JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

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

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 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.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.

Original languageEnglish
Pages (from-to)8383-8401
Number of pages19
JournalNucleic acids research
Volume51
Issue number16
DOIs
StatePublished - Sep 8 2023

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