Overview

This is the Sept 2007 release of the draft genome and annotation of Vitis vinifera by the French-Italian Public Consortium for Grapevine Genome Characterization. Please see Genoscope and Jaillon, et. al. for more information.

Statistics

Genome

487Mb arranged in 19 chromosomes

Loci

30434 loci containing protein-coding transcripts

Transcripts

30434 protein-coding transcripts

Exploring Grape

Grape in the context of Green Plant evolution

Grape genes will be found in clusters defined at the Viridiplantae, Embryophyte, Tracheophyte, Angiosperm, and Rosid nodes. If you know something about the grape gene you're interested in (e.g., its TIGR or RefSeq name, its gene symbol, a descriptive phrase), you can select "search" from the menu at the top of the page, enter your search terms, pick one of the above nodes (or All nodes), and search. The gene clusters you find can then be examined in detail, with summary pages that include descriptive and functional (domain) annotation, syntenic context, and links to each cluster's ancestors and descendants. If you don't have keyword information but do have a gene or gene product sequence, you can search for related gene clusters using BLAST (click on "search" and then select the BLAST tab).

The Grape Genome

Use the Browse the Genome button at the top of this page to view grape gene models in their full genomic context. Alternatively, if you'd like to search the genome for regions homologous to a particular sequence, use the BLAST against the genome button. The browsing environment, Gbrowse, provides overview and detailed views of gene structure. Gbrowse provides a search interface allowing you to look up grape models by name, identifier, or location. Once you've located a gene model of interest, click on it to go to its detail page (e.g, here). The detail page provides sequence information on the model and its translated peptide. From the detail page you can also jump to viewing grape genes in their evolutionary context. To see this gene's orthologs at the Angiosperm node, click on the Cluster link on the detail page. If you'd like to see what other ancestral gene's share sequence similarity with this gene, click on the detail page's Phytozome BLAST link, which will pull up similar gene clusters at whichever Phytozome node you choose.

Downloading Data

CDS and peptide sequence for individual genes is available from the details page of the grape Gbrowse environment. To get there from a Cluster Summary page, however, you'll need to click the "Display Options" tab and make sure that "Reference ID" column is selected. Then expand all the "Genes in the Cluster" rows (by clicking on the icon near the Org heading) and click on the "[PAC]" link, which will take you to the detail page for that model. You can also get gene sequences for all the members of one or more clusters from any Cluster Summary, Phytozome BLAST results, or Search Results page, by launching Jalview (by clicking links for Multiple Sequence Alignments"), which will provide access to CDS sequence or peptide sequence of the members of the gene clusters you selected.