordingly, PUMPs were regrouped into plant UCP1 to UCP3 and plant DIC1 to DIC3 (Supplemental Fig. S1) (Palmieri et al. 2008). UCP1 and UCP2 are highly similar in sequence and share 72\% amino acid identity (Supplemental Fig. S2A) (Monné et al. 2018). We provide evidence that UCP2 localizes to the Golgi unlike UCP1, which localizes to the mitochondria, and we provide perspectives on UCP protein function, Golgi membrane transport, and subcellular targeting principles of membrane proteins.},
	number = {2},
	urldate = {2024-02-02},
	journal = {Plant Physiology},
	author = {Fuchs, Philippe and Feixes-Prats, Elisenda and Arruda, Paulo and Feitosa-Araújo, Elias and Fernie, Alisdair R and Grefen, Christopher and Lichtenauer, Sophie and Linka, Nicole and de Godoy Maia, Ivan and Meyer, Andreas J and Schilasky, Sören and Sweetlove, Lee J and Wege, Stefanie and Weber, Andreas P M and Millar, A Harvey and Keech, Olivier and Florez-Sarasa, Igor and Barreto, Pedro and Schwarzländer, Markus},
	month = feb,
	year = {2024},
	pages = {623--628},
}

Mitochondria act as cellular hubs of energy transformation and metabolite conversion in most eukaryotes. Plant mitochondrial electron transport chains are particularly flexible, featuring components that can bypass proton translocation steps, such as ALTERNATIVE NAD(P)H DEHYDROGENASES and ALTERNATIVE OXIDASES (AOXs). PLANT UNCOUPLING MITOCHONDRIAL PROTEINS (PUMPs or plant UNCOUPLING PROTEINS [UCPs]) have been identified in plants as homologs of mammalian UCPs, and their physiological roles have been investigated in the context of mitochondrial energy metabolism. To dissect UCP function in Arabidopsis (Arabidopsis thaliana), the 2 most conserved family members, UCP1 and UCP2, have been genetically ablated assuming that they both reside in the inner mitochondrial membrane. Yet, contradicting results have been reported on plant UCP2 localization. After UCP1 (Maia et al. 1998) and UCP2 (Watanabe et al. 1999) were identified as plant homologs of mammalian UCP1, 6 Arabidopsis isogenes were named PUMP1 to PUMP6 (Borecký et al. 2006). However, PUMP4 to PUMP6 exhibit properties typical of the phylogenetically related mitochondrial dicarboxylate carrier (DIC) proteins (Palmieri et al. 2008). Accordingly, PUMPs were regrouped into plant UCP1 to UCP3 and plant DIC1 to DIC3 (Supplemental Fig. S1) (Palmieri et al. 2008). UCP1 and UCP2 are highly similar in sequence and share 72% amino acid identity (Supplemental Fig. S2A) (Monné et al. 2018). We provide evidence that UCP2 localizes to the Golgi unlike UCP1, which localizes to the mitochondria, and we provide perspectives on UCP protein function, Golgi membrane transport, and subcellular targeting principles of membrane proteins.

@article{estravis_barcala_whole-genome_2024,
	title = {Whole-genome resequencing facilitates the development of a {50K} single nucleotide polymorphism genotyping array for {Scots} pine ({Pinus} sylvestris {L}.) and its transferability to other pine species},
	volume = {117},
	copyright = {© 2023 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.16535},
	doi = {10.1111/tpj.16535},
	abstract = {Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84\%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.},
	language = {en},
	number = {3},
	urldate = {2024-02-02},
	journal = {The Plant Journal},
	author = {Estravis Barcala, Maximiliano and van der Valk, Tom and Chen, Zhiqiang and Funda, Tomas and Chaudhary, Rajiv and Klingberg, Adam and Fundova, Irena and Suontama, Mari and Hallingbäck, Henrik and Bernhardsson, Carolina and Nystedt, Björn and Ingvarsson, Pär K. and Sherwood, Ellen and Street, Nathaniel and Gyllensten, Ulf and Nilsson, Ove and Wu, Harry X.},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.16535},
	keywords = {Pinus sylvestris, SNP array, genome resequencing, genome-wide association studies, genomic selection, pines},
	pages = {944--955},
}

Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.

@article{oikonomou_esoil_2024,
	title = {{eSoil}: {A} low-power bioelectronic growth scaffold that enhances crop seedling growth},
	volume = {121},
	shorttitle = {{eSoil}},
	url = {https://www.pnas.org/doi/10.1073/pnas.2304135120},
	doi = {10.1073/pnas.2304135120},
	abstract = {Active hydroponic substrates that stimulate on demand the plant growth have not been demonstrated so far. Here, we developed the eSoil, a low-power bioelectronic growth scaffold that can provide electrical stimulation to the plants’ root system and growth environment in hydroponics settings. eSoil’s active material is an organic mixed ionic electronic conductor while its main structural component is cellulose, the most abundant biopolymer. We demonstrate that barley seedlings that are widely used for fodder grow within the eSoil with the root system integrated within its porous matrix. Simply by polarizing the eSoil, seedling growth is accelerated resulting in increase of dry weight on average by 50\% after 15 d of growth. The effect is evident both on root and shoot development and occurs during the growth period after the stimulation. The stimulated plants reduce and assimilate NO3− more efficiently than controls, a finding that may have implications on minimizing fertilizer use. However, more studies are required to provide a mechanistic understanding of the physical and biological processes involved. eSoil opens the pathway for the development of active hydroponic scaffolds that may increase crop yield in a sustainable manner.},
	number = {2},
	urldate = {2023-12-29},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {Oikonomou, Vasileios K. and Huerta, Miriam and Sandéhn, Alexandra and Dreier, Till and Daguerre, Yohann and Lim, Hyungwoo and Berggren, Magnus and Pavlopoulou, Eleni and Näsholm, Torgny and Bech, Martin and Stavrinidou, Eleni},
	month = jan,
	year = {2024},
	pages = {e2304135120},
}

Active hydroponic substrates that stimulate on demand the plant growth have not been demonstrated so far. Here, we developed the eSoil, a low-power bioelectronic growth scaffold that can provide electrical stimulation to the plants’ root system and growth environment in hydroponics settings. eSoil’s active material is an organic mixed ionic electronic conductor while its main structural component is cellulose, the most abundant biopolymer. We demonstrate that barley seedlings that are widely used for fodder grow within the eSoil with the root system integrated within its porous matrix. Simply by polarizing the eSoil, seedling growth is accelerated resulting in increase of dry weight on average by 50% after 15 d of growth. The effect is evident both on root and shoot development and occurs during the growth period after the stimulation. The stimulated plants reduce and assimilate NO3− more efficiently than controls, a finding that may have implications on minimizing fertilizer use. However, more studies are required to provide a mechanistic understanding of the physical and biological processes involved. eSoil opens the pathway for the development of active hydroponic scaffolds that may increase crop yield in a sustainable manner.

@article{niemi_quantitative_2024,
	title = {Quantitative and qualitative saccharide analysis of {North} {Atlantic} brown seaweed by gas chromatography/mass spectrometry and infrared spectroscopy},
	volume = {254},
	issn = {0141-8130},
	url = {https://www.sciencedirect.com/science/article/pii/S0141813023047694},
	doi = {10.1016/j.ijbiomac.2023.127870},
	abstract = {Brown seaweeds contain a variety of saccharides which have potential industrial uses. The most abundant polysaccharide in brown seaweed is typically alginate, consisting of mannuronic (M) and guluronic acid (G). The ratio of these residues fundamentally determines the physicochemical properties of alginate. In the present study, gas chromatography/mass spectrometry (GC/MS) was used to give a detailed breakdown of the monosaccharide species in North Atlantic brown seaweeds. The anthrone method was used for determination of crystalline cellulose. The experimental data was used to calibrate multivariate prediction models for estimation of total carbohydrates, crystalline cellulose, total alginate and alginate M/G ratio directly in dried, brown seaweed using three types of infrared spectroscopy, using relative error (RE) as a measure of predictive accuracy. Diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) performed well for the estimation of total alginate (RE = 0.12, R2 = 0.82), and attenuated total reflectance (ATR) showed good prediction of M/G ratio (RE = 0.14, R2 = 0.86). Both DRIFTS, ATR and near infrared (NIR) were unable to predict crystalline cellulose and only DRIFTS performed better in determining total carbohydrates. Multivariate spectral analysis is a promising method for easy and rapid characterization of alginate and M/G ratio in seaweed.},
	urldate = {2023-11-17},
	journal = {International Journal of Biological Macromolecules},
	author = {Niemi, Calle and Takahashi, Junko and Gorzsás, András and Gentili, Francesco G.},
	month = jan,
	year = {2024},
	keywords = {Alginate, FTIR, GC/MS, MG ratio, North Atlantic brown seaweed},
	pages = {127870},
}

Brown seaweeds contain a variety of saccharides which have potential industrial uses. The most abundant polysaccharide in brown seaweed is typically alginate, consisting of mannuronic (M) and guluronic acid (G). The ratio of these residues fundamentally determines the physicochemical properties of alginate. In the present study, gas chromatography/mass spectrometry (GC/MS) was used to give a detailed breakdown of the monosaccharide species in North Atlantic brown seaweeds. The anthrone method was used for determination of crystalline cellulose. The experimental data was used to calibrate multivariate prediction models for estimation of total carbohydrates, crystalline cellulose, total alginate and alginate M/G ratio directly in dried, brown seaweed using three types of infrared spectroscopy, using relative error (RE) as a measure of predictive accuracy. Diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) performed well for the estimation of total alginate (RE = 0.12, R2 = 0.82), and attenuated total reflectance (ATR) showed good prediction of M/G ratio (RE = 0.14, R2 = 0.86). Both DRIFTS, ATR and near infrared (NIR) were unable to predict crystalline cellulose and only DRIFTS performed better in determining total carbohydrates. Multivariate spectral analysis is a promising method for easy and rapid characterization of alginate and M/G ratio in seaweed.

@article{jin_complex_2023,
	title = {Complex genetic architecture underlying the plasticity of maize agronomic traits},
	volume = {4},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S2590346222003108},
	doi = {10.1016/j.xplc.2022.100473},
	abstract = {Phenotypic plasticity is the ability of a given genotype to produce multiple phenotypes in response to changing environmental conditions. Understanding the genetic basis of phenotypic plasticity and establishing a predictive model is highly relevant to future agriculture under a changing climate. Here we report findings on the genetic basis of phenotypic plasticity for 23 complex traits using a diverse maize population planted at five sites with distinct environmental conditions. We found that latitude-related environmental factors were the main drivers of across-site variation in flowering time traits but not in plant architecture or yield traits. For the 23 traits, we detected 109 quantitative trait loci (QTLs), 29 for mean values, 66 for plasticity, and 14 for both parameters, and 80\% of the QTLs interacted with latitude. The effects of several QTLs changed in magnitude or sign, driving variation in phenotypic plasticity. We experimentally validated one plastic gene, ZmTPS14.1, whose effect was likely mediated by the compensation effect of ZmSPL6 from a downstream pathway. By integrating genetic diversity, environmental variation, and their interaction into a joint model, we could provide site-specific predictions with increased accuracy by as much as 9.9\%, 2.2\%, and 2.6\% for days to tassel, plant height, and ear weight, respectively. This study revealed a complex genetic architecture involving multiple alleles, pleiotropy, and genotype-by-environment interaction that underlies variation in the mean and plasticity of maize complex traits. It provides novel insights into the dynamic genetic architecture of agronomic traits in response to changing environments, paving a practical way toward precision agriculture.},
	number = {3},
	urldate = {2026-05-19},
	journal = {Plant Communications},
	author = {Jin, Minliang and Liu, Haijun and Liu, Xiangguo and Guo, Tingting and Guo, Jia and Yin, Yuejia and Ji, Yan and Li, Zhenxian and Zhang, Jinhong and Wang, Xiaqing and Qiao, Feng and Xiao, Yingjie and Zan, Yanjun and Yan, Jianbing},
	month = may,
	year = {2023},
	keywords = {QTL-by-environment interaction, complex traits, crop improvement, phenotypic plasticity},
	pages = {100473},
}

Phenotypic plasticity is the ability of a given genotype to produce multiple phenotypes in response to changing environmental conditions. Understanding the genetic basis of phenotypic plasticity and establishing a predictive model is highly relevant to future agriculture under a changing climate. Here we report findings on the genetic basis of phenotypic plasticity for 23 complex traits using a diverse maize population planted at five sites with distinct environmental conditions. We found that latitude-related environmental factors were the main drivers of across-site variation in flowering time traits but not in plant architecture or yield traits. For the 23 traits, we detected 109 quantitative trait loci (QTLs), 29 for mean values, 66 for plasticity, and 14 for both parameters, and 80% of the QTLs interacted with latitude. The effects of several QTLs changed in magnitude or sign, driving variation in phenotypic plasticity. We experimentally validated one plastic gene, ZmTPS14.1, whose effect was likely mediated by the compensation effect of ZmSPL6 from a downstream pathway. By integrating genetic diversity, environmental variation, and their interaction into a joint model, we could provide site-specific predictions with increased accuracy by as much as 9.9%, 2.2%, and 2.6% for days to tassel, plant height, and ear weight, respectively. This study revealed a complex genetic architecture involving multiple alleles, pleiotropy, and genotype-by-environment interaction that underlies variation in the mean and plasticity of maize complex traits. It provides novel insights into the dynamic genetic architecture of agronomic traits in response to changing environments, paving a practical way toward precision agriculture.

@article{kang_pan-genome_2023,
	title = {The pan-genome and local adaptation of {Arabidopsis} thaliana},
	volume = {14},
	copyright = {2023 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-42029-4},
	doi = {10.1038/s41467-023-42029-4},
	abstract = {Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution of genomic structural variations (SVs) and their associate genes to the local adaptation of this widely distribute species remains unclear. Here, we de novo assemble chromosome-level genomes of 32 A. thaliana ecotypes and determine that variable genes expand the gene pool in different ecotypes and thus assist local adaptation. We develop a graph-based pan-genome and identify 61,332 SVs that overlap with 18,883 genes, some of which are highly involved in ecological adaptation of this species. For instance, we observe a specific 332 bp insertion in the promoter region of the HPCA1 gene in the Tibet-0 ecotype that enhances gene expression, thereby promotes adaptation to alpine environments. These findings augment our understanding of the molecular mechanisms underlying the local adaptation of A. thaliana across diverse habitats.},
	language = {en},
	number = {1},
	urldate = {2026-05-19},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Kang, Minghui and Wu, Haolin and Liu, Huanhuan and Liu, Wenyu and Zhu, Mingjia and Han, Yu and Liu, Wei and Chen, Chunlin and Song, Yan and Tan, Luna and Yin, Kangqun and Zhao, Yusen and Yan, Zhen and Lou, Shangling and Zan, Yanjun and Liu, Jianquan},
	month = oct,
	year = {2023},
	keywords = {Evolutionary biology, Natural variation in plants, Plant evolution, Structural variation},
	pages = {6259},
}

Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution of genomic structural variations (SVs) and their associate genes to the local adaptation of this widely distribute species remains unclear. Here, we de novo assemble chromosome-level genomes of 32 A. thaliana ecotypes and determine that variable genes expand the gene pool in different ecotypes and thus assist local adaptation. We develop a graph-based pan-genome and identify 61,332 SVs that overlap with 18,883 genes, some of which are highly involved in ecological adaptation of this species. For instance, we observe a specific 332 bp insertion in the promoter region of the HPCA1 gene in the Tibet-0 ecotype that enhances gene expression, thereby promotes adaptation to alpine environments. These findings augment our understanding of the molecular mechanisms underlying the local adaptation of A. thaliana across diverse habitats.

@article{ronneburg_low-coverage_2023,
	title = {Low-coverage sequencing in a deep intercross of the {Virginia} body weight lines provides insight to the polygenic genetic architecture of growth: novel loci revealed by increased power and improved genome-coverage},
	volume = {102},
	issn = {0032-5791},
	shorttitle = {Low-coverage sequencing in a deep intercross of the {Virginia} body weight lines provides insight to the polygenic genetic architecture of growth},
	url = {https://www.sciencedirect.com/science/article/pii/S0032579122004990},
	doi = {10.1016/j.psj.2022.102203},
	abstract = {Genetic dissection of highly polygenic traits is a challenge, in part due to the power necessary to confidently identify loci with minor effects. Experimental crosses are valuable resources for mapping such traits. Traditionally, genome-wide analyses of experimental crosses have targeted major loci using data from a single generation (often the F2) with individuals from later generations being generated for replication and fine-mapping. Here, we aim to confidently identify minor-effect loci contributing to the highly polygenic basis of the long-term, bi-directional selection responses for 56-d body weight in the Virginia body weight chicken lines. To achieve this, a strategy was developed to make use of data from all generations (F2–F18) of the advanced intercross line, developed by crossing the low and high selected lines after 40 generations of selection. A cost-efficient low-coverage sequencing based approach was used to obtain high-confidence genotypes in 1Mb bins across 99.3\% of the chicken genome for {\textgreater}3,300 intercross individuals. In total, 12 genome-wide significant, and 30 additional suggestive QTL reaching a 10\% FDR threshold, were mapped for 56-d body weight. Only 2 of these QTL reached genome-wide significance in earlier analyses of the F2 generation. The minor-effect QTL mapped here were generally due to an overall increase in power by integrating data across generations, with contributions from increased genome-coverage and improved marker information content. The 12 significant QTL explain {\textgreater}37\% of the difference between the parental lines, three times more than 2 previously reported significant QTL. The 42 significant and suggestive QTL together explain {\textgreater}80\%. Making integrated use of all available samples from multiple generations in experimental crosses are economically feasible using the low-cost, sequencing-based genotyping strategies outlined here. Our empirical results illustrate the value of this strategy for mapping novel minor-effect loci contributing to complex traits to provide a more confident, comprehensive view of the individual loci that form the genetic basis of the highly polygenic, long-term selection responses for 56-d body weight in the Virginia body weight chicken lines.},
	number = {5},
	urldate = {2026-05-19},
	journal = {Poultry Science},
	author = {Rönneburg, T. and Zan, Y. and Honaker, C. F. and Siegel, P. B. and Carlborg, Ö.},
	month = may,
	year = {2023},
	keywords = {QTL mapping, advanced intercross line, body weight, low-coverage sequencing},
	pages = {102203},
}

Genetic dissection of highly polygenic traits is a challenge, in part due to the power necessary to confidently identify loci with minor effects. Experimental crosses are valuable resources for mapping such traits. Traditionally, genome-wide analyses of experimental crosses have targeted major loci using data from a single generation (often the F2) with individuals from later generations being generated for replication and fine-mapping. Here, we aim to confidently identify minor-effect loci contributing to the highly polygenic basis of the long-term, bi-directional selection responses for 56-d body weight in the Virginia body weight chicken lines. To achieve this, a strategy was developed to make use of data from all generations (F2–F18) of the advanced intercross line, developed by crossing the low and high selected lines after 40 generations of selection. A cost-efficient low-coverage sequencing based approach was used to obtain high-confidence genotypes in 1Mb bins across 99.3% of the chicken genome for \textgreater3,300 intercross individuals. In total, 12 genome-wide significant, and 30 additional suggestive QTL reaching a 10% FDR threshold, were mapped for 56-d body weight. Only 2 of these QTL reached genome-wide significance in earlier analyses of the F2 generation. The minor-effect QTL mapped here were generally due to an overall increase in power by integrating data across generations, with contributions from increased genome-coverage and improved marker information content. The 12 significant QTL explain \textgreater37% of the difference between the parental lines, three times more than 2 previously reported significant QTL. The 42 significant and suggestive QTL together explain \textgreater80%. Making integrated use of all available samples from multiple generations in experimental crosses are economically feasible using the low-cost, sequencing-based genotyping strategies outlined here. Our empirical results illustrate the value of this strategy for mapping novel minor-effect loci contributing to complex traits to provide a more confident, comprehensive view of the individual loci that form the genetic basis of the highly polygenic, long-term selection responses for 56-d body weight in the Virginia body weight chicken lines.

@article{li_pig_2023,
	title = {The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation},
	volume = {33},
	issn = {1088-9051, 1549-5469},
	url = {https://genome.cshlp.org/content/genome/33/10/1833},
	doi = {10.1101/gr.277638.122},
	abstract = {{\textless}p{\textgreater}Structural variations have emerged as an important driving force for genome evolution and phenotypic variation in various organisms, yet their contributions to genetic diversity and adaptation in domesticated animals remain largely unknown. Here we constructed a pangenome based on 250 sequenced individuals from 32 pig breeds in Eurasia and systematically characterized coding sequence presence/absence variations (PAVs) within pigs. We identified 308.3-Mb nonreference sequences and 3438 novel genes absent from the current reference genome. Gene PAV analysis showed that 16.8\% of the genes in the pangene catalog undergo PAV. A number of newly identified dispensable genes showed close associations with adaptation. For instance, several novel swine leukocyte antigen (SLA) genes discovered in nonreference sequences potentially participate in immune responses to productive and respiratory syndrome virus (PRRSV) infection. We delineated previously unidentified features of the pig mobilome that contained 490,480 transposable element insertion polymorphisms (TIPs) resulting from recent mobilization of 970 TE families, and investigated their population dynamics along with influences on population differentiation and gene expression. In addition, several candidate adaptive TE insertions were detected to be co-opted into genes responsible for responses to hypoxia, skeletal development, regulation of heart contraction, and neuronal cell development, likely contributing to local adaptation of Tibetan wild boars. These findings enhance our understanding on hidden layers of the genetic diversity in pigs and provide novel insights into the role of SVs in the evolutionary adaptation of mammals.{\textless}/p{\textgreater}},
	language = {en},
	number = {10},
	urldate = {2026-05-19},
	journal = {Genome Research},
	publisher = {Cold Spring Harbor Laboratory Press},
	author = {Li, Zhengcao and Liu, Xiaohong and Wang, Chen and Li, Zhenyang and Jiang, Bo and Zhang, Ruifeng and Tong, Lu and Qu, Youping and He, Sheng and Chen, Haifan and Mao, Yafei and Li, Qingnan and Pook, Torsten and Wu, Yu and Zan, Yanjun and Zhang, Hui and Li, Lu and Wen, Keying and Chen, Yaosheng},
	month = nov,
	year = {2023},
	pages = {1833--1847},
}

\textlessp\textgreaterStructural variations have emerged as an important driving force for genome evolution and phenotypic variation in various organisms, yet their contributions to genetic diversity and adaptation in domesticated animals remain largely unknown. Here we constructed a pangenome based on 250 sequenced individuals from 32 pig breeds in Eurasia and systematically characterized coding sequence presence/absence variations (PAVs) within pigs. We identified 308.3-Mb nonreference sequences and 3438 novel genes absent from the current reference genome. Gene PAV analysis showed that 16.8% of the genes in the pangene catalog undergo PAV. A number of newly identified dispensable genes showed close associations with adaptation. For instance, several novel swine leukocyte antigen (SLA) genes discovered in nonreference sequences potentially participate in immune responses to productive and respiratory syndrome virus (PRRSV) infection. We delineated previously unidentified features of the pig mobilome that contained 490,480 transposable element insertion polymorphisms (TIPs) resulting from recent mobilization of 970 TE families, and investigated their population dynamics along with influences on population differentiation and gene expression. In addition, several candidate adaptive TE insertions were detected to be co-opted into genes responsible for responses to hypoxia, skeletal development, regulation of heart contraction, and neuronal cell development, likely contributing to local adaptation of Tibetan wild boars. These findings enhance our understanding on hidden layers of the genetic diversity in pigs and provide novel insights into the role of SVs in the evolutionary adaptation of mammals.\textless/p\textgreater

@article{zan_combining_2023,
	title = {Combining a {Frailty} {Index} {Based} on {Laboratory} {Data} and {Pneumonia} {Severity} {Assessments} to {Predict} {In}-{Hospital} {Outcomes} in {Older} {Adults} with {Community}-{Acquired} {Pneumonia}},
	volume = {27},
	issn = {1279-7707},
	url = {https://www.sciencedirect.com/science/article/pii/S1279770723002920},
	doi = {10.1007/s12603-023-1905-1},
	abstract = {Objectives
Due to the increased morbidity, mortality, and cost of community-acquired pneumonia (CAP) in older people, strategies directed at improving disease evaluation and prevention are imperative. We independently compared the 30-day in-hospital mortality prediction ability of a frailty index based on laboratory data (FI-Lab) with that of the CURB-65 and the Pneumonia Severity Index (PSI) and then proposed combining them to further improve prediction efficiency.
Design
Retrospective cohort study.
Setting and Participants
Patients aged ≥ 65 years (n = 2039) with CAP who were admitted to Jiangsu Provincial People's Hospital of Nanjing Medical University and Jiangsu Provincial Hospital of Chinese Medicine from January 2019 to June 2022.
Measures
The 29-item FI-Lab, PSI and, CURB-65 were administered at admission. We defined frailty by the cut-off value of the FI-Lab score ({\textgreater} 0.43). Multivariable logistic regression analysis, together with the calculation of the area under the receiver operating characteristic curve (ROC-AUC), was conducted to identify stratified risks and relationships between the three indices and 30-day mortality. Participants were divided into the following three groups based on age: 65–74 years, 75–84 years, and ≥ 85 years. Hazard ratios (HRs) and 95\% confidence intervals (CIs) for mortality due to frailty were calculated.
Results
A total of 495 participants ranging from 65 to 100 years of age were ultimately included and divided into age groups (65–74 years, n = 190, 38.4\%; 75–84 years, n = 183, 37.0\%; ≥ 85 years, n = 122, 24.6\%). A total of 142 (28.7\%) of the 495 patients were defined as having frailty. All three scores tested in this study were significantly associated with 30-day mortality in the total sample. The ORs were as follows: 1.06 (95\% CI: 1.03–1.09, P {\textless} 0.001) and 2.33 (95\% CI: 1.26–4.31, P = 0.007) for the FI-Lab when the score was treated as a continuous and categorical variable, respectively; 1.04 (95\% CI: 1.02–1.05, P {\textless} 0.001) for the PSI; and 3.70 (95\% CI: 2.48–5.50, P {\textless} 0.001) for the CURB-65. In the total sample, the ROC-AUCs were 0.783 (95\% CI: 0.744–0.819) for the FI-Lab, 0.812 (95\% CI: 0.775–0.845) for the PSI, and 0.799 (95\% CI: 0.761–0.834) for the CURB-65 (P {\textless} 0.001). The ROC-AUC slightly improved when the FI-Lab was added to the PSI (AUC 0.850, 95\% CI: 0.809–0.892, P = 0.031) and to the CURB-65 (AUC 0.839, 95\% CI: 0.794–0.885, P = 0.002). Older patients with frailty showed a higher risk of in-hospital mortality, with an HR of 2.25 (95\% CI: 1.14–3.58, P {\textless} 0.001).
Conclusion and Implications
The FI-Lab seems to generate simple and readily available data, suggesting that it could be a useful complement to the CURB-65 and the PSI as effective predictors of 30-day mortality due to CAP in older populations.},
	number = {4},
	urldate = {2026-05-19},
	journal = {The Journal of nutrition, health and aging},
	author = {Zan, Y. M. and Zheng, T. P. and Wang, Y. and Shao, J. F. and Wang, Z. Y. and Zhao, W. H. and Wu, J. Q. and Xu, Wei},
	month = apr,
	year = {2023},
	keywords = {30-day mortality, CURB-65, Community-acquired pneumonia, Frailty index, Pneumonia Severity Index},
	pages = {270--276},
}

Objectives Due to the increased morbidity, mortality, and cost of community-acquired pneumonia (CAP) in older people, strategies directed at improving disease evaluation and prevention are imperative. We independently compared the 30-day in-hospital mortality prediction ability of a frailty index based on laboratory data (FI-Lab) with that of the CURB-65 and the Pneumonia Severity Index (PSI) and then proposed combining them to further improve prediction efficiency. Design Retrospective cohort study. Setting and Participants Patients aged ≥ 65 years (n = 2039) with CAP who were admitted to Jiangsu Provincial People's Hospital of Nanjing Medical University and Jiangsu Provincial Hospital of Chinese Medicine from January 2019 to June 2022. Measures The 29-item FI-Lab, PSI and, CURB-65 were administered at admission. We defined frailty by the cut-off value of the FI-Lab score (\textgreater 0.43). Multivariable logistic regression analysis, together with the calculation of the area under the receiver operating characteristic curve (ROC-AUC), was conducted to identify stratified risks and relationships between the three indices and 30-day mortality. Participants were divided into the following three groups based on age: 65–74 years, 75–84 years, and ≥ 85 years. Hazard ratios (HRs) and 95% confidence intervals (CIs) for mortality due to frailty were calculated. Results A total of 495 participants ranging from 65 to 100 years of age were ultimately included and divided into age groups (65–74 years, n = 190, 38.4%; 75–84 years, n = 183, 37.0%; ≥ 85 years, n = 122, 24.6%). A total of 142 (28.7%) of the 495 patients were defined as having frailty. All three scores tested in this study were significantly associated with 30-day mortality in the total sample. The ORs were as follows: 1.06 (95% CI: 1.03–1.09, P \textless 0.001) and 2.33 (95% CI: 1.26–4.31, P = 0.007) for the FI-Lab when the score was treated as a continuous and categorical variable, respectively; 1.04 (95% CI: 1.02–1.05, P \textless 0.001) for the PSI; and 3.70 (95% CI: 2.48–5.50, P \textless 0.001) for the CURB-65. In the total sample, the ROC-AUCs were 0.783 (95% CI: 0.744–0.819) for the FI-Lab, 0.812 (95% CI: 0.775–0.845) for the PSI, and 0.799 (95% CI: 0.761–0.834) for the CURB-65 (P \textless 0.001). The ROC-AUC slightly improved when the FI-Lab was added to the PSI (AUC 0.850, 95% CI: 0.809–0.892, P = 0.031) and to the CURB-65 (AUC 0.839, 95% CI: 0.794–0.885, P = 0.002). Older patients with frailty showed a higher risk of in-hospital mortality, with an HR of 2.25 (95% CI: 1.14–3.58, P \textless 0.001). Conclusion and Implications The FI-Lab seems to generate simple and readily available data, suggesting that it could be a useful complement to the CURB-65 and the PSI as effective predictors of 30-day mortality due to CAP in older populations.

