title: Gramene: a growing plant comparative genomics resource.
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.
authors.affiliation: Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.
authors.forename: Chengzhi
authors.initials: C
authors.lastname: Liang
authors.forename: Pankaj
authors.initials: P
authors.lastname: Jaiswal
authors.forename: Claire
authors.initials: C
authors.lastname: Hebbard
authors.forename: Shuly
authors.initials: S
authors.lastname: Avraham
authors.forename: Edward S
authors.initials: ES
authors.lastname: Buckler
authors.forename: Terry
authors.initials: T
authors.lastname: Casstevens
authors.forename: Bonnie
authors.initials: B
authors.lastname: Hurwitz
authors.forename: Susan
authors.initials: S
authors.lastname: McCouch
authors.forename: Junjian
authors.initials: J
authors.lastname: Ni
authors.forename: Anuradha
authors.initials: A
authors.lastname: Pujar
authors.forename: Dean
authors.initials: D
authors.lastname: Ravenscroft
authors.forename: Liya
authors.initials: L
authors.lastname: Ren
authors.forename: William
authors.initials: W
authors.lastname: Spooner
authors.forename: Isaak
authors.initials: I
authors.lastname: Tecle
authors.forename: Jim
authors.initials: J
authors.lastname: Thomason
authors.forename: Chih-wei
authors.initials: CW
authors.lastname: Tung
authors.forename: Xuehong
authors.initials: X
authors.lastname: Wei
authors.forename: Immanuel
authors.initials: I
authors.lastname: Yap
authors.forename: Ken
authors.initials: K
authors.lastname: Youens-Clark
authors.forename: Doreen
authors.initials: D
authors.lastname: Ware
authors.forename: Lincoln
authors.initials: L
authors.lastname: Stein
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D002874:Chromosome Mapping; D018556:Crops, Agricultural / Q000235:genetics* / Q000378:metabolism; D030541:Databases, Genetic; D005819:Genetic Markers; D014644:Genetic Variation; D018745:Genome, Plant; D023281:Genomics; D020407:Internet; D012275:Oryza / Q000235:genetics; D006109:Poaceae / Q000235:genetics; D014908:Triticum / Q000235:genetics; D014584:User-Computer Interface; D003313:Zea mays / Q000235:genetics
chemical_list: D005819:Genetic Markers