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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 #337632
Title: Gramene database: navigating plant comparative genomics resources

Author
item GUPTA, PARUL - Oregon State University
item NAITHANI, SUSHMA - Oregon State University
item TELLO-RUIZ, MARCELA KAREY - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item D'EUSTACHIO, PETER - New York University School Of Medicine
item FABREGAT, ANTONIO - European Molecular Biology Laboratory
item JIAO, JINPING - Cold Spring Harbor Laboratory
item KEAYS, MARIA - European Molecular Biology Laboratory
item LEE, YOUNG KOUNG - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item MULVANEY, JOSEPH - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item PREECE, JUSTIN - Oregon State University
item STEIN, JOSHUA - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item WEISER, JOEL - European Molecular Biology Laboratory
item HUERTA, LAURA - European Molecular Biology Laboratory
item PETRYSZAK, ROBERT - European Molecular Biology Laboratory
item KERSEY, PAUL - European Molecular Biology Laboratory
item STEIN, LINCOLN - Ontario Cancer Institute
item Ware, Doreen
item JAISWAL, PANKAJ - Oregon State University

Submitted to: Current Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/10/2016
Publication Date: 12/14/2016
Citation: Gupta, P., Naithani, S., Tello-Ruiz, M., Chougule, K., D'Eustachio, P., Fabregat, A., Jiao, J., Keays, M., Lee, Y., Kumari, S., Mulvaney, J., Olson, A., Preece, J., Stein, J., Wei, S., Weiser, J., Huerta, L., Petryszak, R., Kersey, P., Stein, L., Ware, D., Jaiswal, P. 2016. Gramene database: navigating plant comparative genomics resources. Current Biology. DOI: 10.1016/j.cpb.2016.12.005.

Interpretive Summary: Gramene (http://www.gramene.org) is an internet resource designed to support researchers working with plant genomics data, performing plant breeding, evolutionary biology, system biology, and metabolic engineering. Data release #52 includes the complete genome sequence for 44 plant reference genome assemblies, including Arabidopsis, rice and maize, wheat, sorghum, barley, potato, tomato, banana, grape, peach, and sugar beet. In addition, the website provides databases of curated pathways (i.e., a series of chemical reactions that are important in the maintenance of a stable environment for a living organism) for rice and homology-based pathway projections for an additional 66 plant species. Together the plant data hosted at the Gramene website, serve as a reference resource for comparative analyses, for the broad scientific community, in support of basic and translational research, which impact societal interests in food security, energy production, and climate change.

Technical Abstract: Gramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationships to enrich the annotation of genomic data and provides tools to perform powerful comparative analyses across a wide spectrum of plant species. It consists of an integrated portal for querying, visualizing and analyzing data for 44 plant reference genomes, genetic variation data sets for 12 species, expression data for 16 species, curated rice pathways and orthology-based pathway projections for 66 plant species including various crops. Here we briefly describe the functions and uses of the Gramene database.