Dataset Information

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

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.

SUBMITTER: Sreedasyam A

PROVIDER: S-EPMC10484672 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

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

Nucleic acids research 20230901 16

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 resou ...[more]

PMID: 37526283

Similar Datasets

Project description:Our current understanding of plant viruses stems largely from those affecting economically important plants. Yet plant species in cultivation represent a small and biased subset of the plant kingdom. Here, we describe virus diversity and abundance in 1,079 transcriptomes from species across the breadth of the plant kingdom (Archaeplastida) by analyzing open-source data from the 1000 Plant Transcriptomes Initiative (1KP). We identified 104 potentially novel viruses, of which 40% were single-stranded positive-sense RNA viruses across eight orders, including members of the Hepelivirales, Tymovirales, Cryppavirales, Martellivirales, and Picornavirales. One-third of the newly described viruses were double-stranded RNA viruses from the orders Durnavirales and Ghabrivirales. The remaining were negative-sense RNA viruses from the Rhabdoviridae, Aspiviridae, Yueviridae, and Phenuiviridae and the newly proposed Viridisbunyaviridae. Our analysis considerably expands the known host range of 13 virus families to include lower plants (e.g., Benyviridae and Secoviridae) and 4 virus families to include alga hosts (e.g., Tymoviridae and Chrysoviridae). More broadly, however, a cophylogeny analysis revealed that the evolutionary history of these families is largely driven by cross-species transmission events. The discovery of the first 30-kDa movement protein in a nonvascular plant suggests that the acquisition of plant virus movement proteins occurred prior to the emergence of the plant vascular system. Together, these data highlight that numerous RNA virus families are associated with older evolutionary plant lineages than previously thought and that the apparent scarcity of RNA viruses found in lower plants likely reflects a lack of investigation rather than their absence. IMPORTANCE Our knowledge of plant viruses is mainly limited to those infecting economically important host species. In particular, we know little about those viruses infecting basal plant lineages such as the ferns, lycophytes, bryophytes, and charophytes. To expand this understanding, we conducted a broad-scale viral survey of species across the breadth of the plant kingdom. We found that basal plants harbor a wide diversity of RNA viruses, including some that are sufficiently divergent to likely compose a new virus family. The basal plant virome revealed offers key insights into the evolutionary history of core plant virus gene modules and genome segments. More broadly, this work emphasizes that the scarcity of viruses found in these species to date most likely reflects the limited research in this area.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets