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 language | English |
|---|---|
| Pages (from-to) | 8383-8401 |
| Number of pages | 19 |
| Journal | Nucleic Acids Research |
| Volume | 51 |
| Issue number | 16 |
| DOIs | |
| State | Published - Sep 8 2023 |
Funding
The work (proposal: 10.46936/10.25585/60000843) conducted by the U.S. Department of Energy Joint Genome Institute ( https://ror.org/04xm1d337 ); a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; the Populus work was partially supported by the BioEnergy Science Center (BESC) and Center for Bioenergy Innovation (CBI); BESC and CBI are Bioenergy Research Centers supported by the Office of Biological and Environmental Research in the US Department of Energy Office of Science; specific funding for the soybean transcriptome atlas was provided by a grant from the United Soybean Board (to G.S.); the switchgrass work was carried out under the support of the BioEnergy Science Center (BESC, a U.S. Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science, U.S. Department of Energy) and funded by the Samuel Roberts Noble Foundation; B.H. work was funded in part by U.S. DOE the Office of Biological and Environmental Research [DE-SC0012629[; the Chlamydomonas work is supported by the US Department of Energy Grant [DE-FC02-02ER63421]; National Institutes of Health (NIH) [R24 GM092473 to S.S.M.]; the Eucalyptus work was supported by the Brazilian Federal District Research Foundation (FAP-DF) NEXTREE grant; the Panicum hallii work was supported by the DOE Office of Science, Office of Biological and Environmental Research (BER) [DE-SC0008451, DE-SC0021126 to T.E.J.]; the sorghum work by JM laboratory was funded in part by the DOE Great Lakes Bioenergy Research Center [DOE BER grant DE-SC0018409]; the Setaria work was funded by the DOE Office of Science [DE-SC0018277, DE-SC0008769]; the Kalanchoë work was partially supported by the DOE Office of Science, Genomic Science Program [DE-SC0008834]; research related to Sphagnum was funded by DOE BER Early Career Research Program; Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the US DOE [DE-AC05-00OR22725]. Funding for open access charge: Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231].