@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{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{bourdon_ectopic_2023,
	title = {Ectopic callose deposition into woody biomass modulates the nano-architecture of macrofibrils},
	volume = {9},
	copyright = {2023 The Author(s)},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-023-01459-0},
	doi = {10.1038/s41477-023-01459-0},
	abstract = {Plant biomass plays an increasingly important role in the circular bioeconomy, replacing non-renewable fossil resources. Genetic engineering of this lignocellulosic biomass could benefit biorefinery transformation chains by lowering economic and technological barriers to industrial processing. However, previous efforts have mostly targeted the major constituents of woody biomass: cellulose, hemicellulose and lignin. Here we report the engineering of wood structure through the introduction of callose, a polysaccharide novel to most secondary cell walls. Our multiscale analysis of genetically engineered poplar trees shows that callose deposition modulates cell wall porosity, water and lignin contents and increases the lignin–cellulose distance, ultimately resulting in substantially decreased biomass recalcitrance. We provide a model of the wood cell wall nano-architecture engineered to accommodate the hydrated callose inclusions. Ectopic polymer introduction into biomass manifests in new physico-chemical properties and offers new avenues when considering lignocellulose engineering.},
	language = {en},
	number = {9},
	urldate = {2023-09-22},
	journal = {Nature Plants},
	publisher = {Nature Publishing Group},
	author = {Bourdon, Matthieu and Lyczakowski, Jan J. and Cresswell, Rosalie and Amsbury, Sam and Vilaplana, Francisco and Le Guen, Marie-Joo and Follain, Nadège and Wightman, Raymond and Su, Chang and Alatorre-Cobos, Fulgencio and Ritter, Maximilian and Liszka, Aleksandra and Terrett, Oliver M. and Yadav, Shri Ram and Vatén, Anne and Nieminen, Kaisa and Eswaran, Gugan and Alonso-Serra, Juan and Müller, Karin H. and Iuga, Dinu and Miskolczi, Pal Csaba and Kalmbach, Lothar and Otero, Sofia and Mähönen, Ari Pekka and Bhalerao, Rishikesh and Bulone, Vincent and Mansfield, Shawn D. and Hill, Stefan and Burgert, Ingo and Beaugrand, Johnny and Benitez-Alfonso, Yoselin and Dupree, Ray and Dupree, Paul and Helariutta, Ykä},
	month = sep,
	year = {2023},
	note = {Number: 9},
	keywords = {Biofuels, Molecular engineering in plants},
	pages = {1530--1546},
}

Plant biomass plays an increasingly important role in the circular bioeconomy, replacing non-renewable fossil resources. Genetic engineering of this lignocellulosic biomass could benefit biorefinery transformation chains by lowering economic and technological barriers to industrial processing. However, previous efforts have mostly targeted the major constituents of woody biomass: cellulose, hemicellulose and lignin. Here we report the engineering of wood structure through the introduction of callose, a polysaccharide novel to most secondary cell walls. Our multiscale analysis of genetically engineered poplar trees shows that callose deposition modulates cell wall porosity, water and lignin contents and increases the lignin–cellulose distance, ultimately resulting in substantially decreased biomass recalcitrance. We provide a model of the wood cell wall nano-architecture engineered to accommodate the hydrated callose inclusions. Ectopic polymer introduction into biomass manifests in new physico-chemical properties and offers new avenues when considering lignocellulose engineering.

@article{su_tree_2023,
	title = {Tree architecture: {A} strigolactone-deficient mutant reveals a connection between branching order and auxin gradient along the tree stem},
	volume = {120},
	shorttitle = {Tree architecture},
	url = {https://www.pnas.org/doi/10.1073/pnas.2308587120},
	doi = {10.1073/pnas.2308587120},
	abstract = {Due to their long lifespan, trees and bushes develop higher order of branches in a perennial manner. In contrast to a tall tree, with a clearly defined main stem and branching order, a bush is shorter and has a less apparent main stem and branching pattern. To address the developmental basis of these two forms, we studied several naturally occurring architectural variants in silver birch (Betula pendula). Using a candidate gene approach, we identified a bushy kanttarelli variant with a loss-of-function mutation in the BpMAX1 gene required for strigolactone (SL) biosynthesis. While kanttarelli is shorter than the wild type (WT), it has the same number of primary branches, whereas the number of secondary branches is increased, contributing to its bush-like phenotype. To confirm that the identified mutation was responsible for the phenotype, we phenocopied kanttarelli in transgenic BpMAX1::RNAi birch lines. SL profiling confirmed that both kanttarelli and the transgenic lines produced very limited amounts of SL. Interestingly, the auxin (IAA) distribution along the main stem differed between WT and BpMAX1::RNAi. In the WT, the auxin concentration formed a gradient, being higher in the uppermost internodes and decreasing toward the basal part of the stem, whereas in the transgenic line, this gradient was not observed. Through modeling, we showed that the different IAA distribution patterns may result from the difference in the number of higher-order branches and plant height. Future studies will determine whether the IAA gradient itself regulates aspects of plant architecture.},
	number = {48},
	urldate = {2023-11-24},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {Su, Chang and Kokosza, Andrzej and Xie, Xiaonan and Pěnčík, Aleš and Zhang, Youjun and Raumonen, Pasi and Shi, Xueping and Muranen, Sampo and Topcu, Melis Kucukoglu and Immanen, Juha and Hagqvist, Risto and Safronov, Omid and Alonso-Serra, Juan and Eswaran, Gugan and Venegas, Mirko Pavicic and Ljung, Karin and Ward, Sally and Mähönen, Ari Pekka and Himanen, Kristiina and Salojärvi, Jarkko and Fernie, Alisdair R. and Novák, Ondřej and Leyser, Ottoline and Pałubicki, Wojtek and Helariutta, Ykä and Nieminen, Kaisa},
	month = nov,
	year = {2023},
	pages = {e2308587120},
}

Due to their long lifespan, trees and bushes develop higher order of branches in a perennial manner. In contrast to a tall tree, with a clearly defined main stem and branching order, a bush is shorter and has a less apparent main stem and branching pattern. To address the developmental basis of these two forms, we studied several naturally occurring architectural variants in silver birch (Betula pendula). Using a candidate gene approach, we identified a bushy kanttarelli variant with a loss-of-function mutation in the BpMAX1 gene required for strigolactone (SL) biosynthesis. While kanttarelli is shorter than the wild type (WT), it has the same number of primary branches, whereas the number of secondary branches is increased, contributing to its bush-like phenotype. To confirm that the identified mutation was responsible for the phenotype, we phenocopied kanttarelli in transgenic BpMAX1::RNAi birch lines. SL profiling confirmed that both kanttarelli and the transgenic lines produced very limited amounts of SL. Interestingly, the auxin (IAA) distribution along the main stem differed between WT and BpMAX1::RNAi. In the WT, the auxin concentration formed a gradient, being higher in the uppermost internodes and decreasing toward the basal part of the stem, whereas in the transgenic line, this gradient was not observed. Through modeling, we showed that the different IAA distribution patterns may result from the difference in the number of higher-order branches and plant height. Future studies will determine whether the IAA gradient itself regulates aspects of plant architecture.

@article{alonso-serra_carbon_2021,
	title = {Carbon sequestration: counterintuitive feedback of plant growth},
	volume = {2},
	issn = {2632-8828},
	shorttitle = {Carbon sequestration},
	url = {https://pmc.ncbi.nlm.nih.gov/articles/PMC10095961/},
	doi = {10.1017/qpb.2021.11},
	abstract = {Interaction between the atmosphere, plants and soils plays an important role in the carbon cycle. Soils contain vast amounts of carbon, but their capacity to keep it belowground depends on the long-term ecosystem dynamics. Plant growth has the potential of adding or releasing carbon from soil stocks. Since plant growth is also stimulated by higher CO2 levels, understanding its impact on soils becomes crucial for estimating carbon sequestration at the ecosystem level. A recent meta-analysis explored the effect CO2 levels have in plant versus soil carbon sequestration. The integration of 108 experiments performed across different environments revealed that the magnitude of plant growth and the nutrient acquisition strategy result in counterintuitive feedback for soil carbon sequestration.},
	urldate = {2025-10-08},
	journal = {Quantitative Plant Biology},
	author = {Alonso-Serra, Juan},
	month = sep,
	year = {2021},
	pages = {e11},
}

Interaction between the atmosphere, plants and soils plays an important role in the carbon cycle. Soils contain vast amounts of carbon, but their capacity to keep it belowground depends on the long-term ecosystem dynamics. Plant growth has the potential of adding or releasing carbon from soil stocks. Since plant growth is also stimulated by higher CO2 levels, understanding its impact on soils becomes crucial for estimating carbon sequestration at the ecosystem level. A recent meta-analysis explored the effect CO2 levels have in plant versus soil carbon sequestration. The integration of 108 experiments performed across different environments revealed that the magnitude of plant growth and the nutrient acquisition strategy result in counterintuitive feedback for soil carbon sequestration.

@article{trinh_how_2021,
	title = {How {Mechanical} {Forces} {Shape} {Plant} {Organs}},
	volume = {31},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982220318200},
	doi = {10.1016/j.cub.2020.12.001},
	abstract = {Plants produce organs of various shapes and sizes. While much has been learned about genetic regulation of organogenesis, the integration of mechanics in the process is also gaining attention. Here, we consider the role of forces as instructive signals in organ morphogenesis. Turgor pressure is the primary cause of mechanical signals in developing organs. Because plant cells are glued to each other, mechanical signals act, in essence, at multiple scales, through cell wall contiguity and water flux. In turn, cells use such signals to resist mechanical stress, for instance, by reinforcing their cell walls. We show that the three elemental shapes behind plant organs — spheres, cylinders and lamina — can be actively maintained by such a mechanical feedback. Combinations of this 3-letter alphabet can generate more complex shapes. Furthermore, mechanical conflicts emerge at the boundary between domains exhibiting different growth rates or directions. These secondary mechanical signals contribute to three other organ shape features — folds, shape reproducibility and growth arrest. The further integration of mechanical signals with the molecular network offers many fruitful prospects for the scientific community, including the role of proprioception in organ shape robustness or the definition of cell and organ identities as a result of an interplay between biochemical and mechanical signals.},
	number = {3},
	urldate = {2025-10-08},
	journal = {Current Biology},
	author = {Trinh, Duy-Chi and Alonso-Serra, Juan and Asaoka, Mariko and Colin, Leia and Cortes, Matthieu and Malivert, Alice and Takatani, Shogo and Zhao, Feng and Traas, Jan and Trehin, Christophe and Hamant, Olivier},
	month = feb,
	year = {2021},
	pages = {R143--R159},
}

Plants produce organs of various shapes and sizes. While much has been learned about genetic regulation of organogenesis, the integration of mechanics in the process is also gaining attention. Here, we consider the role of forces as instructive signals in organ morphogenesis. Turgor pressure is the primary cause of mechanical signals in developing organs. Because plant cells are glued to each other, mechanical signals act, in essence, at multiple scales, through cell wall contiguity and water flux. In turn, cells use such signals to resist mechanical stress, for instance, by reinforcing their cell walls. We show that the three elemental shapes behind plant organs — spheres, cylinders and lamina — can be actively maintained by such a mechanical feedback. Combinations of this 3-letter alphabet can generate more complex shapes. Furthermore, mechanical conflicts emerge at the boundary between domains exhibiting different growth rates or directions. These secondary mechanical signals contribute to three other organ shape features — folds, shape reproducibility and growth arrest. The further integration of mechanical signals with the molecular network offers many fruitful prospects for the scientific community, including the role of proprioception in organ shape robustness or the definition of cell and organ identities as a result of an interplay between biochemical and mechanical signals.

