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

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dc.contributor.authorSreedasyam, Avinashen
dc.contributor.authorPlott, Christopheren
dc.contributor.authorHossain, Md Shakhawaten
dc.contributor.authorLovell, John T.en
dc.contributor.authorGrimwood, Janeen
dc.contributor.authorJenkins, Jerry W.en
dc.contributor.authorDaum, Christopheren
dc.contributor.authorBarry, Kerrieen
dc.contributor.authorCarlson, Josephen
dc.contributor.authorShu, Shengqiangen
dc.contributor.authorPhillips, Jeremyen
dc.contributor.authorAmirebrahimi, Mojganen
dc.contributor.authorZane, Matthewen
dc.contributor.authorWang, Meien
dc.contributor.authorGoodstein, Daviden
dc.contributor.authorHaas, Fabian B.en
dc.contributor.authorHiss, Manuelen
dc.contributor.authorPerroud, Pierre-Francoisen
dc.contributor.authorJawdy, Sara S.en
dc.contributor.authorYang, Yongilen
dc.contributor.authorHu, Rongbinen
dc.contributor.authorJohnson, Jeniferen
dc.contributor.authorKropat, Janetteen
dc.contributor.authorGallaher, Sean D.en
dc.contributor.authorLipzen, Annaen
dc.contributor.authorShakirov, Eugeneen
dc.contributor.authorWeng, Xiaoyuen
dc.contributor.authorTorres-Jerez, Ivoneen
dc.contributor.authorWeers, Brocken
dc.contributor.authorConde, Danielen
dc.contributor.authorPappas, Marilia R.en
dc.contributor.authorLiu, Lifengen
dc.contributor.authorMuchlinski, Andrewen
dc.contributor.authorJiang, Huien
dc.contributor.authorShyu, Christineen
dc.contributor.authorHuang, Puen
dc.contributor.authorSebastian, Joseen
dc.contributor.authorLaiben, Carolen
dc.contributor.authorMedlin, Alyssaen
dc.contributor.authorCarey, Sankalpien
dc.contributor.authorCarrell, Alyssa A.en
dc.contributor.authorChen, Jin-Guien
dc.contributor.authorPerales, Marianoen
dc.contributor.authorSwaminathan, Kankshitaen
dc.contributor.authorAllona, Isabelen
dc.contributor.authorGrattapaglia, Darioen
dc.contributor.authorCooper, Elizabeth A.en
dc.contributor.authorTholl, Dorotheaen
dc.contributor.authorVogel, John P.en
dc.contributor.authorWeston, David J.en
dc.contributor.authorYang, Xiaohanen
dc.contributor.authorBrutnell, Thomas P.en
dc.contributor.authorKellogg, Elizabeth A.en
dc.contributor.authorBaxter, Ivanen
dc.contributor.authorUdvardi, Michaelen
dc.contributor.authorTang, Yuhongen
dc.contributor.authorMockler, Todd C.en
dc.contributor.authorJuenger, Thomas E.en
dc.contributor.authorMullet, Johnen
dc.contributor.authorRensing, Stefan A.en
dc.contributor.authorTuskan, Gerald A.en
dc.contributor.authorMerchant, Sabeeha S.en
dc.contributor.authorStacey, Garyen
dc.contributor.authorSchmutz, Jeremyen
dc.date.accessioned2024-02-09T13:22:01Zen
dc.date.available2024-02-09T13:22:01Zen
dc.date.issued2023-08-01en
dc.description.abstractGene 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.en
dc.description.versionPublished versionen
dc.format.extentPages 8383-8401en
dc.format.extent19 page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/nar/gkad616en
dc.identifier.eissn1362-4962en
dc.identifier.issn0305-1048en
dc.identifier.issue16en
dc.identifier.orcidTholl, Dorothea [0000-0003-2636-6345]en
dc.identifier.other7234521 (PII)en
dc.identifier.pmid37526283en
dc.identifier.urihttps://hdl.handle.net/10919/117905en
dc.identifier.volume51en
dc.language.isoenen
dc.publisherOxford University Pressen
dc.relation.urihttps://www.ncbi.nlm.nih.gov/pubmed/37526283en
dc.rightsCreative Commons Attribution-NonCommercial 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/en
dc.subject.meshPhylogenyen
dc.subject.meshGene Expression Regulation, Planten
dc.subject.meshGenes, Planten
dc.subject.meshGenome, Planten
dc.subject.meshSoftwareen
dc.subject.meshAtlases as Topicen
dc.subject.meshTranscriptomeen
dc.titleJGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdomen
dc.title.serialNucleic Acids Researchen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherArticleen
dc.type.otherJournalen
dcterms.dateAccepted2023-07-11en
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Scienceen
pubs.organisational-group/Virginia Tech/Science/Biological Sciencesen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Science/COS T&R Facultyen

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