Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

Authors: TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory; NAITHANI, SUSHMA - Oregon State University; GUPTA, PARUL - Oregon State University; OLSON, ANDREW - Cold Spring Harbor Laboratory; WEI, SHARON - Cold Spring Harbor Laboratory; PREECE, JUSTIN - Oregon State University; JIAO, YINPING - Cold Spring Harbor Laboratory; WANG, BO - Cold Spring Harbor Laboratory; CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory; GARG, PRIYANKA - Oregon State University; ELSER, JUSTIN - Oregon State University; KUMARI, SUNITA - Cold Spring Harbor Laboratory; KUMAR, VIVEK - Cold Spring Harbor Laboratory; CONTRERAS-MOREIRA, BRUNO - Embl-Ebi; NAAMATI, GUY - Embl-Ebi; GEORGE, NANCY - Embl-Ebi; COOK, JUSTIN - Ontario Cancer Institute; BOLSER, DANIEL - Embl-Ebi; D'EUSTACHIO, PETER - New York University School Of Medicine; STEIN, LINCOLN - University Of Toronto; GUPTA, AMIT - University Of Texas At Austin; XU, WEIJA - University Of Texas At Austin; REGALA, JENNIFER - American Society Of Plant Biologists; PAPATHEODOROU, IRENE - Embl-Ebi; KERSEY, PAUL - Embl-Ebi; FLICEK, PAUL - Embl-Ebi; TAYLOR, CRISPIN - American Society Of Plant Biologists; JAISWAL, PANKAJ - Oregon State University; Ware, Doreen

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/9/2020
Publication Date: 11/10/2020
Citation: Tello-Ruiz, M.K., Naithani, S., Gupta, P., Olson, A., Wei, S., Preece, J., Jiao, Y., Wang, B., Chougule, K., Garg, P., Elser, J., Kumari, S., Kumar, V., Contreras-Moreira, B., Naamati, G., George, N., Cook, J., Bolser, D.M., D'Eustachio, P., Stein, L.D., Gupta, A., Xu, W., Regala, J., Papatheodorou, I., Kersey, P.J., Flicek, P., Taylor, C., Jaiswal, P., Ware, D. 2020. Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Research. 49:D1452-D1463. https://doi.org/10.1093/nar/gkaa979.
DOI: https://doi.org/10.1093/nar/gkaa979

Interpretive Summary: Gramene is an internet resource for plant researchers to study and compare the physical, genetic, and functional properties of genes, proteins, markers, and biological pathways in diverse crops and model plants. Data is available at the Gramene website (http://www.gramene.org) via graphical interfaces (genome and pathway browsers), customizable dumps (GrameneMart), and bulk downloads (FTP server); in addition to various analysis tools. Data release #63 includes the complete genome sequence and corresponding gene annotation for 93 reference genomes, including Arabidopsis, rice, maize, wheat, sorghum, barley, Brachypodium, grape, cotton, tomato, banana, and apple. The total number of genes exceeds 3.9 million, and they are grouped in 122,947 families. Gramene's pathways portal is called Plant Reactome, and it provides 320 manually curated rice pathways projected to another 106 plant species. Together, the data hosted at the Gramene website, serve as a reference resource for comparative analyses for plant researchers and breeders, and supports basic and translational research, which impact societal interests including food security, bioenergy production, and climate change.

Technical Abstract: Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases; doubled the genome portal's content; expanded curated genes, pathways and expression sets; and implemented the Domain Informational Vocabulary Extraction (DIVE) algorithm for extracting gene function information from publications. The current release, #63 (October 2020), hosts 93 reference genomes-over 3.9 million genes in 122 947 families with orthologous and paralogous classifications. Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species. The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of gene-gene interactions. Gramene integrates ontology-based protein structure-function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused journals using DIVE. We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome.