JGI Plant Gene Atlas: An updateable transcriptome resource to improve structural annotations and functional gene descriptions across the plant kingdom
Authors: Sreedasyam Avinash , Plott Christopher , Hossain Md Shakhawat , Lovell John T. , Grimwood Jane , Jenkins Jerry W. , Daum Christopher , Barry Kerrie , Carlson Joseph , Shu Shengqiang , Phillips Jeremy , Amirebrahimi Mojgan , Zane Matthew , Wang Mei , Goodstein David , Haas Fabian B. , Hiss Manuel , Perroud Pierre-François , Jawdy Sara S. , Hu Rongbin , Johnson Jenifer , Kropat Janette , Gallaher Sean D. , Lipzen Anna , Tillman Ryan , Shakirov Eugene V. , Weng Xiaoyu , Torres-Jerez Ivone , Weers Brock , Conde Daniel , Pappas Marilia R. , Liu Lifeng , Muchlinski Andrew , Jiang Hui , Shyu Christine , Huang Pu , Sebastian Jose , Laiben Carol , Medlin Alyssa , Carey Sankalpi , Carrell Alyssa A. , Perales Mariano , Swaminathan Kankshita , Allona Isabel , Grattapaglia Dario , Cooper Elizabeth A. , Tholl Dorothea , Vogel John P. , Weston David J , Yang Xiaohan , Brutnell Thomas P. , Kellogg Elizabeth A. , Baxter Ivan , Udvardi Michael , Tang Yuhong , Mockler Todd C. , Juenger Thomas E. , Mullet John , Rensing Stefan A. , Tuskan Gerald A. , Merchant Sabeeha S. , Stacey Gary , Schmutz Jeremy 
Published: October 2022

Gene functional descriptions, which are typically derived from sequence similarity to experimentally validated genes in a handful of model species, offer a crucial line of evidence when searching for candidate genes that underlie trait variation. Plant responses to environmental cues, including gene expression regulatory variation, represent important resources for understanding gene function and crucial targets for plant improvement through gene editing and other biotechnologies. However, even after years of effort and numerous large-scale functional characterization studies, biological roles of large proportions of protein coding genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, a public and updateable data resource consisting of transcript abundance assays from 2,090 samples derived from 604 tissues or conditions across 18 diverse species. We integrated across these diverse conditions and genotypes by analyzing expression profiles, building gene clusters that exhibited tissue/condition specific expression, and testing for transcriptional modulation in response to environmental queues. For example, we discovered extensive phylogenetically constrained and condition-specific expression profiles across many gene families and genes without any functional annotation. Such conserved expression patterns and other tightly co-expressed gene clusters let us assign expression derived functional descriptions to 64,620 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome-next.jgi.doe.gov), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.