@article{frew_soil_2023,
	title = {Soil abounds with life–and supports all life above it. {But} {Australian} soils need urgent repair},
	journal = {Conversation},
	author = {Frew, Adam and Birnbaum, Christina and Egidi, Eleonora and Heuck, Meike Katharina},
	month = jan,
	year = {2023},
}

@article{heuck_friends_2023,
	title = {Friends to the rescue: using arbuscular mycorrhizal fungi to future-proof {Australian} agriculture},
	volume = {44},
	issn = {1324-4272},
	shorttitle = {Friends to the rescue},
	url = {https://doi.org/10.1071/MA23002},
	doi = {10.1071/MA23002},
	abstract = {With a rising global population and the challenges of climate change, there is an increasing need to find solutions to maintain crop yields in an ecologically sustainable way. Although many studies have focussed on this issue, comparatively few are conducted in the southern hemisphere. This is worrisome because the geographical and geomorphological conditions within Australia differ greatly from the northern hemisphere. To ensure food security, approaches can rely on conventional agricultural methods as well as commercial arbuscular mycorrhizal (AM) fungal inoculants. Both approaches lack the capacity to be successful in the long term or could have unknown negative effects on the naturally occurring microbial communities. We advocate for a sustainable and holistic approach that combines the effective management of functionally diverse AM fungal communities with precision farming techniques while integrating landscape elements into agricultural fields. In addition, landowners and scientists should collaborate and communicate their work with industry and government to take forward the shift to a more-sustainable agriculture. In this way, we will be better able to secure our food production while restoring our soil ecosystems.},
	number = {1},
	urldate = {2026-03-17},
	journal = {Microbiology Australia},
	author = {Heuck, Meike Katharina and Birnbaum, Christina and Frew, Adam},
	month = mar,
	year = {2023},
	pages = {5--8},
}

With a rising global population and the challenges of climate change, there is an increasing need to find solutions to maintain crop yields in an ecologically sustainable way. Although many studies have focussed on this issue, comparatively few are conducted in the southern hemisphere. This is worrisome because the geographical and geomorphological conditions within Australia differ greatly from the northern hemisphere. To ensure food security, approaches can rely on conventional agricultural methods as well as commercial arbuscular mycorrhizal (AM) fungal inoculants. Both approaches lack the capacity to be successful in the long term or could have unknown negative effects on the naturally occurring microbial communities. We advocate for a sustainable and holistic approach that combines the effective management of functionally diverse AM fungal communities with precision farming techniques while integrating landscape elements into agricultural fields. In addition, landowners and scientists should collaborate and communicate their work with industry and government to take forward the shift to a more-sustainable agriculture. In this way, we will be better able to secure our food production while restoring our soil ecosystems.

@article{ng_belowground_2023,
	title = {Belowground crop responses to root herbivory are associated with the community structure of native arbuscular mycorrhizal fungi},
	volume = {185},
	issn = {0929-1393},
	url = {https://www.sciencedirect.com/science/article/pii/S0929139322004139},
	doi = {10.1016/j.apsoil.2022.104797},
	abstract = {There is growing interest in managing arbuscular mycorrhizal (AM) fungi in agriculture to support plant production. These fungi can support crop growth and nutrient uptake, but also affect plant-herbivore interactions. While our understanding of how AM fungi affect plant responses to herbivory advances, it is less clear how different naturally-occurring (native) fungal communities differentially influence crop responses to root-feeding insects. To explore this, plants (Sorghum bicolor) were grown in a glasshouse experiment without AM fungi (‘no AM fungi’) or with one of three natural soil inocula sourced either from a sclerophyll forest (‘forest inoculum’), a cropped field (‘field inoculum’), or a field in fallow (‘fallow inoculum’), while half the plants were subjected to a root herbivore (Dermolepida albohirtum). We assessed the effects of soil inoculum and root herbivory on root-colonising AM fungal diversity, plant growth, and nutrient content. Root herbivory did not affect AM fungal diversity or composition. Plants grown with the field or fallow inocula were both dominated by the genera Glomus and Claroideoglomus. These plants exhibited reduced biomass in response to inoculation, but were not impacted by root herbivory. In contrast, plants with the forest inoculum had AM fungal communities dominated by Paraglomus and Ambispora. When subjected to root herbivory, the forest inoculated plants and plants without AM fungi exhibited reductions of 44 \% and 61 \% in root biomass, and reductions of 65 \% and 59 \% in root phosphorus, respectively. Our study shows inoculation-driven plant responses to root herbivory that were associated with the community structure of their root-colonising AM fungi. Results suggest associations with communities dominated by Claroideoglomus and Glomus may mitigate the impacts of a root-feeding insect. More exploration of how natural assemblages of AM fungi mediate plant-herbivore interactions is needed if we are to effectively manage soil fungi in agriculture.},
	urldate = {2026-03-17},
	journal = {Applied Soil Ecology},
	author = {Ng, Anna and Wilson, Bree A. L. and Frew, Adam},
	month = may,
	year = {2023},
	keywords = {Arbuscular mycorrhizal fungi, Dermolepida albohirtum, Plant defence, Root herbivory},
	pages = {104797},
}

There is growing interest in managing arbuscular mycorrhizal (AM) fungi in agriculture to support plant production. These fungi can support crop growth and nutrient uptake, but also affect plant-herbivore interactions. While our understanding of how AM fungi affect plant responses to herbivory advances, it is less clear how different naturally-occurring (native) fungal communities differentially influence crop responses to root-feeding insects. To explore this, plants (Sorghum bicolor) were grown in a glasshouse experiment without AM fungi (‘no AM fungi’) or with one of three natural soil inocula sourced either from a sclerophyll forest (‘forest inoculum’), a cropped field (‘field inoculum’), or a field in fallow (‘fallow inoculum’), while half the plants were subjected to a root herbivore (Dermolepida albohirtum). We assessed the effects of soil inoculum and root herbivory on root-colonising AM fungal diversity, plant growth, and nutrient content. Root herbivory did not affect AM fungal diversity or composition. Plants grown with the field or fallow inocula were both dominated by the genera Glomus and Claroideoglomus. These plants exhibited reduced biomass in response to inoculation, but were not impacted by root herbivory. In contrast, plants with the forest inoculum had AM fungal communities dominated by Paraglomus and Ambispora. When subjected to root herbivory, the forest inoculated plants and plants without AM fungi exhibited reductions of 44 % and 61 % in root biomass, and reductions of 65 % and 59 % in root phosphorus, respectively. Our study shows inoculation-driven plant responses to root herbivory that were associated with the community structure of their root-colonising AM fungi. Results suggest associations with communities dominated by Claroideoglomus and Glomus may mitigate the impacts of a root-feeding insect. More exploration of how natural assemblages of AM fungi mediate plant-herbivore interactions is needed if we are to effectively manage soil fungi in agriculture.

@article{frew_host_2023,
	title = {Host filtering, not competitive exclusion, may be the main driver of arbuscular mycorrhizal fungal community assembly under high phosphorus},
	volume = {37},
	copyright = {© 2023 The Authors. Functional Ecology published by John Wiley \& Sons Ltd on behalf of British Ecological Society.},
	issn = {1365-2435},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2435.14349},
	doi = {10.1111/1365-2435.14349},
	abstract = {A major goal in ecology is understanding the factors which determine the diversity and distribution of organisms. The outcome of the symbiotic relationship between plants and arbuscular mycorrhizal (AM) fungi is strongly influenced by soil phosphorus (P) availability. Despite this knowledge, there is still much to uncover about how soil P status can shape the taxonomic and phylogenetic assembly of root-colonising AM fungi. Additionally, there is a paucity of understanding about the implications of these changes for the outcome of the AM symbiosis in terms of plant growth, nutrient status and defence traits. We conducted a factorial pot experiment where sorghum (Sorghum bicolor) was grown under three different P treatments (low, medium and high), in the presence or absence of a natural AM fungal community. By analysing the diversity and community structure of the fungal community colonising roots, we aimed to determine if and how soil P influences the relatedness of these communities and whether competitive exclusion or environmental filtering play a more significant role in their assembly. Additionally, we evaluated the concomitant outcomes for plant growth, nutrient acquisition and defensive chemistry (phenolics). Increasing P availability reduced AM fungal richness and increased community evenness. Root-colonising AM fungal communities under the high P treatment had significantly reduced phylogenetic diversity and comparatively lower mean pairwise distances among all treatments. This indicated that AM fungal communities became more closely related (phylogenetically clustered) with increasing soil P. The mycorrhizal growth and mycorrhizal P responses of plants were positive under low and medium P, but this was lost under high P, however, plant phenolics were increased. Our results suggest that under high P conditions, environmental filtering plays an important role in AM fungal community assembly as host plants alter their selectivity of fungal functional groups prioritising those associated with enhancing plant stress resistance and defences, rather than nutrient acquisition. Here we demonstrated how soil P status can shape taxonomic and phylogenetic assembly of AM fungi and the associated functional outcomes for the host. Read the free Plain Language Summary for this article on the Journal blog.},
	language = {en},
	number = {7},
	urldate = {2026-03-17},
	journal = {Functional Ecology},
	author = {Frew, Adam and Heuck, Meike Katharina and Aguilar-Trigueros, Carlos A.},
	year = {2023},
	note = {\_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2435.14349},
	keywords = {arbuscular mycorrhizal fungi, community assembly, phylogenetic diversity, plant defence, plant phosphorus},
	pages = {1856--1869},
}

A major goal in ecology is understanding the factors which determine the diversity and distribution of organisms. The outcome of the symbiotic relationship between plants and arbuscular mycorrhizal (AM) fungi is strongly influenced by soil phosphorus (P) availability. Despite this knowledge, there is still much to uncover about how soil P status can shape the taxonomic and phylogenetic assembly of root-colonising AM fungi. Additionally, there is a paucity of understanding about the implications of these changes for the outcome of the AM symbiosis in terms of plant growth, nutrient status and defence traits. We conducted a factorial pot experiment where sorghum (Sorghum bicolor) was grown under three different P treatments (low, medium and high), in the presence or absence of a natural AM fungal community. By analysing the diversity and community structure of the fungal community colonising roots, we aimed to determine if and how soil P influences the relatedness of these communities and whether competitive exclusion or environmental filtering play a more significant role in their assembly. Additionally, we evaluated the concomitant outcomes for plant growth, nutrient acquisition and defensive chemistry (phenolics). Increasing P availability reduced AM fungal richness and increased community evenness. Root-colonising AM fungal communities under the high P treatment had significantly reduced phylogenetic diversity and comparatively lower mean pairwise distances among all treatments. This indicated that AM fungal communities became more closely related (phylogenetically clustered) with increasing soil P. The mycorrhizal growth and mycorrhizal P responses of plants were positive under low and medium P, but this was lost under high P, however, plant phenolics were increased. Our results suggest that under high P conditions, environmental filtering plays an important role in AM fungal community assembly as host plants alter their selectivity of fungal functional groups prioritising those associated with enhancing plant stress resistance and defences, rather than nutrient acquisition. Here we demonstrated how soil P status can shape taxonomic and phylogenetic assembly of AM fungi and the associated functional outcomes for the host. Read the free Plain Language Summary for this article on the Journal blog.

@article{frew_water_2023,
	title = {Water availability alters the community structure of arbuscular mycorrhizal fungi and determines plant mycorrhizal benefit},
	volume = {5},
	copyright = {© 2023 The Authors. Plants, People, Planet published by John Wiley \& Sons Ltd on behalf of New Phytologist Foundation.},
	issn = {2572-2611},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ppp3.10372},
	doi = {10.1002/ppp3.10372},
	abstract = {Societal Impact Statement The world faces major changes in rainfall patterns and water availability, posing a significant threat to plant productions systems and food security. The arbuscular mycorrhizal (AM) fungi associate with most major crops and can support plant nutrient and water uptake. Here, AM fungi were shown to mitigate the negative effects of low water availability on sorghum growth and phosphorus uptake, an effect that was associated with shifts in the fungal community structure. To realise the potential of AM fungi in sustainable agriculture requires more examination of their interactions with edaphic stresses in crop systems.},
	language = {en},
	number = {5},
	urldate = {2026-03-17},
	journal = {PLANTS, PEOPLE, PLANET},
	author = {Frew, Adam},
	year = {2023},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1002/ppp3.10372},
	keywords = {arbuscular mycorrhiza, community structure, fungal community, sorghum, sustainable agriculture, water availability},
	pages = {683--689},
}

Societal Impact Statement The world faces major changes in rainfall patterns and water availability, posing a significant threat to plant productions systems and food security. The arbuscular mycorrhizal (AM) fungi associate with most major crops and can support plant nutrient and water uptake. Here, AM fungi were shown to mitigate the negative effects of low water availability on sorghum growth and phosphorus uptake, an effect that was associated with shifts in the fungal community structure. To realise the potential of AM fungi in sustainable agriculture requires more examination of their interactions with edaphic stresses in crop systems.

@article{greenwood_fire_2023,
	title = {Fire shapes fungal guild diversity and composition through direct and indirect pathways},
	volume = {32},
	copyright = {© 2023 The Authors. Molecular Ecology published by John Wiley \& Sons Ltd.},
	issn = {1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.17068},
	doi = {10.1111/mec.17068},
	abstract = {Fire has shaped global ecosystems for millennia by directly killing organisms and indirectly altering habitats and resources. All terrestrial ecosystems, including fire-prone ecosystems, rely on soil-inhabiting fungi, where they play vital roles in ecological processes. Yet our understanding of how fire regimes influence soil fungi remains limited and our knowledge of these interactions in semiarid landscapes is virtually absent. We collected soil samples and vegetation measurements from sites across a gradient in time-since-fire ages (0–75 years-since-fire) and fire frequency (burnt 0–5 times during the recent 29-year period) in a semiarid heathland of south-eastern Australia. We characterized fungal communities using ITS amplicon-sequencing and assigned fungi taxonomically to trophic guilds. We used structural equation models to examine direct, indirect and total effects of time-since-fire and fire frequency on total fungal, ectomycorrhizal, saprotrophic and pathogenic richness. We used multivariate analyses to investigate how total fungal, ectomycorrhizal, saprotrophic and pathogenic species composition differed between post-fire successional stages and fire frequency classes. Time-since-fire was an important driver of saprotrophic richness; directly, saprotrophic richness increased with time-since-fire, and indirectly, saprotrophic richness declined with time-since-fire (resulting in a positive total effect), mediated through the impact of fire on substrates. Frequently burnt sites had lower numbers of saprotrophic and pathogenic species. Post-fire successional stages and fire frequency classes were characterized by distinct fungal communities, with large differences in ectomycorrhizal species composition. Understanding the complex responses of fungal communities to fire can be improved by exploring how the effects of fire flow through ecosystems. Diverse fire histories may be important for maintaining the functional diversity of fungi in semiarid regions.},
	language = {en},
	number = {17},
	urldate = {2026-03-17},
	journal = {Molecular Ecology},
	author = {Greenwood, Leanne and Nimmo, Dale G. and Egidi, Eleonora and Price, Jodi N. and McIntosh, Rachel and Frew, Adam},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.17068},
	keywords = {fire frequency, fungal composition, fungal ecology, fungal guilds, fungal richness, time-since-fire},
	pages = {4921--4939},
}

Fire has shaped global ecosystems for millennia by directly killing organisms and indirectly altering habitats and resources. All terrestrial ecosystems, including fire-prone ecosystems, rely on soil-inhabiting fungi, where they play vital roles in ecological processes. Yet our understanding of how fire regimes influence soil fungi remains limited and our knowledge of these interactions in semiarid landscapes is virtually absent. We collected soil samples and vegetation measurements from sites across a gradient in time-since-fire ages (0–75 years-since-fire) and fire frequency (burnt 0–5 times during the recent 29-year period) in a semiarid heathland of south-eastern Australia. We characterized fungal communities using ITS amplicon-sequencing and assigned fungi taxonomically to trophic guilds. We used structural equation models to examine direct, indirect and total effects of time-since-fire and fire frequency on total fungal, ectomycorrhizal, saprotrophic and pathogenic richness. We used multivariate analyses to investigate how total fungal, ectomycorrhizal, saprotrophic and pathogenic species composition differed between post-fire successional stages and fire frequency classes. Time-since-fire was an important driver of saprotrophic richness; directly, saprotrophic richness increased with time-since-fire, and indirectly, saprotrophic richness declined with time-since-fire (resulting in a positive total effect), mediated through the impact of fire on substrates. Frequently burnt sites had lower numbers of saprotrophic and pathogenic species. Post-fire successional stages and fire frequency classes were characterized by distinct fungal communities, with large differences in ectomycorrhizal species composition. Understanding the complex responses of fungal communities to fire can be improved by exploring how the effects of fire flow through ecosystems. Diverse fire histories may be important for maintaining the functional diversity of fungi in semiarid regions.

@article{frew_australia_2023,
	title = {Australia offers unique insight into the ecology of arbuscular mycorrhizal fungi: {An} opportunity not to be lost},
	volume = {48},
	copyright = {© 2023 The Authors. Austral Ecology published by John Wiley \& Sons Australia, Ltd on behalf of Ecological Society of Australia.},
	issn = {1442-9993},
	shorttitle = {Australia offers unique insight into the ecology of arbuscular mycorrhizal fungi},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/aec.13451},
	doi = {10.1111/aec.13451},
	abstract = {Typified by ancient soils and unique assemblages of flora, Australia provides opportunities to expand our understanding of arbuscular mycorrhizal (AM) fungi. Despite their ubiquity, key aspects of Australian AM fungal ecology remain buried due to our limited knowledge of their biogeography and their potential adaptation to Australia's environmental conditions. This knowledge gap is particularly extraordinary given that the characteristics of the Australian environment are likely to provide unique insights into AM fungal ecology and evolution. Extensive exploration of the diversity and distribution of AM fungi across the continent is overdue. In pursuit of this goal, ecologists should employ the most effective and pragmatic molecular approaches, while making use of well-curated databases. We urge researchers to examine the biogeography of Australian AM fungi meaningfully, leveraging the distinctive attributes of Australian landscapes, such as the demographics of plant mycorrhizal types and the characteristic interplay with fire. Documenting AM fungal communities across Australia will not only provide unique insights into their ecology but is also pivotal to being able to incorporate these organisms into land management for conservation, restoration and sustainable agriculture.},
	language = {en},
	number = {8},
	urldate = {2026-03-17},
	journal = {Austral Ecology},
	author = {Frew, Adam and Aguilar-Trigueros, Carlos A.},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/aec.13451},
	keywords = {Australia, SSU, arbuscular mycorrhizal fungi, dual mycorrhizal, fire ecology, fungal ecology, metabarcoding},
	pages = {1713--1720},
}

Typified by ancient soils and unique assemblages of flora, Australia provides opportunities to expand our understanding of arbuscular mycorrhizal (AM) fungi. Despite their ubiquity, key aspects of Australian AM fungal ecology remain buried due to our limited knowledge of their biogeography and their potential adaptation to Australia's environmental conditions. This knowledge gap is particularly extraordinary given that the characteristics of the Australian environment are likely to provide unique insights into AM fungal ecology and evolution. Extensive exploration of the diversity and distribution of AM fungi across the continent is overdue. In pursuit of this goal, ecologists should employ the most effective and pragmatic molecular approaches, while making use of well-curated databases. We urge researchers to examine the biogeography of Australian AM fungi meaningfully, leveraging the distinctive attributes of Australian landscapes, such as the demographics of plant mycorrhizal types and the characteristic interplay with fire. Documenting AM fungal communities across Australia will not only provide unique insights into their ecology but is also pivotal to being able to incorporate these organisms into land management for conservation, restoration and sustainable agriculture.

@article{blaschek_different_2023,
	title = {Different combinations of laccase paralogs nonredundantly control the amount and composition of lignin in specific cell types and cell wall layers in {Arabidopsis}},
	volume = {35},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koac344},
	doi = {10.1093/plcell/koac344},
	abstract = {Vascular plants reinforce the cell walls of the different xylem cell types with lignin phenolic polymers. Distinct lignin chemistries differ between each cell wall layer and each cell type to support their specific functions. Yet the mechanisms controlling the tight spatial localization of specific lignin chemistries remain unclear. Current hypotheses focus on control by monomer biosynthesis and/or export, while cell wall polymerization is viewed as random and nonlimiting. Here, we show that combinations of multiple individual laccases (LACs) are nonredundantly and specifically required to set the lignin chemistry in different cell types and their distinct cell wall layers. We dissected the roles of Arabidopsis thaliana LAC4, 5, 10, 12, and 17 by generating quadruple and quintuple loss-of-function mutants. Loss of these LACs in different combinations led to specific changes in lignin chemistry affecting both residue ring structures and/or aliphatic tails in specific cell types and cell wall layers. Moreover, we showed that LAC-mediated lignification has distinct functions in specific cell types, waterproofing fibers, and strengthening vessels. Altogether, we propose that the spatial control of lignin chemistry depends on different combinations of LACs with nonredundant activities immobilized in specific cell types and cell wall layers.},
	number = {2},
	urldate = {2026-01-30},
	journal = {The Plant Cell},
	author = {Blaschek, Leonard and Murozuka, Emiko and Serk, Henrik and Ménard, Delphine and Pesquet, Edouard},
	month = feb,
	year = {2023},
	pages = {889--909},
}

Vascular plants reinforce the cell walls of the different xylem cell types with lignin phenolic polymers. Distinct lignin chemistries differ between each cell wall layer and each cell type to support their specific functions. Yet the mechanisms controlling the tight spatial localization of specific lignin chemistries remain unclear. Current hypotheses focus on control by monomer biosynthesis and/or export, while cell wall polymerization is viewed as random and nonlimiting. Here, we show that combinations of multiple individual laccases (LACs) are nonredundantly and specifically required to set the lignin chemistry in different cell types and their distinct cell wall layers. We dissected the roles of Arabidopsis thaliana LAC4, 5, 10, 12, and 17 by generating quadruple and quintuple loss-of-function mutants. Loss of these LACs in different combinations led to specific changes in lignin chemistry affecting both residue ring structures and/or aliphatic tails in specific cell types and cell wall layers. Moreover, we showed that LAC-mediated lignification has distinct functions in specific cell types, waterproofing fibers, and strengthening vessels. Altogether, we propose that the spatial control of lignin chemistry depends on different combinations of LACs with nonredundant activities immobilized in specific cell types and cell wall layers.

@article{pedersen_cellulose_2023,
	series = {“{Celebrating} 15 {Years} of {Publication}” {Special} {Issue}},
	title = {Cellulose synthesis in land plants},
	volume = {16},
	issn = {1674-2052},
	url = {https://www.sciencedirect.com/science/article/pii/S1674205222004506},
	doi = {10.1016/j.molp.2022.12.015},
	abstract = {All plant cells are surrounded by a cell wall that provides cohesion, protection, and a means of directional growth to plants. Cellulose microfibrils contribute the main biomechanical scaffold for most of these walls. The biosynthesis of cellulose, which typically is the most prominent constituent of the cell wall and therefore Earth’s most abundant biopolymer, is finely attuned to developmental and environmental cues. Our understanding of the machinery that catalyzes and regulates cellulose biosynthesis has substantially improved due to recent technological advances in, for example, structural biology and microscopy. Here, we provide a comprehensive overview of the structure, function, and regulation of the cellulose synthesis machinery and its regulatory interactors. We aim to highlight important knowledge gaps in the field, and outline emerging approaches that promise a means to close those gaps.},
	number = {1},
	urldate = {2026-01-30},
	journal = {Molecular Plant},
	author = {Pedersen, Gustav B. and Blaschek, Leonard and Frandsen, Kristian E. H. and Noack, Lise C. and Persson, Staffan},
	month = jan,
	year = {2023},
	keywords = {cellulose microfibrils, cellulose synthases, cytoskeleton, membrane proteins, plant cell wall, protein interaction},
	pages = {206--231},
}

All plant cells are surrounded by a cell wall that provides cohesion, protection, and a means of directional growth to plants. Cellulose microfibrils contribute the main biomechanical scaffold for most of these walls. The biosynthesis of cellulose, which typically is the most prominent constituent of the cell wall and therefore Earth’s most abundant biopolymer, is finely attuned to developmental and environmental cues. Our understanding of the machinery that catalyzes and regulates cellulose biosynthesis has substantially improved due to recent technological advances in, for example, structural biology and microscopy. Here, we provide a comprehensive overview of the structure, function, and regulation of the cellulose synthesis machinery and its regulatory interactors. We aim to highlight important knowledge gaps in the field, and outline emerging approaches that promise a means to close those gaps.

@article{mcevoy_chromosome-level_2023,
	title = {Chromosome-level reference genome of stinkwort, {Dittrichia} graveolens ({L}.) {Greuter}: {A} resource for studies on invasion, range expansion, and evolutionary adaptation under global change},
	volume = {114},
	issn = {1465-7333},
	shorttitle = {Chromosome-level reference genome of stinkwort, {Dittrichia} graveolens ({L}.) {Greuter}},
	url = {https://doi.org/10.1093/jhered/esad033},
	doi = {10.1093/jhered/esad033},
	abstract = {Dittrichia graveolens (L.) Greuter, or stinkwort, is a weedy annual plant within the family Asteraceae. The species is recognized for the rapid expansion of both its native and introduced ranges: in Europe, it has expanded its native distribution northward from the Mediterranean basin by nearly 7 °C latitude since the mid-20th century, while in California and Australia the plant is an invasive weed of concern. Here, we present the first de novo D. graveolens genome assembly (1N = 9 chromosomes), including complete chloroplast (151,013 bp) and partial mitochondrial genomes (22,084 bp), created using Pacific Biosciences HiFi reads and Dovetail Omni-C data. The final primary assembly is 835 Mbp in length, of which 98.1\% are represented by 9 scaffolds ranging from 66 to 119 Mbp. The contig N50 is 74.9 Mbp and the scaffold N50 is 96.9 Mbp, which, together with a 98.8\% completeness based on the BUSCO embryophyta10 database containing 1,614 orthologs, underscores the high quality of this assembly. This pseudo-molecule-scale genome assembly is a valuable resource for our fundamental understanding of the genomic consequences of range expansion under global change, as well as comparative genomic studies in the Asteraceae.},
	number = {5},
	urldate = {2026-01-16},
	journal = {Journal of Heredity},
	author = {McEvoy, Susan L and Lustenhouwer, Nicky and Melen, Miranda K and Nguyen, Oanh and Marimuthu, Mohan P A and Chumchim, Noravit and Beraut, Eric and Parker, Ingrid M and Meyer, Rachel S},
	month = sep,
	year = {2023},
	pages = {561--569},
}

Dittrichia graveolens (L.) Greuter, or stinkwort, is a weedy annual plant within the family Asteraceae. The species is recognized for the rapid expansion of both its native and introduced ranges: in Europe, it has expanded its native distribution northward from the Mediterranean basin by nearly 7 °C latitude since the mid-20th century, while in California and Australia the plant is an invasive weed of concern. Here, we present the first de novo D. graveolens genome assembly (1N = 9 chromosomes), including complete chloroplast (151,013 bp) and partial mitochondrial genomes (22,084 bp), created using Pacific Biosciences HiFi reads and Dovetail Omni-C data. The final primary assembly is 835 Mbp in length, of which 98.1% are represented by 9 scaffolds ranging from 66 to 119 Mbp. The contig N50 is 74.9 Mbp and the scaffold N50 is 96.9 Mbp, which, together with a 98.8% completeness based on the BUSCO embryophyta10 database containing 1,614 orthologs, underscores the high quality of this assembly. This pseudo-molecule-scale genome assembly is a valuable resource for our fundamental understanding of the genomic consequences of range expansion under global change, as well as comparative genomic studies in the Asteraceae.

@article{vuruputoor_welcome_2023,
	title = {Welcome to the big leaves: {Best} practices for improving genome annotation in non-model plant genomes},
	volume = {11},
	copyright = {© 2023 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.},
	issn = {2168-0450},
	shorttitle = {Welcome to the big leaves},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aps3.11533},
	doi = {10.1002/aps3.11533},
	abstract = {Premise Robust standards to evaluate quality and completeness are lacking in eukaryotic structural genome annotation, as genome annotation software is developed using model organisms and typically lacks benchmarking to comprehensively evaluate the quality and accuracy of the final predictions. The annotation of plant genomes is particularly challenging due to their large sizes, abundant transposable elements, and variable ploidies. This study investigates the impact of genome quality, complexity, sequence read input, and method on protein-coding gene predictions. Methods The impact of repeat masking, long-read and short-read inputs, and de novo and genome-guided protein evidence was examined in the context of the popular BRAKER and MAKER workflows for five plant genomes. The annotations were benchmarked for structural traits and sequence similarity. Results Benchmarks that reflect gene structures, reciprocal similarity search alignments, and mono-exonic/multi-exonic gene counts provide a more complete view of annotation accuracy. Transcripts derived from RNA-read alignments alone are not sufficient for genome annotation. Gene prediction workflows that combine evidence-based and ab initio approaches are recommended, and a combination of short and long reads can improve genome annotation. Adding protein evidence from de novo assemblies, genome-guided transcriptome assemblies, or full-length proteins from OrthoDB generates more putative false positives as implemented in the current workflows. Post-processing with functional and structural filters is highly recommended. Discussion While the annotation of non-model plant genomes remains complex, this study provides recommendations for inputs and methodological approaches. We discuss a set of best practices to generate an optimal plant genome annotation and present a more robust set of metrics to evaluate the resulting predictions.},
	language = {en},
	number = {4},
	urldate = {2026-01-16},
	journal = {Applications in Plant Sciences},
	author = {Vuruputoor, Vidya S. and Monyak, Daniel and Fetter, Karl C. and Webster, Cynthia and Bhattarai, Akriti and Shrestha, Bikash and Zaman, Sumaira and Bennett, Jeremy and McEvoy, Susan L. and Caballero, Madison and Wegrzyn, Jill L.},
	year = {2023},
	note = {\_eprint: https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.1002/aps3.11533},
	keywords = {BRAKER, MAKER, StringTie2, TSEBRA, gene identification, genome annotation, plant genomes},
	pages = {e11533},
}

Premise Robust standards to evaluate quality and completeness are lacking in eukaryotic structural genome annotation, as genome annotation software is developed using model organisms and typically lacks benchmarking to comprehensively evaluate the quality and accuracy of the final predictions. The annotation of plant genomes is particularly challenging due to their large sizes, abundant transposable elements, and variable ploidies. This study investigates the impact of genome quality, complexity, sequence read input, and method on protein-coding gene predictions. Methods The impact of repeat masking, long-read and short-read inputs, and de novo and genome-guided protein evidence was examined in the context of the popular BRAKER and MAKER workflows for five plant genomes. The annotations were benchmarked for structural traits and sequence similarity. Results Benchmarks that reflect gene structures, reciprocal similarity search alignments, and mono-exonic/multi-exonic gene counts provide a more complete view of annotation accuracy. Transcripts derived from RNA-read alignments alone are not sufficient for genome annotation. Gene prediction workflows that combine evidence-based and ab initio approaches are recommended, and a combination of short and long reads can improve genome annotation. Adding protein evidence from de novo assemblies, genome-guided transcriptome assemblies, or full-length proteins from OrthoDB generates more putative false positives as implemented in the current workflows. Post-processing with functional and structural filters is highly recommended. Discussion While the annotation of non-model plant genomes remains complex, this study provides recommendations for inputs and methodological approaches. We discuss a set of best practices to generate an optimal plant genome annotation and present a more robust set of metrics to evaluate the resulting predictions.

@article{bhowmick_structural_2023,
	title = {Structural evidence for intermediates during {O2} formation in photosystem {II}},
	volume = {617},
	copyright = {2023 The Author(s)},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/s41586-023-06038-z},
	doi = {10.1038/s41586-023-06038-z},
	abstract = {In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn4CaO5 cluster first stores four oxidizing equivalents, the S0 to S4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O–O bond formation chemistry1–3. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok’s photosynthetic water oxidation cycle, the S3→[S4]→S0 transition where O2 is formed and Kok’s water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn4CaO5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom Ox, which was introduced as a bridging ligand between Ca and Mn1 during the S2→S3 transition4–6, disappears or relocates in parallel with Yz reduction starting at approximately 700 μs after the third flash. The onset of O2 evolution, as indicated by the shortening of the Mn1–Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.},
	language = {en},
	number = {7961},
	urldate = {2024-10-16},
	journal = {Nature},
	publisher = {Nature Publishing Group},
	author = {Bhowmick, Asmit and Hussein, Rana and Bogacz, Isabel and Simon, Philipp S. and Ibrahim, Mohamed and Chatterjee, Ruchira and Doyle, Margaret D. and Cheah, Mun Hon and Fransson, Thomas and Chernev, Petko and Kim, In-Sik and Makita, Hiroki and Dasgupta, Medhanjali and Kaminsky, Corey J. and Zhang, Miao and Gätcke, Julia and Haupt, Stephanie and Nangca, Isabela I. and Keable, Stephen M. and Aydin, A. Orkun and Tono, Kensuke and Owada, Shigeki and Gee, Leland B. and Fuller, Franklin D. and Batyuk, Alexander and Alonso-Mori, Roberto and Holton, James M. and Paley, Daniel W. and Moriarty, Nigel W. and Mamedov, Fikret and Adams, Paul D. and Brewster, Aaron S. and Dobbek, Holger and Sauter, Nicholas K. and Bergmann, Uwe and Zouni, Athina and Messinger, Johannes and Kern, Jan and Yano, Junko and Yachandra, Vittal K.},
	month = may,
	year = {2023},
	keywords = {Bioenergetics, Nanocrystallography},
	pages = {629--636},
}

In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn4CaO5 cluster first stores four oxidizing equivalents, the S0 to S4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O–O bond formation chemistry1–3. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok’s photosynthetic water oxidation cycle, the S3→[S4]→S0 transition where O2 is formed and Kok’s water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn4CaO5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom Ox, which was introduced as a bridging ligand between Ca and Mn1 during the S2→S3 transition4–6, disappears or relocates in parallel with Yz reduction starting at approximately 700 μs after the third flash. The onset of O2 evolution, as indicated by the shortening of the Mn1–Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.

@article{bag_flavodiiron-mediated_2023,
	title = {Flavodiiron-mediated {O2} photoreduction at photosystem {I} acceptor-side provides photoprotection to conifer thylakoids in early spring},
	volume = {14},
	copyright = {2023 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-38938-z},
	doi = {10.1038/s41467-023-38938-z},
	abstract = {Green organisms evolve oxygen (O2) via photosynthesis and consume it by respiration. Generally, net O2 consumption only becomes dominant when photosynthesis is suppressed at night. Here, we show that green thylakoid membranes of Scots pine (Pinus sylvestris L) and Norway spruce (Picea abies) needles display strong O2 consumption even in the presence of light when extremely low temperatures coincide with high solar irradiation during early spring (ES). By employing different electron transport chain inhibitors, we show that this unusual light-induced O2 consumption occurs around photosystem (PS) I and correlates with higher abundance of flavodiiron (Flv) A protein in ES thylakoids. With P700 absorption changes, we demonstrate that electron scavenging from the acceptor-side of PSI via O2 photoreduction is a major alternative pathway in ES. This photoprotection mechanism in vascular plants indicates that conifers have developed an adaptative evolution trajectory for growing in harsh environments.},
	language = {en},
	number = {1},
	urldate = {2023-06-09},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Bag, Pushan and Shutova, Tatyana and Shevela, Dmitry and Lihavainen, Jenna and Nanda, Sanchali and Ivanov, Alexander G. and Messinger, Johannes and Jansson, Stefan},
	month = jun,
	year = {2023},
	note = {Number: 1},
	keywords = {Abiotic, Light responses, Photosystem I},
	pages = {3210},
}

Green organisms evolve oxygen (O2) via photosynthesis and consume it by respiration. Generally, net O2 consumption only becomes dominant when photosynthesis is suppressed at night. Here, we show that green thylakoid membranes of Scots pine (Pinus sylvestris L) and Norway spruce (Picea abies) needles display strong O2 consumption even in the presence of light when extremely low temperatures coincide with high solar irradiation during early spring (ES). By employing different electron transport chain inhibitors, we show that this unusual light-induced O2 consumption occurs around photosystem (PS) I and correlates with higher abundance of flavodiiron (Flv) A protein in ES thylakoids. With P700 absorption changes, we demonstrate that electron scavenging from the acceptor-side of PSI via O2 photoreduction is a major alternative pathway in ES. This photoprotection mechanism in vascular plants indicates that conifers have developed an adaptative evolution trajectory for growing in harsh environments.

@article{bhowmick_going_2023,
	title = {Going around the {Kok} cycle of the water oxidation reaction with femtosecond {X}-ray crystallography},
	volume = {10},
	copyright = {https://creativecommons.org/licenses/by/4.0/},
	issn = {2052-2525},
	url = {https://journals.iucr.org/m/issues/2023/06/00/it5029/},
	doi = {10.1107/S2052252523008928},
	abstract = {The water oxidation reaction in photosystem II (PS II) produces most of the molecular oxygen in the atmosphere, which sustains life on Earth, and in this process releases four electrons and four protons that drive the downstream process of CO2 fixation in the photosynthetic apparatus. The catalytic center of PS II is an oxygen-bridged Mn4Ca complex (Mn4CaO5) which is progressively oxidized upon the absorption of light by the chloro­phyll of the PS II reaction center, and the accumulation of four oxidative equivalents in the catalytic center results in the oxidation of two waters to di­oxy­gen in the last step. The recent emergence of X-ray free-electron lasers (XFELs) with intense femtosecond X-ray pulses has opened up opportunities to visualize this reaction in PS II as it proceeds through the catalytic cycle. In this review, we summarize our recent studies of the catalytic reaction in PS II by following the structural changes along the reaction pathway via room-temperature X-ray crystallography using XFELs. The evolution of the electron density changes at the Mn complex reveals notable structural changes, including the insertion of OX from a new water molecule, which disappears on completion of the reaction, implicating it in the O—O bond formation reaction. We were also able to follow the structural dynamics of the protein coordinating with the catalytic complex and of channels within the protein that are important for substrate and product transport, revealing well orchestrated conformational changes in response to the electronic changes at the Mn4Ca cluster.},
	language = {en},
	number = {6},
	urldate = {2024-10-16},
	journal = {IUCrJ},
	publisher = {International Union of Crystallography},
	author = {Bhowmick, A. and Simon, P. S. and Bogacz, I. and Hussein, R. and Zhang, M. and Makita, H. and Ibrahim, M. and Chatterjee, R. and Doyle, M. D. and Cheah, M. H. and Chernev, P. and Fuller, F. D. and Fransson, T. and Alonso-Mori, R. and Brewster, A. S. and Sauter, N. K. and Bergmann, U. and Dobbek, H. and Zouni, A. and Messinger, J. and Kern, J. and Yachandra, V. K. and Yano, J.},
	month = nov,
	year = {2023},
	note = {Number: 6},
	pages = {642--655},
}

The water oxidation reaction in photosystem II (PS II) produces most of the molecular oxygen in the atmosphere, which sustains life on Earth, and in this process releases four electrons and four protons that drive the downstream process of CO2 fixation in the photosynthetic apparatus. The catalytic center of PS II is an oxygen-bridged Mn4Ca complex (Mn4CaO5) which is progressively oxidized upon the absorption of light by the chloro­phyll of the PS II reaction center, and the accumulation of four oxidative equivalents in the catalytic center results in the oxidation of two waters to di­oxy­gen in the last step. The recent emergence of X-ray free-electron lasers (XFELs) with intense femtosecond X-ray pulses has opened up opportunities to visualize this reaction in PS II as it proceeds through the catalytic cycle. In this review, we summarize our recent studies of the catalytic reaction in PS II by following the structural changes along the reaction pathway via room-temperature X-ray crystallography using XFELs. The evolution of the electron density changes at the Mn complex reveals notable structural changes, including the insertion of OX from a new water molecule, which disappears on completion of the reaction, implicating it in the O—O bond formation reaction. We were also able to follow the structural dynamics of the protein coordinating with the catalytic complex and of channels within the protein that are important for substrate and product transport, revealing well orchestrated conformational changes in response to the electronic changes at the Mn4Ca cluster.