@article{fal_tissue_2021,
	title = {Tissue folding at the organ–meristem boundary results in nuclear compression and chromatin compaction},
	volume = {118},
	url = {https://www.pnas.org/doi/10.1073/pnas.2017859118},
	doi = {10.1073/pnas.2017859118},
	abstract = {Artificial mechanical perturbations affect chromatin in animal cells in culture. Whether this is also relevant to growing tissues in living organisms remains debated. In plants, aerial organ emergence occurs through localized outgrowth at the periphery of the shoot apical meristem, which also contains a stem cell niche. Interestingly, organ outgrowth has been proposed to generate compression in the saddle-shaped organ–meristem boundary domain. Yet whether such growth-induced mechanical stress affects chromatin in plant tissues is unknown. Here, by imaging the nuclear envelope in vivo over time and quantifying nucleus deformation, we demonstrate the presence of active nuclear compression in that domain. We developed a quantitative pipeline amenable to identifying a subset of very deformed nuclei deep in the boundary and in which nuclei become gradually narrower and more elongated as the cell contracts transversely. In this domain, we find that the number of chromocenters is reduced, as shown by chromatin staining and labeling, and that the expression of linker histone H1.3 is induced. As further evidence of the role of forces on chromatin changes, artificial compression with a MicroVice could induce the ectopic expression of H1.3 in the rest of the meristem. Furthermore, while the methylation status of chromatin was correlated with nucleus deformation at the meristem boundary, such correlation was lost in the h1.3 mutant. Altogether, we reveal that organogenesis in plants generates compression that is able to have global effects on chromatin in individual cells.},
	number = {8},
	urldate = {2025-10-08},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {Fal, Kateryna and Korsbo, Niklas and Alonso-Serra, Juan and Teles, Jose and Liu, Mengying and Refahi, Yassin and Chabouté, Marie-Edith and Jönsson, Henrik and Hamant, Olivier},
	month = feb,
	year = {2021},
	pages = {e2017859118},
}

Artificial mechanical perturbations affect chromatin in animal cells in culture. Whether this is also relevant to growing tissues in living organisms remains debated. In plants, aerial organ emergence occurs through localized outgrowth at the periphery of the shoot apical meristem, which also contains a stem cell niche. Interestingly, organ outgrowth has been proposed to generate compression in the saddle-shaped organ–meristem boundary domain. Yet whether such growth-induced mechanical stress affects chromatin in plant tissues is unknown. Here, by imaging the nuclear envelope in vivo over time and quantifying nucleus deformation, we demonstrate the presence of active nuclear compression in that domain. We developed a quantitative pipeline amenable to identifying a subset of very deformed nuclei deep in the boundary and in which nuclei become gradually narrower and more elongated as the cell contracts transversely. In this domain, we find that the number of chromocenters is reduced, as shown by chromatin staining and labeling, and that the expression of linker histone H1.3 is induced. As further evidence of the role of forces on chromatin changes, artificial compression with a MicroVice could induce the ectopic expression of H1.3 in the rest of the meristem. Furthermore, while the methylation status of chromatin was correlated with nucleus deformation at the meristem boundary, such correlation was lost in the h1.3 mutant. Altogether, we reveal that organogenesis in plants generates compression that is able to have global effects on chromatin in individual cells.

@article{alonso-serra_elimaki_2020,
	title = {{ELIMÄKI} {Locus} {Is} {Required} for {Vertical} {Proprioceptive} {Response} in {Birch} {Trees}},
	volume = {30},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982219316112},
	doi = {10.1016/j.cub.2019.12.016},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Alonso-Serra, Juan and Shi, Xueping and Peaucelle, Alexis and Rastas, Pasi and Bourdon, Matthieu and Immanen, Juha and Takahashi, Junko and Koivula, Hanna and Eswaran, Gugan and Muranen, Sampo and Help, Hanna and Smolander, Olli-Pekka and Su, Chang and Safronov, Omid and Gerber, Lorenz and Salojärvi, Jarkko and Hagqvist, Risto and Mähönen, Ari Pekka and Helariutta, Ykä and Nieminen, Kaisa},
	month = feb,
	year = {2020},
	pages = {589--599.e5},
}

@inproceedings{hyvonen_coded_2019,
	title = {Coded {Acoustic} {Microscopy} to {Study} {Wood} {Mechanics} and {Development}},
	issn = {1948-5727},
	url = {https://ieeexplore.ieee.org/document/8926285},
	doi = {10.1109/ULTSYM.2019.8926285},
	abstract = {We have developed a coded excitation scanning acoustic microscope (CESAM) that operates in range of 0.1 to 1 GHz. We used a focusing transducer with 375 MHz central frequency to image two different tree species (birch and hybrid aspen) at different stem height to study their micromechanical difference. The method was able to capture the fresh wood anatomy with cellular resolution. A full stem section scan revealed the heterogeneity of micromechanical properties throughout tissues, and highlighted the higher stiffness of the phloem fibers compared to other vascular cells. This demonstrates the applicability of the method for plant developmental biology.},
	urldate = {2025-10-08},
	booktitle = {2019 {IEEE} {International} {Ultrasonics} {Symposium} ({IUS})},
	author = {Hyvönen, Jere and Serra, Juan Alonso and Meriläinen, Antti and Help-Rinta-Rahko, Hanna and Nieminen, Kaisa and Salmi, Ari and Svedström, Kirsi and Helariutta, Yrjö and Haeggström, Edward},
	month = oct,
	year = {2019},
	keywords = {Acoustic impedance, Acoustic microscopy, Acoustics, Image resolution, Imaging, Impedance, Microscopy, Optical microscopy, Vegetation, Wood developmental biology},
	pages = {1989--1991},
}

