File:PAG2011 URGI Grapevine.pdf

Bio-informatic resources for genomic and genetic information system in grapevine

Presentation given by Anne-Francoise Adam-Blondon, of INRA-URGI at PAG 2011.

Abstract

Nathalie Choisne, Aminah Keliet, Marc Bras, Nacer Mohellibi, Sandie Arnoux, Olivier Inizan, Joelle Anselem, Baptiste Brault, Daphné Verdelet, Francoise Alfama, Laetitia Brigitte, Sophie Durand, Erik Kimmel, Isabelle Luyten, Cyril Pommier, Sebastien Reboux, Delphine Steinbach, Thierry Lacombe, Anne-Francoise Adam-Blondon, Hadi Quesneville, all of INRA.

The INRA-URGI bioinformatics unit is in charge of development and maintenance of a genomic and genetic information system (GnpIS, http://urgi.versailles.inra.fr/gnpis) for the grape scientific community. The GnpIS information system is composed of integrated genetic and genomic modules. The accessions held at our national collection for grapevine genetic resources are available in the SIReGal database with their primary descriptors. Genetic, physical maps and associated markers are stored in the GnpMap database and their links viewable using CMap. The GnpGenome module is a multispecies database relying on the international open source GMOD database (Chado) and interface (GBrowse) (http://www.gmod.org). It contains the 12X Vitis vinifera genomic sequence assembly and its public structural annotation. A system was developed for the distributed manual curation of the grapevine genome sequence annotation based on Apollo graphical editing interface and Chado (GMOD) allowing curators to change the gene structures according to various evidences (ESTs, short-reads, protein similarity, comparative genomics). The results can be saved and shared in real time with other members of the community of curators. When validated, genes/pseudogenes curated models are committed in a second database publicly accessible by GBrowse. SNP and small indels are stored in the GnpSNP database and a pipeline for SNPs detection from short reads, integrated in Galaxy workflow manager (http://main.g2.bx.psu.edu/) is under development. Quick and complexe queries are possible through GnpIS using respectively QuickSearch and BioMart (GMOD).