Gramene: A growing plant comparative genomics resource

Chengzhi Liang, Pankaj Jaiswal, Claire Hebbard, Shuly Avraham, Edward S. Buckler, Terry Casstevens, Bonnie Hurwitz, Susan Mccouch, Junjian Ni, Anuradha Pujar, Dean Ravenscroft, Liya Ren, William Spooner, Isaak Tecle, Jim Thomason, Chih Wei Tung, Xuehong Wei, Immanuel Yap, Ken Youens-Clark, Doreen WareLincoln Stein

Research output: Contribution to journalArticle

128 Scopus citations

Abstract

Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use without restriction. Gramene's core data types include 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 2 years ago, we have updated these data types to include new datasets and new connections among them. Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose). We have significantly improved the web interface in order to provide 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.

Original languageEnglish (US)
Pages (from-to)D947-D953
JournalNucleic acids research
Volume36
Issue numberSUPPL. 1
DOIs
StatePublished - Jan 2008

ASJC Scopus subject areas

  • Genetics

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    Liang, C., Jaiswal, P., Hebbard, C., Avraham, S., Buckler, E. S., Casstevens, T., Hurwitz, B., Mccouch, S., Ni, J., Pujar, A., Ravenscroft, D., Ren, L., Spooner, W., Tecle, I., Thomason, J., Tung, C. W., Wei, X., Yap, I., Youens-Clark, K., ... Stein, L. (2008). Gramene: A growing plant comparative genomics resource. Nucleic acids research, 36(SUPPL. 1), D947-D953. https://doi.org/10.1093/nar/gkm968