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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 #217782
Title: Gramene: a growing plant comparative genomics resource

Author
item JAISWAL, PANKAJ - CORNELL UNIVERSITY
item AVRAHAM, SHULAMIT - COLD SPRINGS HARBOR LAB
item Buckler, Edward - Ed
item CASSTEVENS, TERRY - CORNELL UNIVERSITY
item HEBBARD, CLAIRE - CORNELL UNIVERSITY
item LIANG, CHENGZHI - COLD SPRINGS HARBOR LAB
item NI, JUNJIAN - CORNELL UNIVERSITY
item RAVENSCROFT, DEAN - CORNELL UNIVERSITY
item REN, LIYA - COLD SPRINGS HARBOR LAB
item STEIN, LINCOLN - COLD SPRINGS HARBOR LAB
item SPOONER, WILLIAM - COLD SPRINGS HARBOR LAB
item TECLE, ISAAK - CORNELL UNIVERSITY
item THOMASON, JIM - COLD SPRINGS HARBOR LAB
item WEI XUEHONG - COLD SPRINGS HARBOR LAB
item Ware, Doreen
item YOUENS-CLARK, KEN - COLD SPRINGS HARBOR LAB
item YAP, IMMANUEL - CORNELL UNIVERSITY
item MCCOUCH, SUSAN - CORNELL UNIVERSITY
item TUNG, CHIH-WEI - CORNELL UNIVERSITY

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/16/2007
Publication Date: 1/12/2008
Citation: Jaiswal, P., Avraham, S., Buckler Iv, E.S., Casstevens, T., Hebbard, C., Liang, C., Ni, J., Ravenscroft, D., Ren, L., Stein, L., Spooner, W., Tecle, I., Thomason, J., Wei Xuehong, Ware, D., Youens-Clark, K., Yap, I., Mccouch, S., Tung, C. 2008. Gramene: a growing plant comparative genomics resource. Nucleic Acids Research. 36:D947-D953.

Interpretive Summary: We present an update on the Gramene (www.gramene.org) project. The Gramene project provides integrated views of public data set for cereals. The data types include genome sequence and assemblies, genetic and physical maps and the associated markers, functional annotations of proteins, and controlled vocabularies to describe protein function, anatomy, and traits. In the past two years the project has had significant updates in content, analysis, and improvements in views and the addition of a new pathway and diversity module. The update communicates these improvements to the scientific community.

Technical Abstract: Gramene (www.gramene.org) is a curated genetic, genomic and comparative genome analysis resource for the major crop species, such as rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project, with all data and software freely downloadable through the ftp site (ftp.gramene.org/pub/gramene). Traditionally, Gramene’s data types included genome assembly and annotations, other DNA/mRNA sequences, genetic and physical maps/markers, genes, quantitative trait loci (QTLs), proteins, ontologies, literature, and comparative mappings. Since our last NAR publication two years ago, updates on these data types include new datasets and new associations among all datasets. Additionally, new features include rice pathways for ultimate functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons between Oryza sativa and its wild relatives for evolutionary studies; and orthologous gene sets between rice, Arabidopsis, maize, poplar and several animal species (for reference purpose) with their phylogenetic trees for gene function annotation. Significant improvements have been made to the web interface in order to provide users with a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions.