The grapevine gene nomenclature system

Jérôme Grimplet (1) , Anne-Francoise Adam-Blondon (2) , Pierre-François Bert (3) , Olivier Bitz (4) , Dario Cantu (5) , Christopher Davies (6) , Serge Delrot (3) , Mario Pezzotti (7) , Stéphane Rombauts (8, 9) , Grant R Cramer (10)

1 Instituto de Ciencias de la Vid y del Vino
2 URGI - Unité de Recherche Génomique Info
3 UMR EGFV - Ecophysiologie et Génomique Fonctionnelle de la Vigne
4 Department of Grapevine Breeding
5 Department of Viticulture and Enology
6 CSIRO Plant Industry
7 Department of Biotechnology
8 Department of Plant Biotechnology
9 Department of Plant Biotechnology
10 Department of Biochemistry and Molecular Biology

Background Grapevine (Vitis vinifera L.) is one of the most important fruit crops in the world and serves as a valuable model for fruit development in woody species. A major breakthrough in grapevine genomics was achieved in 2007 with the sequencing of the Vitis vinifera cv. PN40024 genome. Subsequently, data on structural and functional characterization of grape genes accumulated exponentially. To better exploit the results obtained by the international community, we think that a coordinated nomenclature for gene naming in species with sequenced genomes is essential. It will pave the way for the accumulation of functional data that will enable effective scientific discussion and discovery. The exploitation of data that were generated independently of the genome release is hampered by their heterogeneous nature and by often incompatible and decentralized storage. Classically, large amounts of data describing gene functions are only available in printed articles and therefore remain hardly accessible for automatic text mining. On the other hand, high throughput “Omics” data are typically stored in public repositories, but should be arranged in compendia to better contribute to the annotation and functional characterization of the genes. Results With the objective of providing a high quality and highly accessible annotation of grapevine genes, the International Grapevine Genome Project (IGGP) commissioned an international Super-Nomenclature Committee for Grape Gene Annotation (sNCGGa) to coordinate the effort of experts to annotate the grapevine genes. The goal of the committee is to provide a standard nomenclature for locus identifiers and to define conventions for a gene naming system in this paper. Conclusions Learning from similar initiatives in other plant species such as Arabidopsis, rice and tomato, a versatile nomenclature system has been developed in anticipation of future genomic developments and annotation issues. The sNCGGa’s first outreach to the grape community has been focused on implementing recommended guidelines for the expert annotators by: (i) providing a common annotation platform that enables community-based gene curation, (ii) developing a gene nomenclature scheme reflecting the biological features of gene products that is consistent with that used in other organisms in order to facilitate comparative analyses.

Mots clés: grapevine gene; nomenclature

Domaines: Sciences du Vivant [q-bio]

Jérôme Grimplet, Anne-Francoise Adam-Blondon, Pierre-François Bert, Olivier Bitz, Dario Cantu, et al.. The grapevine gene nomenclature system. BMC Genomics, 2014, 15 (1077), ⟨10.1186/1471-2164-15-1077⟩. ⟨hal-01128546v2⟩