@article{hussein_evolutionary_2023,
	title = {Evolutionary diversity of proton and water channels on the oxidizing side of photosystem {II} and their relevance to function},
	volume = {158},
	issn = {1573-5079},
	url = {https://doi.org/10.1007/s11120-023-01018-w},
	doi = {10.1007/s11120-023-01018-w},
	abstract = {One of the reasons for the high efficiency and selectivity of biological catalysts arise from their ability to control the pathways of substrates and products using protein channels, and by modulating the transport in the channels using the interaction with the protein residues and the water/hydrogen-bonding network. This process is clearly demonstrated in Photosystem II (PS II), where its light-driven water oxidation reaction catalyzed by the Mn4CaO5 cluster occurs deep inside the protein complex and thus requires the transport of two water molecules to and four protons from the metal center to the bulk water. Based on the recent advances in structural studies of PS II from X-ray crystallography and cryo-electron microscopy, in this review we compare the channels that have been proposed to facilitate this mass transport in cyanobacteria, red and green algae, diatoms, and higher plants. The three major channels (O1, O4, and Cl1 channels) are present in all species investigated; however, some differences exist in the reported structures that arise from the different composition and arrangement of membrane extrinsic subunits between the species. Among the three channels, the Cl1 channel, including the proton gate, is the most conserved among all photosynthetic species. We also found at least one branch for the O1 channel in all organisms, extending all the way from Ca/O1 via the ‘water wheel’ to the lumen. However, the extending path after the water wheel varies between most species. The O4 channel is, like the Cl1 channel, highly conserved among all species while having different orientations at the end of the path near the bulk. The comparison suggests that the previously proposed functionality of the channels in T. vestitus (Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Hussein et al., Nat Commun 12:6531, 2021) is conserved through the species, i.e. the O1-like channel is used for substrate water intake, and the tighter Cl1 and O4 channels for proton release. The comparison does not eliminate the potential role of O4 channel as a water intake channel. However, the highly ordered hydrogen-bonded water wire connected to the Mn4CaO5 cluster via the O4 may strongly suggest that it functions in proton release, especially during the S0 → S1 transition (Saito et al., Nat Commun 6:8488, 2015; Kern et al., Nature 563:421–425, 2018; Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Sakashita et al., Phys Chem Chem Phys 22:15831–15841, 2020; Hussein et al., Nat Commun 12:6531, 2021).},
	language = {en},
	number = {2},
	urldate = {2024-10-16},
	journal = {Photosynthesis Research},
	author = {Hussein, Rana and Ibrahim, Mohamed and Bhowmick, Asmit and Simon, Philipp S. and Bogacz, Isabel and Doyle, Margaret D. and Dobbek, Holger and Zouni, Athina and Messinger, Johannes and Yachandra, Vittal K. and Kern, Jan F. and Yano, Junko},
	month = nov,
	year = {2023},
	keywords = {Evolution, Oxygen evolving complex, Photosystem II, Water oxidation, Water transport},
	pages = {91--107},
}

One of the reasons for the high efficiency and selectivity of biological catalysts arise from their ability to control the pathways of substrates and products using protein channels, and by modulating the transport in the channels using the interaction with the protein residues and the water/hydrogen-bonding network. This process is clearly demonstrated in Photosystem II (PS II), where its light-driven water oxidation reaction catalyzed by the Mn4CaO5 cluster occurs deep inside the protein complex and thus requires the transport of two water molecules to and four protons from the metal center to the bulk water. Based on the recent advances in structural studies of PS II from X-ray crystallography and cryo-electron microscopy, in this review we compare the channels that have been proposed to facilitate this mass transport in cyanobacteria, red and green algae, diatoms, and higher plants. The three major channels (O1, O4, and Cl1 channels) are present in all species investigated; however, some differences exist in the reported structures that arise from the different composition and arrangement of membrane extrinsic subunits between the species. Among the three channels, the Cl1 channel, including the proton gate, is the most conserved among all photosynthetic species. We also found at least one branch for the O1 channel in all organisms, extending all the way from Ca/O1 via the ‘water wheel’ to the lumen. However, the extending path after the water wheel varies between most species. The O4 channel is, like the Cl1 channel, highly conserved among all species while having different orientations at the end of the path near the bulk. The comparison suggests that the previously proposed functionality of the channels in T. vestitus (Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Hussein et al., Nat Commun 12:6531, 2021) is conserved through the species, i.e. the O1-like channel is used for substrate water intake, and the tighter Cl1 and O4 channels for proton release. The comparison does not eliminate the potential role of O4 channel as a water intake channel. However, the highly ordered hydrogen-bonded water wire connected to the Mn4CaO5 cluster via the O4 may strongly suggest that it functions in proton release, especially during the S0 → S1 transition (Saito et al., Nat Commun 6:8488, 2015; Kern et al., Nature 563:421–425, 2018; Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Sakashita et al., Phys Chem Chem Phys 22:15831–15841, 2020; Hussein et al., Nat Commun 12:6531, 2021).

@article{shevela_solar_2023,
	title = {Solar energy conversion by photosystem {II}: principles and structures},
	volume = {156},
	issn = {1573-5079},
	shorttitle = {Solar energy conversion by photosystem {II}},
	url = {https://doi.org/10.1007/s11120-022-00991-y},
	doi = {10.1007/s11120-022-00991-y},
	abstract = {Photosynthetic water oxidation by Photosystem II (PSII) is a fascinating process because it sustains life on Earth and serves as a blue print for scalable synthetic catalysts required for renewable energy applications. The biophysical, computational, and structural description of this process, which started more than 50 years ago, has made tremendous progress over the past two decades, with its high-resolution crystal structures being available not only of the dark-stable state of PSII, but of all the semi-stable reaction intermediates and even some transient states. Here, we summarize the current knowledge on PSII with emphasis on the basic principles that govern the conversion of light energy to chemical energy in PSII, as well as on the illustration of the molecular structures that enable these reactions. The important remaining questions regarding the mechanism of biological water oxidation are highlighted, and one possible pathway for this fundamental reaction is described at a molecular level.},
	language = {en},
	number = {3},
	urldate = {2024-10-16},
	journal = {Photosynthesis Research},
	author = {Shevela, Dmitry and Kern, Jan F. and Govindjee, Govindjee and Messinger, Johannes},
	month = jun,
	year = {2023},
	keywords = {Educational review, Function of Photosystem II, Mechanism of water oxidation, Oxygen evolution, Photosynthesis, Primary photochemistry},
	pages = {279--307},
}

Photosynthetic water oxidation by Photosystem II (PSII) is a fascinating process because it sustains life on Earth and serves as a blue print for scalable synthetic catalysts required for renewable energy applications. The biophysical, computational, and structural description of this process, which started more than 50 years ago, has made tremendous progress over the past two decades, with its high-resolution crystal structures being available not only of the dark-stable state of PSII, but of all the semi-stable reaction intermediates and even some transient states. Here, we summarize the current knowledge on PSII with emphasis on the basic principles that govern the conversion of light energy to chemical energy in PSII, as well as on the illustration of the molecular structures that enable these reactions. The important remaining questions regarding the mechanism of biological water oxidation are highlighted, and one possible pathway for this fundamental reaction is described at a molecular level.

@article{guo_alternative_2023,
	title = {Alternative {Mechanism} for {O2} {Formation} in {Natural} {Photosynthesis} via {Nucleophilic} {Oxo}–{Oxo} {Coupling}},
	volume = {145},
	issn = {0002-7863},
	url = {https://doi.org/10.1021/jacs.2c12174},
	doi = {10.1021/jacs.2c12174},
	abstract = {O2 formation in photosystem II (PSII) is a vital event on Earth, but the exact mechanism remains unclear. The presently prevailing theoretical model is “radical coupling” (RC) involving a Mn(IV)-oxyl unit in an “open-cubane” Mn4CaO6 cluster, which is supported experimentally by the S3 state of cyanobacterial PSII featuring an additional Mn-bound oxygenic ligand. However, it was recently proposed that the major structural form of the S3 state of higher plants lacks this extra ligand, and that the resulting S4 state would feature instead a penta-coordinate dangler Mn(V)=oxo, covalently linked to a “closed-cubane” Mn3CaO4 cluster. For this proposal, we explore here a large number of possible pathways of O–O bond formation and demonstrate that the “nucleophilic oxo–oxo coupling” (NOOC) between Mn(V)=oxo and μ3-oxo is the only eligible mechanism in such a system. The reaction is facilitated by a specific conformation of the cluster and concomitant water binding, which is delayed compared to the RC mechanism. An energetically feasible process is described starting from the valid S4 state through the sequential formation of peroxide and superoxide, followed by O2 release and a second water insertion. The newly found mechanism is consistent with available experimental thermodynamic and kinetic data and thus a viable alternative pathway for O2 formation in natural photosynthesis, in particular for higher plants.},
	number = {7},
	urldate = {2024-10-16},
	journal = {Journal of the American Chemical Society},
	publisher = {American Chemical Society},
	author = {Guo, Yu and Messinger, Johannes and Kloo, Lars and Sun, Licheng},
	month = feb,
	year = {2023},
	pages = {4129--4141},
}

O2 formation in photosystem II (PSII) is a vital event on Earth, but the exact mechanism remains unclear. The presently prevailing theoretical model is “radical coupling” (RC) involving a Mn(IV)-oxyl unit in an “open-cubane” Mn4CaO6 cluster, which is supported experimentally by the S3 state of cyanobacterial PSII featuring an additional Mn-bound oxygenic ligand. However, it was recently proposed that the major structural form of the S3 state of higher plants lacks this extra ligand, and that the resulting S4 state would feature instead a penta-coordinate dangler Mn(V)=oxo, covalently linked to a “closed-cubane” Mn3CaO4 cluster. For this proposal, we explore here a large number of possible pathways of O–O bond formation and demonstrate that the “nucleophilic oxo–oxo coupling” (NOOC) between Mn(V)=oxo and μ3-oxo is the only eligible mechanism in such a system. The reaction is facilitated by a specific conformation of the cluster and concomitant water binding, which is delayed compared to the RC mechanism. An energetically feasible process is described starting from the valid S4 state through the sequential formation of peroxide and superoxide, followed by O2 release and a second water insertion. The newly found mechanism is consistent with available experimental thermodynamic and kinetic data and thus a viable alternative pathway for O2 formation in natural photosynthesis, in particular for higher plants.

@article{simon_capturing_2023,
	title = {Capturing the sequence of events during the water oxidation reaction in photosynthesis using {XFELs}},
	volume = {597},
	copyright = {© 2022 Federation of European Biochemical Societies.},
	issn = {1873-3468},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/1873-3468.14527},
	doi = {10.1002/1873-3468.14527},
	abstract = {Ever since the discovery that Mn was required for oxygen evolution in plants by Pirson in 1937 and the period-four oscillation in flash-induced oxygen evolution by Joliot and Kok in the 1970s, understanding of this process has advanced enormously using state-of-the-art methods. The most recent in this series of innovative techniques was the introduction of X-ray free-electron lasers (XFELs) a decade ago, which led to another quantum leap in the understanding in this field, by enabling operando X-ray structural and X-ray spectroscopy studies at room temperature. This review summarizes the current understanding of the structure of Photosystem II (PS II) and its catalytic centre, the Mn4CaO5 complex, in the intermediate Si (i = 0–4)-states of the Kok cycle, obtained using XFELs.},
	language = {en},
	number = {1},
	urldate = {2024-10-16},
	journal = {FEBS Letters},
	author = {Simon, Philipp S. and Makita, Hiroki and Bogacz, Isabel and Fuller, Franklin and Bhowmick, Asmit and Hussein, Rana and Ibrahim, Mohamed and Zhang, Miao and Chatterjee, Ruchira and Cheah, Mun Hon and Chernev, Petko and Doyle, Margaret D. and Brewster, Aaron S. and Alonso-Mori, Roberto and Sauter, Nicholas K. and Bergmann, Uwe and Dobbek, Holger and Zouni, Athina and Messinger, Johannes and Kern, Jan and Yachandra, Vittal K. and Yano, Junko},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/1873-3468.14527},
	keywords = {X-ray free-electron laser, X-ray spectroscopy, manganese metalloenzymes, oxygen evolving complex, photosystem II, water-oxidation/splitting},
	pages = {30--37},
}

Ever since the discovery that Mn was required for oxygen evolution in plants by Pirson in 1937 and the period-four oscillation in flash-induced oxygen evolution by Joliot and Kok in the 1970s, understanding of this process has advanced enormously using state-of-the-art methods. The most recent in this series of innovative techniques was the introduction of X-ray free-electron lasers (XFELs) a decade ago, which led to another quantum leap in the understanding in this field, by enabling operando X-ray structural and X-ray spectroscopy studies at room temperature. This review summarizes the current understanding of the structure of Photosystem II (PS II) and its catalytic centre, the Mn4CaO5 complex, in the intermediate Si (i = 0–4)-states of the Kok cycle, obtained using XFELs.

@article{vukasinovic_cracking_2023,
	title = {Cracking the green wall code: insights into cell wall integrity across organisms},
	volume = {1},
	issn = {2813-821X},
	shorttitle = {Cracking the green wall code},
	url = {https://www.frontiersin.org/journals/plant-physiology/articles/10.3389/fphgy.2023.1323899/full},
	doi = {10.3389/fphgy.2023.1323899},
	abstract = {{\textless}p{\textgreater}Cell walls are not just passive barriers; they are dynamic and adaptable structures that are actively remodeled in response to both internal and external cues. They are crucial in defining cellular identity, ensuring structural integrity, and mediating interactions with the environment. The concept of cell wall integrity (CWI) encompasses the mechanisms by which cells monitor and maintain their walls, ensuring proper function and response to challenges. While significant knowledge has been accumulated on CWI in certain model organisms, there remains a vast landscape of uncharted territory in others. In this review, we aim to bridge this gap, offering a comparative perspective on CWI across different evolutionary lineages, from the well-studied yeasts to the diverse world of plants. We focus especially on the green lineage –the group of green algae and land plants, hence the {\textless}italic{\textgreater}green wall{\textless}/italic{\textgreater}–, but also consider some insights from organisms with radically different lifestyles and cell wall arrangements, which serves as a base to some intriguing questions about the role of CWI across evolution and environmental adaptation.{\textless}/p{\textgreater}},
	language = {English},
	urldate = {2024-10-02},
	journal = {Frontiers in Plant Physiology},
	publisher = {Frontiers},
	author = {Vukašinović, Nemanja and Serif, Manuel and Bacete, Laura},
	month = nov,
	year = {2023},
	keywords = {Bacillariophyceae, Cell wall physicochemical properties, Cell wall plasticity, Charophyceae, Mechanosensing, Streptophyta, Zygnematophyceae, cell wall dynamics},
}

\textlessp\textgreaterCell walls are not just passive barriers; they are dynamic and adaptable structures that are actively remodeled in response to both internal and external cues. They are crucial in defining cellular identity, ensuring structural integrity, and mediating interactions with the environment. The concept of cell wall integrity (CWI) encompasses the mechanisms by which cells monitor and maintain their walls, ensuring proper function and response to challenges. While significant knowledge has been accumulated on CWI in certain model organisms, there remains a vast landscape of uncharted territory in others. In this review, we aim to bridge this gap, offering a comparative perspective on CWI across different evolutionary lineages, from the well-studied yeasts to the diverse world of plants. We focus especially on the green lineage –the group of green algae and land plants, hence the \textlessitalic\textgreatergreen wall\textless/italic\textgreater–, but also consider some insights from organisms with radically different lifestyles and cell wall arrangements, which serves as a base to some intriguing questions about the role of CWI across evolution and environmental adaptation.\textless/p\textgreater

@article{shahid_copper-treated_2023,
	title = {Copper-{Treated} {Environmentally} {Friendly} {Antipathogenic} {Cotton} {Fabric} with {Modified} {Reactive} {Blue} 4 {Dye} to {Improve} {Its} {Antibacterial} and {Aesthetic} {Properties}},
	volume = {13},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2079-6412},
	url = {https://www.mdpi.com/2079-6412/13/1/133},
	doi = {10.3390/coatings13010133},
	abstract = {The objectives of the present study were to develop an environmentally friendly, low-price, easy, and fast method for developing antipathogenic (antibacterial, antifungal, and antiviral) cuprous-oxide-coated multifunctional fabrics. The fabrics were first sensitized with citric acid, and then Cu2O particles were formed using the Fehling solution method. The cuprous oxide particles were then applied to the cotton fabrics. To create the Cu2O particles, three different kinds of reducing agents with varying concentrations were used. SEM, dynamic light scattering, FTIR, EDS, and XRD were used to examine the surface morphologies and metal presences. In the second step, a reactive antibacterial dye was made (by reacting Reactive Blue 4 with triclosan). The molecular structure of the modified dye was confirmed with FTIR. The resultant antibacterial dye was applied on the copper-treated cotton fabrics in accordance with the exhaust dyeing protocol. The dyed fabrics were characterized through the colorimetric data (L*, a*, b*, C, H, and K/S), levelness of dye, fastness properties as well as exhaustion and fixation rates. Cuprous-oxide-coated fabrics were tested for antipathogenic activity using quantitative and qualitative measurement results. The fabrics treated with cuprous oxide particles reduced with sodium hydrosulfite at 1 g/L seemed to have the highest antipathogenic effect. Moreover, the versatility of the hygienically developed bioactive fabrics in terms of their comfort properties such as air permeability and stiffness were investigated. Finally, the coating’s durability was confirmed by evaluating its antibacterial properties and performing an SEM analysis after laundry.},
	language = {en},
	number = {1},
	urldate = {2024-08-30},
	journal = {Coatings},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Shahid, Muhammad and Ali, Azam and Zahid, Nageena and Anjam, Muhammad Shahzad and Militky, Jiri and Wiener, Jakub and Palanisamy, Sundaramoorthy and Tomkova, Blanka},
	month = jan,
	year = {2023},
	note = {Number: 1},
	keywords = {antimicrobial, color analysis, cuprous oxide particles, hospital-acquired infections, medical textiles},
	pages = {133},
}

The objectives of the present study were to develop an environmentally friendly, low-price, easy, and fast method for developing antipathogenic (antibacterial, antifungal, and antiviral) cuprous-oxide-coated multifunctional fabrics. The fabrics were first sensitized with citric acid, and then Cu2O particles were formed using the Fehling solution method. The cuprous oxide particles were then applied to the cotton fabrics. To create the Cu2O particles, three different kinds of reducing agents with varying concentrations were used. SEM, dynamic light scattering, FTIR, EDS, and XRD were used to examine the surface morphologies and metal presences. In the second step, a reactive antibacterial dye was made (by reacting Reactive Blue 4 with triclosan). The molecular structure of the modified dye was confirmed with FTIR. The resultant antibacterial dye was applied on the copper-treated cotton fabrics in accordance with the exhaust dyeing protocol. The dyed fabrics were characterized through the colorimetric data (L*, a*, b*, C, H, and K/S), levelness of dye, fastness properties as well as exhaustion and fixation rates. Cuprous-oxide-coated fabrics were tested for antipathogenic activity using quantitative and qualitative measurement results. The fabrics treated with cuprous oxide particles reduced with sodium hydrosulfite at 1 g/L seemed to have the highest antipathogenic effect. Moreover, the versatility of the hygienically developed bioactive fabrics in terms of their comfort properties such as air permeability and stiffness were investigated. Finally, the coating’s durability was confirmed by evaluating its antibacterial properties and performing an SEM analysis after laundry.

@article{polacek_automation_2023,
	title = {Automation of tree-ring detection and measurements using deep learning},
	volume = {14},
	copyright = {© 2023 GMI - Gregor Mendel Institute of Molecular Plant Biology. Methods in Ecology and Evolution published by John Wiley \& Sons Ltd on behalf of British Ecological Society.},
	issn = {2041-210X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.14183},
	doi = {10.1111/2041-210X.14183},
	abstract = {Core samples from trees are a critical reservoir of ecological information, informing our understanding of past climates, as well as contemporary ecosystem responses to global change. Manual measurements of annual growth rings in trees are slow, labour-intensive and subject to human bias, hindering the generation of big datasets. We present an alternative, neural network-based implementation that automates detection and measurement of tree-ring boundaries from coniferous species. We trained our Mask R-CNN extensively on over 8000 manually annotated ring boundaries from microscope-imaged Norway Spruce Picea abies increment cores. We assessed the performance of the trained model after post-processing on real-world data generated from our core processing pipeline. The CNN after post-processing performed well, with recognition of over 98\% of ring boundaries (recall) with a precision in detection of 96\% when tested on real-world data. Additionally, we have implemented automatic measurements based on minimum distance between rings. With minimal editing for missed ring detections, these measurements were 98\% correlated with human measurements of the same samples. Tests on other three conifer species demonstrate that the CNN generalizes well to other species with similar structure. We demonstrate the efficacy of automating the measurement of growth increment in tree core samples. Our CNN-based system provides high predictive performance in terms of both tree-ring detection and growth rate determination. Our application is readily deployable as a Docker container and requires only basic command line skills. Additionally, an easy re-training option allows users to expand capabilities to other wood types. Application outputs include both editable annotations of predictions as well as ring-width measurements in a commonly used .pos format, facilitating the efficient generation of large ring-width measurement datasets from increment core samples, an important source of environmental data.},
	language = {en},
	number = {9},
	urldate = {2024-03-22},
	journal = {Methods in Ecology and Evolution},
	author = {Poláček, Miroslav and Arizpe, Alexis and Hüther, Patrick and Weidlich, Lisa and Steindl, Sonja and Swarts, Kelly},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.14183},
	keywords = {automation, computer vision, mask R-CNN, phenotyping, tree rings},
	pages = {2233--2242},
}

Core samples from trees are a critical reservoir of ecological information, informing our understanding of past climates, as well as contemporary ecosystem responses to global change. Manual measurements of annual growth rings in trees are slow, labour-intensive and subject to human bias, hindering the generation of big datasets. We present an alternative, neural network-based implementation that automates detection and measurement of tree-ring boundaries from coniferous species. We trained our Mask R-CNN extensively on over 8000 manually annotated ring boundaries from microscope-imaged Norway Spruce Picea abies increment cores. We assessed the performance of the trained model after post-processing on real-world data generated from our core processing pipeline. The CNN after post-processing performed well, with recognition of over 98% of ring boundaries (recall) with a precision in detection of 96% when tested on real-world data. Additionally, we have implemented automatic measurements based on minimum distance between rings. With minimal editing for missed ring detections, these measurements were 98% correlated with human measurements of the same samples. Tests on other three conifer species demonstrate that the CNN generalizes well to other species with similar structure. We demonstrate the efficacy of automating the measurement of growth increment in tree core samples. Our CNN-based system provides high predictive performance in terms of both tree-ring detection and growth rate determination. Our application is readily deployable as a Docker container and requires only basic command line skills. Additionally, an easy re-training option allows users to expand capabilities to other wood types. Application outputs include both editable annotations of predictions as well as ring-width measurements in a commonly used .pos format, facilitating the efficient generation of large ring-width measurement datasets from increment core samples, an important source of environmental data.

@article{vallebueno-estrada_domestication_2023,
	title = {Domestication and lowland adaptation of coastal preceramic maize from {Paredones}, {Peru}},
	volume = {12},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.83149},
	doi = {10.7554/eLife.83149},
	abstract = {Archaeological cobs from Paredones and Huaca Prieta (Peru) represent some of the oldest maize known to date, yet they present relevant phenotypic traits corresponding to domesticated maize. This contrasts with the earliest Mexican macro-specimens from Guila Naquitz and San Marcos, which are phenotypically intermediate for these traits, even though they date more recently in time. To gain insights into the origins of ancient Peruvian maize, we sequenced DNA from three Paredones specimens dating {\textasciitilde}6700–5000 calibrated years before present (BP), conducting comparative analyses with two teosinte subspecies (Zea mays ssp. mexicana and parviglumis) and extant maize, that include highland and lowland landraces from Mesoamerica and South America. We show that Paredones maize originated from the same domestication event as Mexican maize and was domesticated by {\textasciitilde}6700 BP, implying rapid dispersal followed by improvement. Paredones maize shows no relevant gene flow from mexicana, smaller than that observed in teosinte parviglumis. Thus, Paredones samples represent the only maize without confounding mexicana variation found to date. It also harbors significantly fewer alleles previously found to be adaptive to highlands, but not of alleles adaptive to lowlands, supporting a lowland migration route. Our overall results imply that Paredones maize originated in Mesoamerica, arrived in Peru without mexicana introgression through a rapid lowland migration route, and underwent improvements in both Mesoamerica and South America.},
	urldate = {2024-03-22},
	journal = {eLife},
	publisher = {eLife Sciences Publications, Ltd},
	author = {Vallebueno-Estrada, Miguel and Hernández-Robles, Guillermo G and González-Orozco, Eduardo and Lopez-Valdivia, Ivan and Rosales Tham, Teresa and Vásquez Sánchez, Víctor and Swarts, Kelly and Dillehay, Tom D and Vielle-Calzada, Jean-Philippe and Montiel, Rafael},
	editor = {Weigel, Detlef},
	month = apr,
	year = {2023},
	keywords = {domestication, lowlands, paleogenomics, paredones},
	pages = {e83149},
}

Archaeological cobs from Paredones and Huaca Prieta (Peru) represent some of the oldest maize known to date, yet they present relevant phenotypic traits corresponding to domesticated maize. This contrasts with the earliest Mexican macro-specimens from Guila Naquitz and San Marcos, which are phenotypically intermediate for these traits, even though they date more recently in time. To gain insights into the origins of ancient Peruvian maize, we sequenced DNA from three Paredones specimens dating ~6700–5000 calibrated years before present (BP), conducting comparative analyses with two teosinte subspecies (Zea mays ssp. mexicana and parviglumis) and extant maize, that include highland and lowland landraces from Mesoamerica and South America. We show that Paredones maize originated from the same domestication event as Mexican maize and was domesticated by ~6700 BP, implying rapid dispersal followed by improvement. Paredones maize shows no relevant gene flow from mexicana, smaller than that observed in teosinte parviglumis. Thus, Paredones samples represent the only maize without confounding mexicana variation found to date. It also harbors significantly fewer alleles previously found to be adaptive to highlands, but not of alleles adaptive to lowlands, supporting a lowland migration route. Our overall results imply that Paredones maize originated in Mesoamerica, arrived in Peru without mexicana introgression through a rapid lowland migration route, and underwent improvements in both Mesoamerica and South America.

@article{guerreiro_unveiling_2023,
	title = {Unveiling the intricate mechanisms of plant defense},
	volume = {1},
	issn = {2813-821X},
	url = {https://www.frontiersin.org/articles/10.3389/fphgy.2023.1285373},
	doi = {10.3389/fphgy.2023.1285373},
	abstract = {Plants may lack mobility, but they are not defenseless against the constant threats posed by pathogens and pests. Pattern Recognition Receptors (PRRs), which are located on the plasma membrane, enable plants to effectively recognize intruders. These receptors function by sensing elicitors or fragments of the cell wall that arise from damage. Recent studies underscore the significance of maintaining cell wall integrity in the coordination of defense mechanisms following the detection of parasitism. Pathogen invasion often triggers alterations in cell wall structure, which leads to the release of molecules like β-glucans and oligogalacturonides. These small molecules are then recognized by PRRs, which stimulate downstream signaling pathways that involve both receptor-like kinases and calcium-dependent signaling. Here, we present the latest insights into plant signaling that play a vital role in immunity: the maintenance of cell wall integrity; the intricate interplay between receptor-like kinases; and the involvement of calcium ions. The goal of the review is to provide readers with a deeper understanding of the intricate mechanisms underlying plant defense strategies.},
	urldate = {2024-02-08},
	journal = {Frontiers in Plant Physiology},
	author = {Guerreiro, Julie and Marhavý, Peter},
	year = {2023},
}

Plants may lack mobility, but they are not defenseless against the constant threats posed by pathogens and pests. Pattern Recognition Receptors (PRRs), which are located on the plasma membrane, enable plants to effectively recognize intruders. These receptors function by sensing elicitors or fragments of the cell wall that arise from damage. Recent studies underscore the significance of maintaining cell wall integrity in the coordination of defense mechanisms following the detection of parasitism. Pathogen invasion often triggers alterations in cell wall structure, which leads to the release of molecules like β-glucans and oligogalacturonides. These small molecules are then recognized by PRRs, which stimulate downstream signaling pathways that involve both receptor-like kinases and calcium-dependent signaling. Here, we present the latest insights into plant signaling that play a vital role in immunity: the maintenance of cell wall integrity; the intricate interplay between receptor-like kinases; and the involvement of calcium ions. The goal of the review is to provide readers with a deeper understanding of the intricate mechanisms underlying plant defense strategies.

