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2014

International,  COM (talks) 08 Jan 2014   Toward the improvement of the gene centered information in grapevine genomics

Jérôme Grimplet1, Anne-Françoise Adam-Blondon2, Pierre-François Bert3, Oliver Bitz4, Dario Cantu5, Grant Cramer6, Chris Davies7, Serge Delrot3, Mario Pezzotti8 and Stéphane Rombauts9

1 Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, 26006, Spain

2 INRA, Units of Research Genomics-Info (URGI), Route de Saint Cyr, 78026 Versailles, France

3 Université de Bordeaux, ISVV, EGFV, UMR 1287, F-33140 Villenave d’Ornon, France

4 Department of Grapevine Breeding, Geisenheim University, 65366 Geisenheim, Germany

5 Department of Viticulture and Enology, University of California Davis, CA 95616 USA

6 Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA

7 CSIRO Plant Industry, Waite Campus, Urrbrae SA 5064, Australia

8 Department of Biotechnology,Università degli Studi di Verona, 37134 Verona, Italy

9a Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium; b Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium

A major breakthrough in grapevine genomics was achieved in 2007 with the sequencing of the Vitis vinifera cv. PN40024 genome. Subsequently, invaluable data related to the structural and functional characterization of the genes accumulated exponentially. Unfortunately, part of this data is episodic by nature or was acquired prior to the genome release. Furthermore, because of heterogeneous sources these data were greatly under-exploited with issues like incompatibility of data but also decentralized storage making retrieval more difficult. Classically, a large amount of useful data describing gene functions only appears in printed articles that describe the experiments carried out to answer the initial question of the publishing research team without being deposited in a common database, then remaining inaccessible for automatic data mining. High throughput “omics” data are typically stored in public repositories, but generally remain confined to their initial aim.

With the objective of providing a high quality and highly accessible annotation of the grapevine genes, the International Grapevine Genome Project (IGGP) commissioned an international Supernomenclature Committee for Grape Gene Annotation to coordinate the expert-annotation effort of the grapevine genes. The goal of the committee is to provide a standard nomenclature for locus identifiers and to define the convention for the gene naming system.

This system will be implemented on a new version of grapevine annotation that is being developed on an improved version of the grapevine genome chromosome assembly.  

Acknowledgements: GRCN NSF program, Grant Plant-KBBE-2008-GrapeReSeq, EU COST FA 1106


Creation date: 08 Jan 2014