@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{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{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{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.

@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{mcevoy_strategies_2022,
	title = {Strategies of tolerance reflected in two {North} {American} maple genomes},
	volume = {109},
	copyright = {© 2021 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.15657},
	doi = {10.1111/tpj.15657},
	abstract = {Maples (the genus Acer) represent important and beloved forest, urban, and ornamental trees distributed throughout the Northern hemisphere. They exist in a diverse array of native ranges and distributions, across spectrums of tolerance or decline, and have varying levels of susceptibility to biotic and abiotic stress. Among Acer species, several stand out in their importance to economic interest. Here we report the first two chromosome-scale genomes for North American species, Acer negundo and Acer saccharum. Both assembled genomes contain scaffolds corresponding to 13 chromosomes, with A. negundo at a length of 442 Mb, an N50 of 32 Mb, and 30 491 genes, and A. saccharum at a length of 626 Mb, an N50 of 46 Mb, and 40 074 genes. No recent whole genome duplications were detected, though A. saccharum has local gene duplication and more recent bursts of transposable elements, as well as a large-scale translocation between two chromosomes. Genomic comparison revealed that A. negundo has a smaller genome with recent gene family evolution that is predominantly contracted and expansions that are potentially related to invasive tendencies and tolerance to abiotic stress. Examination of RNA sequencing data obtained from A. saccharum given long-term aluminum and calcium soil treatments at the Hubbard Brook Experimental Forest provided insights into genes involved in the aluminum stress response at the systemic level, as well as signs of compromised processes upon calcium deficiency, a condition contributing to maple decline.},
	language = {de},
	number = {6},
	urldate = {2026-01-16},
	journal = {The Plant Journal},
	author = {McEvoy, Susan L. and Sezen, U. Uzay and Trouern-Trend, Alexander and McMahon, Sean M. and Schaberg, Paul G. and Yang, Jie and Wegrzyn, Jill L. and Swenson, Nathan G.},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.15657},
	keywords = {Acer negundo, Acer saccharum, abiotic stress, aluminum, calcium, differential expression, genome, nutrient stress, plasticity, tolerance},
	pages = {1591--1613},
}

Maples (the genus Acer) represent important and beloved forest, urban, and ornamental trees distributed throughout the Northern hemisphere. They exist in a diverse array of native ranges and distributions, across spectrums of tolerance or decline, and have varying levels of susceptibility to biotic and abiotic stress. Among Acer species, several stand out in their importance to economic interest. Here we report the first two chromosome-scale genomes for North American species, Acer negundo and Acer saccharum. Both assembled genomes contain scaffolds corresponding to 13 chromosomes, with A. negundo at a length of 442 Mb, an N50 of 32 Mb, and 30 491 genes, and A. saccharum at a length of 626 Mb, an N50 of 46 Mb, and 40 074 genes. No recent whole genome duplications were detected, though A. saccharum has local gene duplication and more recent bursts of transposable elements, as well as a large-scale translocation between two chromosomes. Genomic comparison revealed that A. negundo has a smaller genome with recent gene family evolution that is predominantly contracted and expansions that are potentially related to invasive tendencies and tolerance to abiotic stress. Examination of RNA sequencing data obtained from A. saccharum given long-term aluminum and calcium soil treatments at the Hubbard Brook Experimental Forest provided insights into genes involved in the aluminum stress response at the systemic level, as well as signs of compromised processes upon calcium deficiency, a condition contributing to maple decline.