Skip to main content
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 #300535

Research Project: Enhancing Plant Genome Function Maps Through Genomic, Genetic, Computational and Collaborative Research

Location: Plant, Soil and Nutrition Research

Title: Gramene 2013: Comparative plant genomics resources

Author
item MONACO, MARCELA - Cold Spring Harbor Laboratory
item STEIN, JOSHUA - Cold Spring Harbor Laboratory
item NAITHANI, SUSHMA - Oregon State University
item WEI, SHARON - Cold Spring Harbor Laboratory
item DHARMAWARDHANA, PALITHA - Oregon State University
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item AMARASINGHE, VINDHYA - Oregon State University
item YOUENS-CLARK, KEN - Cold Spring Harbor Laboratory
item THOMASON, JAMES - Cold Spring Harbor Laboratory
item PREECE, JUSTIN - Oregon State University
item PASTERNAK, SHIRAN - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item JIAO, YINPING - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item BOLSER, DAN - Cold Spring Harbor Laboratory
item KERHORNOU, ARNAUD - European Bioinformatics Institute
item STAINES, DAN - European Bioinformatics Institute
item WATTS, BRANDON - European Bioinformatics Institute
item WU, GUANMING - Ontario Cancer Institute
item D'EUSTACHIO, PETER - New York University School Of Medicine
item HAW, ROBIN - Ontario Cancer Institute
item CROFT, DAVID - European Bioinformatics Institute
item KERSEY, PAUL - European Biological Control Laboratory (EBCL)
item STEIN, LINCOLN - Ontario Cancer Institute
item JAISWAL, PANKAJ - Oregon State University
item Ware, Doreen

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/21/2013
Publication Date: 1/2/2014
Publication URL: http://DOI: 10.1093/nar/gkt1110
Citation: Monaco, M.K., Stein, J., Naithani, S., Wei, S., Dharmawardhana, P., Kumari, S., Amarasinghe, V., Youens-Clark, K., Thomason, J., Preece, J., Pasternak, S., Olson, A., Jiao, Y., Lu, Z., Bolser, D., Kerhornou, A., Staines, D., Watts, B., Wu, G., D'Eustachio, P., Haw, R., Croft, D., Kersey, P., Stein, L., Jaiswal, P., Ware, D. 2014. Gramene 2013: Comparative plant genomics resources. Nucleic Acids Research. 42:D1193-D1199.

Interpretive Summary: Gramene (http://www.gramene.org) is an internet resource for plant researchers to study the location, functional properties, and evolutionary history of genes, proteins, and genetic markers of diversity across crops and model plants. Data available at the Gramene website also include biological pathways, i.e., how the above interact with one another and with the environment to control the appearance and function of a plant. This wealth of data is provided in graphical interfaces (genome browser), customizable dumps (GrameneMart), and bulk downloads (FTP server). Data release #38 includes the complete genome sequence for 27 reference genomes, including Arabidopsis, rice and maize, sorghum, barley, tomato, potato, banana, and grape, as well as the partial sequence of 10 distinct varieties of wild rices. In addition, the website provides databases of pathways (i.e., a series of chemical reactions that are important in the maintenance of a stable environment for a living organism) for 10 plant species. Recently, a new pathways portal called the Plant Reactome was incorporated into Gramene for pathways created by manual curation of the published literature or derived by computationally projecting already curated pathways in other 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 a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. Whole-genome alignments complemented by phylogenetic gene family trees help infer syntenic and orthologous relationships. Genetic variation data, sequences and genome mappings available for 10 species, including Arabidopsis, rice and maize, help infer putative variant effects on genes and transcripts. The pathways section also hosts 10 species-specific metabolic pathways databases developed in-house or by our collaborators using Pathway Tools software, which facilitates searches for pathway, reaction and metabolite annotations, and allows analyses of user-defined expression datasets. Recently, we released a Plant Reactome portal featuring 133 curated rice pathways. This portal will be expanded for Arabidopsis, maize and other plant species. We continue to provide genetic and QTL maps and marker datasets developed by crop researchers. The project provides a unique community platform to support scientific research in plant genomics including studies in evolution, genetics, plant breeding, molecular biology, biochemistry and systems biology.