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 Vitis vinifera

Vitis vinifera in the context of Green Plant evolution

Gene families containing Vitis vinifera genes can be found by searching at the Viridiplantae, Embryophyte, Tracheophyte, Angiosperm, Rosid Pre- and Post-hexaploidy and Grape nodes. Keyword searches (the default) can be performed using either a gene identifier, a gene symbol, ontology id (e.g, GO, PFAM, Panther) or full or partial defline. If you don't have this type of information for your gene of interest, but know something about its functional classification, you can perform an ontology search using a descriptive phrase (e.g., "developmental regulator", "apoptosis inhibition","alkaline phospatase"). This will search the selected ontologies for these phrases, and then use the resulting set of ontology identifiers (e.g, "PF05918", "KOG3913") to search for gene families whose members carry these classifications. Finally, if you don't have keyword or functional information but do have a gene or gene product sequence, you can search for homologous gene families by BLASTing against the (peptide) gene family consensus sequeuences.

The Vitis vinifera Genome

Use the BROWSE GENOME button at the top of this page to view Vitis vinifera 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 GENOME button. The browsing environment, Gbrowse, provides overview and detailed views of gene structure. Gbrowse provides a search interface allowing you to look up Vitis vinifera models by gene name, external identifier, or genomic location. Once you've located a gene model of interest, click on it to go to its detail page. The detail page provides sequence information on the model and its translated peptide. From the detail page you can also jump to viewing the gene in its 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

Bulk data downloads are available from a number of locations:

• BioMart: Choose "Phytozome Genomes" and use the Filter to restrict the data to Vitis vinifera. You can use other filters to further restrict the data, and then choose which data Attributes to download.
• FTP Site: Phytozome Data. Contains Phytozome-specific data as well as annotation and assembly files for JGI-sourced genomes.
• External Site: Genoscope Grape Data Page. Contains annotation and assembly files

Single Gene Family and Genomic Region data:

• Gene Family page
  • Go to the "Get Data" tab and select either "Get Sequences" or "Get Cluster Data" (which launches BioMart).
  • Go to the "Align Cluster Members" tab and select either "Load Member protein sequences" or "Load Member coding sequences." This will launch Jalview, from which sequences can be downloaded.
• Keyword and BLAST search results page: Data for one or more of the Gene Families found via a keyword search or a BLAST search against a gene family consensus database can be downloaded by selecting "ANALYZE RESULTS/GET DATA" and clicking "Get data for selected families". This will launch BioMart with filters set to retrieve data only for the selected families.
• Gbrowse region page: Use the "Download Alignments", "Download Decorated Fasta", or "Download Sequence" plugins under the "Reports and Analysis" pulldown.