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Open Access Research article

Comparative analysis of grapevine whole-genome gene predictions, functional annotation, categorization and integration of the predicted gene sequences

Jérôme Grimplet1*, John Van Hemert2, Pablo Carbonell-Bejerano13, José Díaz-Riquelme1, Julie Dickerson2, Anne Fennell4, Mario Pezzotti5 and José M Martínez-Zapater13

Author Affiliations

1 Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), CCT, C/Madre de Dios 51, Logroño, España, 26006, Vietnam

2 Bioinformatics and Computational Biology Department, Iowa State University, Ames, IA, 50011, USA

3 Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, (CNB-CSIC), C/Darwin 3, Madrid, España, 28049, Vietnam

4 Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA

5 Department of Biotechnology, University of Verona, Strada le Grazie 15, Verona, 37134, Italy

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BMC Research Notes 2012, 5:213  doi:10.1186/1756-0500-5-213

Published: 3 May 2012

Abstract

Background

The first draft assembly and gene prediction of the grapevine genome (8X base coverage) was made available to the scientific community in 2007, and functional annotation was developed on this gene prediction. Since then additional Sanger sequences were added to the 8X sequences pool and a new version of the genomic sequence with superior base coverage (12X) was produced.

Results

In order to more efficiently annotate the function of the genes predicted in the new assembly, it is important to build on as much of the previous work as possible, by transferring 8X annotation of the genome to the 12X version. The 8X and 12X assemblies and gene predictions of the grapevine genome were compared to answer the question, “Can we uniquely map 8X predicted genes to 12X predicted genes?” The results show that while the assemblies and gene structure predictions are too different to make a complete mapping between them, most genes (18,725) showed a one-to-one relationship between 8X predicted genes and the last version of 12X predicted genes. In addition, reshuffled genomic sequence structures appeared. These highlight regions of the genome where the gene predictions need to be taken with caution. Based on the new grapevine gene functional annotation and in-depth functional categorization, twenty eight new molecular networks have been created for VitisNet while the existing networks were updated.

Conclusions

The outcomes of this study provide a functional annotation of the 12X genes, an update of VitisNet, the system of the grapevine molecular networks, and a new functional categorization of genes. Data are available at the VitisNet website (http://www.sdstate.edu/ps/research/vitis/pathways.cfm webcite).