We have developed a coded excitation scanning acoustic microscope (CESAM) that operates in range of 0.1 to 1 GHz. We used a focusing transducer with 375 MHz central frequency to image two different tree species (birch and hybrid aspen) at different stem height to study their micromechanical difference. The method was able to capture the fresh wood anatomy with cellular resolution. A full stem section scan revealed the heterogeneity of micromechanical properties throughout tissues, and highlighted the higher stiffness of the phloem fibers compared to other vascular cells. This demonstrates the applicability of the method for plant developmental biology.

@article{alonso-serra_tissue-specific_2019,
	title = {Tissue-specific study across the stem reveals the chemistry and transcriptome dynamics of birch bark},
	volume = {222},
	copyright = {© 2019 The Authors. New Phytologist © 2019 New Phytologist Trust},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.15725},
	doi = {10.1111/nph.15725},
	abstract = {Tree bark is a highly specialized array of tissues that plays important roles in plant protection and development. Bark tissues develop from two lateral meristems; the phellogen (cork cambium) produces the outermost stem–environment barrier called the periderm, while the vascular cambium contributes with phloem tissues. Although bark is diverse in terms of tissues, functions and species, it remains understudied at higher resolution. We dissected the stem of silver birch (Betula pendula) into eight major tissue types, and characterized these by a combined transcriptomics and metabolomics approach. We further analyzed the varying bark types within the Betulaceae family. The two meristems had a distinct contribution to the stem transcriptomic landscape. Furthermore, inter- and intraspecies analyses illustrated the unique molecular profile of the phellem. We identified multiple tissue-specific metabolic pathways, such as the mevalonate/betulin biosynthesis pathway, that displayed differential evolution within the Betulaceae. A detailed analysis of suberin and betulin biosynthesis pathways identified a set of underlying regulators and highlighted the important role of local, small-scale gene duplication events in the evolution of metabolic pathways. This work reveals the transcriptome and metabolic diversity among bark tissues and provides insights to its development and evolution, as well as its biotechnological applications.},
	language = {en},
	number = {4},
	urldate = {2025-10-08},
	journal = {New Phytologist},
	author = {Alonso-Serra, Juan and Safronov, Omid and Lim, Kean-Jin and Fraser-Miller, Sara J. and Blokhina, Olga B. and Campilho, Ana and Chong, Sun-Li and Fagerstedt, Kurt and Haavikko, Raisa and Helariutta, Ykä and Immanen, Juha and Kangasjärvi, Jaakko and Kauppila, Tiina J. and Lehtonen, Mari and Ragni, Laura and Rajaraman, Sitaram and Räsänen, Riikka-Marjaana and Safdari, Pezhman and Tenkanen, Maija and Yli-Kauhaluoma, Jari T. and Teeri, Teemu H. and Strachan, Clare J. and Nieminen, Kaisa and Salojärvi, Jarkko},
	year = {2019},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15725},
	keywords = {Betula pendula (silver birch), bark, cambium, genome evolution, metabolic pathways, periderm, phellem, phellogen},
	pages = {1816--1831},
}

Tree bark is a highly specialized array of tissues that plays important roles in plant protection and development. Bark tissues develop from two lateral meristems; the phellogen (cork cambium) produces the outermost stem–environment barrier called the periderm, while the vascular cambium contributes with phloem tissues. Although bark is diverse in terms of tissues, functions and species, it remains understudied at higher resolution. We dissected the stem of silver birch (Betula pendula) into eight major tissue types, and characterized these by a combined transcriptomics and metabolomics approach. We further analyzed the varying bark types within the Betulaceae family. The two meristems had a distinct contribution to the stem transcriptomic landscape. Furthermore, inter- and intraspecies analyses illustrated the unique molecular profile of the phellem. We identified multiple tissue-specific metabolic pathways, such as the mevalonate/betulin biosynthesis pathway, that displayed differential evolution within the Betulaceae. A detailed analysis of suberin and betulin biosynthesis pathways identified a set of underlying regulators and highlighted the important role of local, small-scale gene duplication events in the evolution of metabolic pathways. This work reveals the transcriptome and metabolic diversity among bark tissues and provides insights to its development and evolution, as well as its biotechnological applications.

@article{zhang_transcriptional_2019,
	title = {Transcriptional regulatory framework for vascular cambium development in {Arabidopsis} roots},
	volume = {5},
	copyright = {2019 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-019-0522-9},
	doi = {10.1038/s41477-019-0522-9},
	abstract = {Vascular cambium, a lateral plant meristem, is a central producer of woody biomass. Although a few transcription factors have been shown to regulate cambial activity1, the phenotypes of the corresponding loss-of-function mutants are relatively modest, highlighting our limited understanding of the underlying transcriptional regulation. Here, we use cambium cell-specific transcript profiling followed by a combination of transcription factor network and genetic analyses to identify 62 new transcription factor genotypes displaying an array of cambial phenotypes. This approach culminated in virtual loss of cambial activity when both WUSCHEL-RELATED HOMEOBOX 4 (WOX4) and KNOTTED-like from Arabidopsis thaliana 1 (KNAT1; also known as BREVIPEDICELLUS) were mutated, thereby unlocking the genetic redundancy in the regulation of cambium development. We also identified transcription factors with dual functions in cambial cell proliferation and xylem differentiation, including WOX4, SHORT VEGETATIVE PHASE (SVP) and PETAL LOSS (PTL). Using the transcription factor network information, we combined overexpression of the cambial activator WOX4 and removal of the putative inhibitor PTL to engineer Arabidopsis for enhanced radial growth. This line also showed ectopic cambial activity, thus further highlighting the central roles of WOX4 and PTL in cambium development.},
	language = {en},
	number = {10},
	urldate = {2025-10-08},
	journal = {Nature Plants},
	publisher = {Nature Publishing Group},
	author = {Zhang, Jing and Eswaran, Gugan and Alonso-Serra, Juan and Kucukoglu, Melis and Xiang, Jiale and Yang, Weibing and Elo, Annakaisa and Nieminen, Kaisa and Damén, Teddy and Joung, Je-Gun and Yun, Jae-Young and Lee, Jung-Hun and Ragni, Laura and Barbier de Reuille, Pierre and Ahnert, Sebastian E. and Lee, Ji-Young and Mähönen, Ari Pekka and Helariutta, Ykä},
	month = oct,
	year = {2019},
	keywords = {Plant development, Plant genetics},
	pages = {1033--1042},
}

Vascular cambium, a lateral plant meristem, is a central producer of woody biomass. Although a few transcription factors have been shown to regulate cambial activity1, the phenotypes of the corresponding loss-of-function mutants are relatively modest, highlighting our limited understanding of the underlying transcriptional regulation. Here, we use cambium cell-specific transcript profiling followed by a combination of transcription factor network and genetic analyses to identify 62 new transcription factor genotypes displaying an array of cambial phenotypes. This approach culminated in virtual loss of cambial activity when both WUSCHEL-RELATED HOMEOBOX 4 (WOX4) and KNOTTED-like from Arabidopsis thaliana 1 (KNAT1; also known as BREVIPEDICELLUS) were mutated, thereby unlocking the genetic redundancy in the regulation of cambium development. We also identified transcription factors with dual functions in cambial cell proliferation and xylem differentiation, including WOX4, SHORT VEGETATIVE PHASE (SVP) and PETAL LOSS (PTL). Using the transcription factor network information, we combined overexpression of the cambial activator WOX4 and removal of the putative inhibitor PTL to engineer Arabidopsis for enhanced radial growth. This line also showed ectopic cambial activity, thus further highlighting the central roles of WOX4 and PTL in cambium development.

