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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #382815

Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

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

Author
item TELLO-RUIZ, MARCELA - COLD SPRING HARBOR LABORATORY
item NAITHANI, SUSHMA - OREGON STATE UNIVERSITY
item GUPTA, PARUL - OREGON STATE UNIVERSITY
item OLSON, ANDREW - COLD SPRING HARBOR LABORATORY
item WEI, SHARON - COLD SPRING HARBOR LABORATORY
item PREECE, JUSTIN - OREGON STATE UNIVERSITY
item JIAO, YINPING - COLD SPRING HARBOR LABORATORY
item WANG, BO - COLD SPRING HARBOR LABORATORY
item CHOUGULE, KAPEEL - COLD SPRING HARBOR LABORATORY
item GARG, PRIYANKA - OREGON STATE UNIVERSITY
item ELSER, JUSTIN - OREGON STATE UNIVERSITY
item KUMARI, SUNITA - COLD SPRING HARBOR LABORATORY
item KUMAR, VIVEK - COLD SPRING HARBOR LABORATORY
item CONTRERAS-MOREIRA, BRUNO - EMBL-EBI
item NAAMATI, GUY - EMBL-EBI
item GEORGE, NANCY - EMBL-EBI
item COOK, JUSTIN - ONTARIO CANCER INSTITUTE
item BOLSER, DANIEL - EMBL-EBI
item D'EUSTACHIO, PETER - NEW YORK UNIVERSITY SCHOOL OF MEDICINE
item STEIN, LINCOLN - UNIVERSITY OF TORONTO
item GUPTA, AMIT - UNIVERSITY OF TEXAS AT AUSTIN
item XU, WEIJA - UNIVERSITY OF TEXAS AT AUSTIN
item REGALA, JENNIFER - AMERICAN SOCIETY OF PLANT BIOLOGISTS
item PAPATHEODOROU, IRENE - EMBL-EBI
item KERSEY, PAUL - EMBL-EBI
item FLICEK, PAUL - EMBL-EBI
item TAYLOR, CRISPIN - AMERICAN SOCIETY OF PLANT BIOLOGISTS
item JAISWAL, PANKAJ - OREGON STATE UNIVERSITY
item 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.