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

The functional description of genes is crucial to evidence candidate genes to determine trait variation in plant species. Gene expression response to environmental signals is an essential resource to decipher its function. Here, we developed a visualization and analysis tool consisting of transcriptomic assays spanning 18 species. Expression profiles were analyzed, genes were grouped based on their tissue/condition-specific expression, and transcriptional changes under different environmental signals were analyzed. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. These conserved expression patterns and clusters of strongly co-expressed genes allow us to assign additional biological information to thousands of genes with otherwise unknown functions. This resource is available in the JGI Plant Gene Atlas and Phytozome. These web tools allow users to access expression profiles, track orthologs, graph co-expressed genes, and visualize their ontology and pathways.


Original Paper:

Sreedasyam, A., Plott, C., Hossain, M.S., Lovell, J.T., Grimwood, J., Jenkins, J.W., Daum, C., Barry, K., Carlson, J., Shu, S., Phillips, J., Amirebrahimi, M., Zane, M., Wang, M., Goodstein, D., Haas, F.B., Hiss, M., Perroud, P.-F., Jawdy, S.S., Yang, Y., Hu, R., Johnson, J., Kropat, J., Gallaher, S.D., Lipzen, A., Shakirov, E.V., Weng, X., Torres-Jerez, I., Weers, B., Conde, D., Pappas, M.R., Liu, L., Muchlinski, A., Jiang, H., Shyu, C., Huang, P., Sebastian, J., Laiben, C., Medlin, A., Carey, S., Carrell, A.A., Chen, J.-G., Perales, M., Swaminathan, K., Allona, I., Grattapaglia, D., Cooper, E.A., Tholl, D., Vogel, J.P., Weston, D.J., Yang, X., Brutnell, T.P., Kellogg, E.A., Baxter, I., Udvardi, M., Tang, Y., Mockler, T.C., Juenger, T.E., Mullet, J., Rensing, S.A., Tuskan, G.A., Merchant, S.S., Stacey, G., Schmutz, J. 2023. JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom. Nucleic Acids Research 51, 8383–8401. DOI: 10.1093/nar/gkad616