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. 2008 Jan;36(Database issue):D947-53.
doi: 10.1093/nar/gkm968. Epub 2007 Nov 4.

Gramene: a growing plant comparative genomics resource

Chengzhi Liang  1 , 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 Ware, Lincoln Stein
Affiliations

Gramene: a growing plant comparative genomics resource

Chengzhi Liang et al. Nucleic Acids Res. 2008 Jan.

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.

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Figures

Figure 1.
Figure 1.
Conceptual data organization and relationship in Gramene. Gramene contains primary data, such as genome sequences, maps, genes, QTLs, proteins and markers, as well as complex data, such as comparative mappings, gene families, genetic diversities and pathways. Ontology terms are used to provide annotations and associations for other data. Gramene also provides literature for the data source. Please note the size of each line segment is not in proportional to the real size of any biological objects it represents.
Figure 2.
Figure 2.
A syntenic region showing related QTLs and genes between rice and maize in CMap. Please refer to CMap tutorial (http://www.gramene.org/tutorials/cmap.html) on how to construct this comparative map view. The maize chromosomes 3 and 8 contain big syntenic regions (including inversions) with rice chromosome 1 as evidenced in Ensembl synteny view http://tinyurl.com/2sl55k. The QTLs are shown in blue and genes in green. The rice markers are shown on the right side of the chromosome, where the markers in red are those also mapped on the maize map. There are many plant height QTLs in rice and maize mapped in this region (PTHT, in blue ovate—the names were enlarged for better viewing). The rice PTHT QTLs are probably contributed by the sd1 gene (McCouch et al., unpublished data), but the maize PTHT QTLs have not been characterized regarding the underlying genes. Note that several maize height genes, d12, d*-N394 and d*-N282 (in brown ovate) are also mapped in the region. Based on the syntenic view, we can expect that the sd1 orthologs in maize will be able to be identified after the maize genome sequence is completed, and they will likely contribute to some of these maize PTHT QTLs.
Figure 3.
Figure 3.
The rice bhlh90 gene tree (partial) showing the orthologous genes between rice, maize, A. thaliana and poplar. The full tree can be viewed at http://tinyurl.com/3clrjv. Note the bhlh90 gene is mapped in the region shown in Figure 2, but its maize gene ortholog is a predicted gene and has not been studied functionally. The solid box on the right shows the aligned regions in the proteins. It is expected that there are more maize orthologs to be identified after the maize genome sequence becomes complete.
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