Gramene database in 2010: updates and extensions

Abstract

Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene began with the addition of an Ensembl genome browser and has expanded in the last decade to become a robust resource for plant genomics hosting a wide array of data sets including quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps from various published studies (genetic, physical, bin, etc.). In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data.

Figure 1.

An Ensembl browser view showing Vitis vinifera SNPs in the context of gene annotation. SNPs are color-coded to indicate position relative to gene features (e.g. `intronic') and consequences of SNP on coding sequence (e.g. `non-synonymous').

Figure 2.

The new multi-species view shows alignments in the context of gene annotations across multiple species. In this case, a region of rice (center) is displayed against homologous regions in sorghum (top) and Brachypodium (bottom). To create such a view from any location-based display, a user would select the `multi-species view' option from the navigation hierarchy. Referent species can be added to and removed from the display using the `select species' option.

Figure 3.

Phylogenetic tree for Arabidopsis gene PNT1, a Glycosyltransferase, showing conservation throughout the eukaryotic lineage.

Figure 4.

The new SNP Query tool returns variation from one or more accessions based on genomic coordinates. The `genes' column contains hyperlinks to the Ensembl genome browser’s gene summary page.

Figure 5.

A comparative map view showing the genetic map of Aegilops tauschii along side the latest O. sativa japonica sequence map and a rice QTL map.

Figure 6.

Gramene’s redesigned home page allows quick access to all our major data sets and quick search.