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United States Department of Agriculture

Agricultural Research Service

Title: Gramene: a growing plant comparative genomics resource

item Jaiswal, Pankaj
item Avraham, Shulamit
item Buckler, Edward - Ed
item Casstevens, Terry
item Hebbard, Claire
item Liang, Chengzhi
item Ni, Junjian
item Ravenscroft, Dean
item Ren, Liya
item Stein, Lincoln
item Spooner, William
item Tecle, Isaak
item Thomason, Jim
item Wei Xuehong
item Ware, Doreen
item Youens-clark, Ken
item Yap, Immanuel
item Mccouch, Susan
item Tung, Chih-wei

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 ( 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 ( 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 ( 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.

Last Modified: 10/18/2017
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