@article{salojarvi_genome_2017,
	title = {Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch},
	volume = {49},
	issn = {1061-4036, 1546-1718},
	url = {http://www.nature.com/articles/ng.3862},
	doi = {10/f96grj},
	abstract = {Abstract
            
              Silver birch (
              Betula pendula
              ) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred
              B. pendula
              individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes
              PHYC
              and
              FRS10
              correlated with latitude and longitude and temperature, and with precipitation for
              PHYC
              . Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes
              KAK
              and
              MED5A
              .},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Nature Genetics},
	author = {Salojärvi, Jarkko and Smolander, Olli-Pekka and Nieminen, Kaisa and Rajaraman, Sitaram and Safronov, Omid and Safdari, Pezhman and Lamminmäki, Airi and Immanen, Juha and Lan, Tianying and Tanskanen, Jaakko and Rastas, Pasi and Amiryousefi, Ali and Jayaprakash, Balamuralikrishna and Kammonen, Juhana I and Hagqvist, Risto and Eswaran, Gugan and Ahonen, Viivi Helena and Serra, Juan Alonso and Asiegbu, Fred O and de Dios Barajas-Lopez, Juan and Blande, Daniel and Blokhina, Olga and Blomster, Tiina and Broholm, Suvi and Brosché, Mikael and Cui, Fuqiang and Dardick, Chris and Ehonen, Sanna E and Elomaa, Paula and Escamez, Sacha and Fagerstedt, Kurt V and Fujii, Hiroaki and Gauthier, Adrien and Gollan, Peter J and Halimaa, Pauliina and Heino, Pekka I and Himanen, Kristiina and Hollender, Courtney and Kangasjärvi, Saijaliisa and Kauppinen, Leila and Kelleher, Colin T and Kontunen-Soppela, Sari and Koskinen, J Patrik and Kovalchuk, Andriy and Kärenlampi, Sirpa O and Kärkönen, Anna K and Lim, Kean-Jin and Leppälä, Johanna and Macpherson, Lee and Mikola, Juha and Mouhu, Katriina and Mähönen, Ari Pekka and Niinemets, Ülo and Oksanen, Elina and Overmyer, Kirk and Palva, E Tapio and Pazouki, Leila and Pennanen, Ville and Puhakainen, Tuula and Poczai, Péter and Possen, Boy J H M and Punkkinen, Matleena and Rahikainen, Moona M and Rousi, Matti and Ruonala, Raili and van der Schoot, Christiaan and Shapiguzov, Alexey and Sierla, Maija and Sipilä, Timo P and Sutela, Suvi and Teeri, Teemu H and Tervahauta, Arja I and Vaattovaara, Aleksia and Vahala, Jorma and Vetchinnikova, Lidia and Welling, Annikki and Wrzaczek, Michael and Xu, Enjun and Paulin, Lars G and Schulman, Alan H and Lascoux, Martin and Albert, Victor A and Auvinen, Petri and Helariutta, Ykä and Kangasjärvi, Jaakko},
	month = jun,
	year = {2017},
	pages = {904--912},
}

Abstract Silver birch ( Betula pendula ) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC . Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A .

@article{fagerstedt_determining_2015,
	title = {Determining the {Composition} of {Lignins} in {Different} {Tissues} of {Silver} {Birch}},
	volume = {4},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/4/2/183},
	doi = {10.3390/plants4020183},
	abstract = {Quantitative and qualitative lignin analyses were carried out on material from the trunks of silver birch (Betula pendula Roth) trees. Two types of material were analyzed. First, whole birch trunk pieces were cryosectioned into cork cambium, non-conductive phloem, the cambial zone (conductive phloem, cambium and differentiating xylem), lignified xylem and the previous year’s xylem; material that would show differences in lignin amount and quality. Second, clonal material from one natural birch population was analyzed to show variations between individuals and between the lignin analysis methods. The different tissues showed marked differences in lignin amount and the syringyl:guaiacyl (S/G) ratio. In the non-conductive phloem tissue containing sclereids, the S/G ratio was very low, and typical for phloem fibers and in the newly-formed xylem, as well as in the previous year’s xylem, the ratio lay between five and seven, typical for broadleaf tree xylem. Clonal material consisting of 88 stems was used to calculate the S/G ratios from the thioacidolysis and CuO methods, which correlated positively with an R2 value of 0.43. Comparisons of the methods indicate clearly that the CuO method is a good alternative to study the monomeric composition and S/G ratio of wood lignins.},
	language = {en},
	number = {2},
	urldate = {2025-10-08},
	journal = {Plants},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Fagerstedt, Kurt V. and Saranpää, Pekka and Tapanila, Tarja and Immanen, Juha and Serra, Juan Antonio Alonso and Nieminen, Kaisa},
	month = jun,
	year = {2015},
	keywords = {\textit{Betula pendula}, acetyl bromide, cupric oxide, lignin analysis methods, phloem, thioacidolysis, xylem},
	pages = {183--195},
}

Quantitative and qualitative lignin analyses were carried out on material from the trunks of silver birch (Betula pendula Roth) trees. Two types of material were analyzed. First, whole birch trunk pieces were cryosectioned into cork cambium, non-conductive phloem, the cambial zone (conductive phloem, cambium and differentiating xylem), lignified xylem and the previous year’s xylem; material that would show differences in lignin amount and quality. Second, clonal material from one natural birch population was analyzed to show variations between individuals and between the lignin analysis methods. The different tissues showed marked differences in lignin amount and the syringyl:guaiacyl (S/G) ratio. In the non-conductive phloem tissue containing sclereids, the S/G ratio was very low, and typical for phloem fibers and in the newly-formed xylem, as well as in the previous year’s xylem, the ratio lay between five and seven, typical for broadleaf tree xylem. Clonal material consisting of 88 stems was used to calculate the S/G ratios from the thioacidolysis and CuO methods, which correlated positively with an R2 value of 0.43. Comparisons of the methods indicate clearly that the CuO method is a good alternative to study the monomeric composition and S/G ratio of wood lignins.

@article{zhang_wood_2015,
	title = {Wood development: {Growth} through knowledge},
	volume = {1},
	copyright = {2015 Macmillan Publishers Limited},
	issn = {2055-0278},
	shorttitle = {Wood development},
	url = {https://www.nature.com/articles/nplants201560},
	doi = {10.1038/nplants.2015.60},
	abstract = {Overexpressing a receptor–ligand pair specifically in their native tissue domains dramatically promotes wood formation and biomass production in trees.},
	language = {en},
	number = {5},
	urldate = {2025-10-08},
	journal = {Nature Plants},
	publisher = {Nature Publishing Group},
	author = {Zhang, Jing and Serra, Juan Antonio Alonso and Helariutta, Ykä},
	month = may,
	year = {2015},
	keywords = {Patterning, Plant biotechnology, Plant stem cell},
	pages = {15060},
}

Overexpressing a receptor–ligand pair specifically in their native tissue domains dramatically promotes wood formation and biomass production in trees.

@article{zhang_formation_2014,
	series = {Growth and development},
	title = {The formation of wood and its control},
	volume = {17},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526613001660},
	doi = {10.1016/j.pbi.2013.11.003},
	abstract = {Wood continues to increase in importance as a sustainable source of energy and shelter. Wood formation is a dynamic process derived from plant secondary (radial) growth. Several experimental systems have been employed to study wood formation and its regulation. The use of genetic manipulation approaches and genome-wide analyses in model plants have significantly advanced our understanding of wood formation. In this review, we provide an update of our knowledge of the genetic and hormonal regulation of wood formation based on research in different plants systems, as well as considering the subject from an evo-devo perspective.},
	urldate = {2025-10-08},
	journal = {Current Opinion in Plant Biology},
	author = {Zhang, Jing and Nieminen, Kaisa and Serra, Juan Antonio Alonso and Helariutta, Ykä},
	month = feb,
	year = {2014},
	pages = {56--63},
}

Wood continues to increase in importance as a sustainable source of energy and shelter. Wood formation is a dynamic process derived from plant secondary (radial) growth. Several experimental systems have been employed to study wood formation and its regulation. The use of genetic manipulation approaches and genome-wide analyses in model plants have significantly advanced our understanding of wood formation. In this review, we provide an update of our knowledge of the genetic and hormonal regulation of wood formation based on research in different plants systems, as well as considering the subject from an evo-devo perspective.