@article{bacete_dynamics_2023,
	title = {Dynamics and mechanics of plant cell walls: insights into plant growth, defence, and stress response},
	volume = {113},
	issn = {1573-5028},
	shorttitle = {Dynamics and mechanics of plant cell walls},
	url = {https://doi.org/10.1007/s11103-023-01395-9},
	doi = {10.1007/s11103-023-01395-9},
	language = {en},
	number = {6},
	urldate = {2024-01-04},
	journal = {Plant Molecular Biology},
	author = {Bacete, Laura and Mélida, Hugo},
	month = dec,
	year = {2023},
	pages = {329--330},
}

@article{skalicky_fluorescence-activated_2023,
	title = {Fluorescence-activated multi-organelle mapping of subcellular plant hormone distribution},
	volume = {116},
	copyright = {© 2023 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.16456},
	doi = {10.1111/tpj.16456},
	abstract = {Auxins and cytokinins are two major families of phytohormones that control most aspects of plant growth, development and plasticity. Their distribution in plants has been described, but the importance of cell- and subcellular-type specific phytohormone homeostasis remains undefined. Herein, we revealed auxin and cytokinin distribution maps showing their different organelle-specific allocations within the Arabidopsis plant cell. To do so, we have developed Fluorescence-Activated multi-Organelle Sorting (FAmOS), an innovative subcellular fractionation technique based on flow cytometric principles. FAmOS allows the simultaneous sorting of four differently labelled organelles based on their individual light scatter and fluorescence parameters while ensuring hormone metabolic stability. Our data showed different subcellular distribution of auxin and cytokinins, revealing the formation of phytohormone gradients that have been suggested by the subcellular localization of auxin and cytokinin transporters, receptors and metabolic enzymes. Both hormones showed enrichment in vacuoles, while cytokinins were also accumulated in the endoplasmic reticulum.},
	language = {en},
	number = {6},
	urldate = {2023-12-22},
	journal = {The Plant Journal},
	author = {Skalický, Vladimír and Antoniadi, Ioanna and Pěnčík, Aleš and Chamrád, Ivo and Lenobel, René and Kubeš, Martin F. and Zatloukal, Marek and Žukauskaitė, Asta and Strnad, Miroslav and Ljung, Karin and Novák, Ondřej},
	month = sep,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.16456},
	keywords = {Arabidopsis thaliana, Auxin, LC–MS/MS, cytokinin, flow cytometry, subcellular fractionation, subcellular homeostasis, technical advances},
	pages = {1825--1841},
}

Auxins and cytokinins are two major families of phytohormones that control most aspects of plant growth, development and plasticity. Their distribution in plants has been described, but the importance of cell- and subcellular-type specific phytohormone homeostasis remains undefined. Herein, we revealed auxin and cytokinin distribution maps showing their different organelle-specific allocations within the Arabidopsis plant cell. To do so, we have developed Fluorescence-Activated multi-Organelle Sorting (FAmOS), an innovative subcellular fractionation technique based on flow cytometric principles. FAmOS allows the simultaneous sorting of four differently labelled organelles based on their individual light scatter and fluorescence parameters while ensuring hormone metabolic stability. Our data showed different subcellular distribution of auxin and cytokinins, revealing the formation of phytohormone gradients that have been suggested by the subcellular localization of auxin and cytokinin transporters, receptors and metabolic enzymes. Both hormones showed enrichment in vacuoles, while cytokinins were also accumulated in the endoplasmic reticulum.

@article{sharma_regulation_2023,
	title = {Regulation of {PIN} polarity in response to abiotic stress},
	volume = {76},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526623001103},
	doi = {10.1016/j.pbi.2023.102445},
	abstract = {Plants have evolved robust adaptive mechanisms to withstand the ever-changing environment. Tightly regulated distribution of the hormone auxin throughout the plant body controls an impressive variety of developmental processes that tailor plant growth and morphology to environmental conditions. The proper flow and directionality of auxin between cells is mainly governed by asymmetrically localized efflux carriers – PINs – ensuring proper coordination of developmental processes in plants. Discerning the molecular players and cellular dynamics involved in the establishment and maintenance of PINs in specific membrane domains, as well as their ability to readjust in response to abiotic stressors is essential for understanding how plants balance adaptability and stability. While much is known about how PINs get polarized, there is still limited knowledge about how abiotic stresses alter PIN polarity by acting on these systems. In this review, we focus on the current understanding of mechanisms involved in (re)establishing and maintaining PIN polarity under abiotic stresses.},
	urldate = {2023-12-22},
	journal = {Current Opinion in Plant Biology},
	author = {Sharma, Manvi and Marhava, Petra},
	month = dec,
	year = {2023},
	pages = {102445},
}

Plants have evolved robust adaptive mechanisms to withstand the ever-changing environment. Tightly regulated distribution of the hormone auxin throughout the plant body controls an impressive variety of developmental processes that tailor plant growth and morphology to environmental conditions. The proper flow and directionality of auxin between cells is mainly governed by asymmetrically localized efflux carriers – PINs – ensuring proper coordination of developmental processes in plants. Discerning the molecular players and cellular dynamics involved in the establishment and maintenance of PINs in specific membrane domains, as well as their ability to readjust in response to abiotic stressors is essential for understanding how plants balance adaptability and stability. While much is known about how PINs get polarized, there is still limited knowledge about how abiotic stresses alter PIN polarity by acting on these systems. In this review, we focus on the current understanding of mechanisms involved in (re)establishing and maintaining PIN polarity under abiotic stresses.

@article{bas_preparation_2023,
	title = {Preparation and {Characterization} of {Softwood} and {Hardwood} {Nanofibril} {Hydrogels}: {Toward} {Wound} {Dressing} {Applications}},
	volume = {24},
	issn = {1525-7797},
	shorttitle = {Preparation and {Characterization} of {Softwood} and {Hardwood} {Nanofibril} {Hydrogels}},
	url = {https://doi.org/10.1021/acs.biomac.3c00596},
	doi = {10.1021/acs.biomac.3c00596},
	abstract = {Hydrogels of cellulose nanofibrils (CNFs) are promising wound dressing candidates due to their biocompatibility, high water absorption, and transparency. Herein, two different commercially available wood species, softwood and hardwood, were subjected to TEMPO-mediated oxidation to proceed with delignification and oxidation in a one-pot process, and thereafter, nanofibrils were isolated using a high-pressure microfluidizer. Furthermore, transparent nanofibril hydrogel networks were prepared by vacuum filtration. Nanofibril properties and network performance correlated with oxidation were investigated and compared with commercially available TEMPO-oxidized pulp nanofibrils and their networks. Softwood nanofibril hydrogel networks exhibited the best mechanical properties, and in vitro toxicological risk assessment showed no detrimental effect for any of the studied hydrogels on human fibroblast or keratinocyte cells. This study demonstrates a straightforward processing route for direct oxidation of different wood species to obtain nanofibril hydrogels for potential use as wound dressings, with softwood having the most potential.},
	number = {12},
	urldate = {2023-12-22},
	journal = {Biomacromolecules},
	publisher = {American Chemical Society},
	author = {Baş, Yağmur and Berglund, Linn and Niittylä, Totte and Zattarin, Elisa and Aili, Daniel and Sotra, Zeljana and Rinklake, Ivana and Junker, Johan and Rakar, Jonathan and Oksman, Kristiina},
	month = dec,
	year = {2023},
	pages = {5605--5619},
}

Hydrogels of cellulose nanofibrils (CNFs) are promising wound dressing candidates due to their biocompatibility, high water absorption, and transparency. Herein, two different commercially available wood species, softwood and hardwood, were subjected to TEMPO-mediated oxidation to proceed with delignification and oxidation in a one-pot process, and thereafter, nanofibrils were isolated using a high-pressure microfluidizer. Furthermore, transparent nanofibril hydrogel networks were prepared by vacuum filtration. Nanofibril properties and network performance correlated with oxidation were investigated and compared with commercially available TEMPO-oxidized pulp nanofibrils and their networks. Softwood nanofibril hydrogel networks exhibited the best mechanical properties, and in vitro toxicological risk assessment showed no detrimental effect for any of the studied hydrogels on human fibroblast or keratinocyte cells. This study demonstrates a straightforward processing route for direct oxidation of different wood species to obtain nanofibril hydrogels for potential use as wound dressings, with softwood having the most potential.

@article{soni_interplay_2023,
	title = {The interplay between cell wall integrity and cell cycle progression in plants},
	volume = {113},
	issn = {1573-5028},
	url = {https://doi.org/10.1007/s11103-023-01394-w},
	doi = {10.1007/s11103-023-01394-w},
	abstract = {Plant cell walls are dynamic structures that play crucial roles in growth, development, and stress responses. Despite our growing understanding of cell wall biology, the connections between cell wall integrity (CWI) and cell cycle progression in plants remain poorly understood. This review aims to explore the intricate relationship between CWI and cell cycle progression in plants, drawing insights from studies in yeast and mammals. We provide an overview of the plant cell cycle, highlight the role of endoreplication in cell wall composition, and discuss recent findings on the molecular mechanisms linking CWI perception to cell wall biosynthesis and gene expression regulation. Furthermore, we address future perspectives and unanswered questions in the field, such as the identification of specific CWI sensing mechanisms and the role of CWI maintenance in the growth-defense trade-off. Elucidating these connections could have significant implications for crop improvement and sustainable agriculture.},
	language = {en},
	number = {6},
	urldate = {2023-12-22},
	journal = {Plant Molecular Biology},
	author = {Soni, Nancy and Bacete, Laura},
	month = dec,
	year = {2023},
	keywords = {Auxin, Cell cycle progression, Cell wall sensing, Cytokinin, Endoreplication, Growth-defense trade-off, Plant cell wall integrity},
	pages = {367--382},
}

Plant cell walls are dynamic structures that play crucial roles in growth, development, and stress responses. Despite our growing understanding of cell wall biology, the connections between cell wall integrity (CWI) and cell cycle progression in plants remain poorly understood. This review aims to explore the intricate relationship between CWI and cell cycle progression in plants, drawing insights from studies in yeast and mammals. We provide an overview of the plant cell cycle, highlight the role of endoreplication in cell wall composition, and discuss recent findings on the molecular mechanisms linking CWI perception to cell wall biosynthesis and gene expression regulation. Furthermore, we address future perspectives and unanswered questions in the field, such as the identification of specific CWI sensing mechanisms and the role of CWI maintenance in the growth-defense trade-off. Elucidating these connections could have significant implications for crop improvement and sustainable agriculture.

@article{bernacki_biotechnological_2023,
	title = {Biotechnological {Potential} of the {Stress} {Response} and {Plant} {Cell} {Death} {Regulators} {Proteins} in the {Biofuel} {Industry}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2073-4409},
	url = {https://www.mdpi.com/2073-4409/12/16/2018},
	doi = {10.3390/cells12162018},
	abstract = {Production of biofuel from lignocellulosic biomass is relatively low due to the limited knowledge about natural cell wall loosening and cellulolytic processes in plants. Industrial separation of cellulose fiber mass from lignin, its saccharification and alcoholic fermentation is still cost-ineffective and environmentally unfriendly. Assuming that the green transformation is inevitable and that new sources of raw materials for biofuels are needed, we decided to study cell death—a natural process occurring in plants in the context of reducing the recalcitrance of lignocellulose for the production of second-generation bioethanol. “Members of the enzyme families responsible for lysigenous aerenchyma formation were identified during the root hypoxia stress in Arabidopsis thaliana cell death mutants. The cell death regulatory genes, LESION SIMULATING DISEASE 1 (LSD1), PHYTOALEXIN DEFICIENT 4 (PAD4) and ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) conditionally regulate the cell wall when suppressed in transgenic aspen. During four years of growth in the field, the following effects were observed: lignin content was reduced, the cellulose fiber polymerization degree increased and the growth itself was unaffected. The wood of transgenic trees was more efficient as a substrate for saccharification, alcoholic fermentation and bioethanol production. The presented results may trigger the development of novel biotechnologies in the biofuel industry.},
	language = {en},
	number = {16},
	urldate = {2023-08-31},
	journal = {Cells},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Bernacki, Maciej Jerzy and Mielecki, Jakub and Antczak, Andrzej and Drożdżek, Michał and Witoń, Damian and Dąbrowska-Bronk, Joanna and Gawroński, Piotr and Burdiak, Paweł and Marchwicka, Monika and Rusaczonek, Anna and Dąbkowska-Susfał, Katarzyna and Strobel, Wacław Roman and Mellerowicz, Ewa J. and Zawadzki, Janusz and Szechyńska-Hebda, Magdalena and Karpiński, Stanisław},
	month = aug,
	year = {2023},
	note = {Number: 16},
	keywords = {bioethanol, biofuels, cell death, cell wall, lignin, poplar, scarification},
	pages = {2018},
}

Production of biofuel from lignocellulosic biomass is relatively low due to the limited knowledge about natural cell wall loosening and cellulolytic processes in plants. Industrial separation of cellulose fiber mass from lignin, its saccharification and alcoholic fermentation is still cost-ineffective and environmentally unfriendly. Assuming that the green transformation is inevitable and that new sources of raw materials for biofuels are needed, we decided to study cell death—a natural process occurring in plants in the context of reducing the recalcitrance of lignocellulose for the production of second-generation bioethanol. “Members of the enzyme families responsible for lysigenous aerenchyma formation were identified during the root hypoxia stress in Arabidopsis thaliana cell death mutants. The cell death regulatory genes, LESION SIMULATING DISEASE 1 (LSD1), PHYTOALEXIN DEFICIENT 4 (PAD4) and ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) conditionally regulate the cell wall when suppressed in transgenic aspen. During four years of growth in the field, the following effects were observed: lignin content was reduced, the cellulose fiber polymerization degree increased and the growth itself was unaffected. The wood of transgenic trees was more efficient as a substrate for saccharification, alcoholic fermentation and bioethanol production. The presented results may trigger the development of novel biotechnologies in the biofuel industry.