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

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.; Yang, Yongil; Hu, Rongbin; Johnson, Jenifer; Kropat, Janette; Gallaher, Sean D.; Lipzen, Anna; 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.; Chen, Jin-Gui; 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

doi:10.1093/nar/gkad616

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

Journal Article · Tue Aug 01 00:00:00 EDT 2023 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkad616· OSTI ID:1993322

;

; Hossain, Md Shakhawat; Lovell, John T.;

; Jenkins, Jerry W.; Daum, Christopher; Barry, Kerrie; Carlson, Joseph;

; Phillips, Jeremy; Amirebrahimi, Mojgan; Zane, Matthew; Wang, Mei; Goodstein, David;

; Hiss, Manuel;

; Jawdy, Sara S.; Yang, Yongil more »

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.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Donald Danforth Plant Science Center, St. Louis, MO (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; SC0012629; FC02-02ER63421; SC0008451; SC0021126; SC0018277; SC0008769; SC0018409; SC0008834; AC05-00OR22725

OSTI ID:: 1993322

Alternate ID(s):: OSTI ID: 1995662; OSTI ID: 2305737; OSTI ID: 2310928

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Vol. 51 Journal Issue: 16; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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