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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 #327938

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

Location: Plant, Soil and Nutrition Research

Title: Gramene 2016: comparative plant genomics and pathway resources

item TELLO-RUIZ, M. - Cold Spring Harbor Laboratory
item STEIN, J. - Cold Spring Harbor Laboratory
item WEI, S. - Cold Spring Harbor Laboratory
item PREECE, J. - Oregon State University
item OLSON, A. - Cold Spring Harbor Laboratory
item NAITHANI, S. - Cold Spring Harbor Laboratory
item AMARASHINGHE, V. - Oregon State University
item DHARMAWARDHANA, P. - Oregon State University
item JIAO, Y. - Cold Spring Harbor Laboratory
item MULVANEY, J. - Cold Spring Harbor Laboratory
item KUMARI, S. - Cold Spring Harbor Laboratory
item CHOUGULE, K. - Cold Spring Harbor Laboratory
item ELSER, J. - Ontario Cancer Institute
item WANG, B. - Cold Spring Harbor Laboratory
item THOMASON, J. - Cold Spring Harbor Laboratory
item BOLSER, DM. - European Bioinformatics Institute
item KERHORNOU, A. - European Bioinformatics Institute
item WALTS, B. - European Bioinformatics Institute
item FONSECA, NA. - European Bioinformatics Institute
item HUERTA, L. - European Bioinformatics Institute
item KEAYS, M. - European Bioinformatics Institute
item TANG, YA. - European Bioinformatics Institute
item PARKINSON, H. - European Bioinformatics Institute
item FABREGAT, A. - European Bioinformatics Institute
item MCKAY, S. - Ontario Cancer Institute
item WEISER, J. - Ontario Cancer Institute
item D'EUSTACHIO, P. - New York University School Of Medicine
item STEIN, L. - Ontario Cancer Institute
item PETRYSZAK, R. - European Bioinformatics Institute
item KERSEY, PJ. - European Bioinformatics Institute
item JAISWAL, P. - Oregon State University
item Ware, Doreen

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/1/2015
Publication Date: 11/8/2015
Citation: Tello-Ruiz, M., Stein, J., Wei, S., Preece, J., Olson, A., Naithani, S., Amarashinghe, V., Dharmawardhana, P., Jiao, Y., Mulvaney, J., Kumari, S., Chougule, K., Elser, J., Wang, B., Thomason, J., Bolser, D., Kerhornou, A., Walts, B., Fonseca, N., Huerta, L., Keays, M., Tang, Y., Parkinson, H., Fabregat, A., Mckay, S., Weiser, J., D'Eustachio, P., Stein, L., Petryszak, R., Kersey, P., Jaiswal, P., Ware, D. 2015. Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Research. doi: 10.1093/nar/gkv1179.

Interpretive Summary: Gramene ( is an internet resource for plant researchers to study the physical location, functional properties, and evolution 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 #47 includes the complete genome sequence for 39 reference genomes, including Arabidopsis, rice and maize, wheat, sorghum, barley, Amborella, potato, tomato, banana, grape and peach. 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 ( is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal ( provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ~200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI’s Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene’s archive website ( continues to provide previously reported resources on comparative maps, markers, and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials.