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

Authors
  • Grimplet, Jérôme1
  • Van Hemert, John2
  • Carbonell-Bejerano, Pablo1, 3
  • Díaz-Riquelme, José1
  • Dickerson, Julie2
  • Fennell, Anne4
  • Pezzotti, Mario5
  • Martínez-Zapater, José M1, 3
  • 1 CCT, Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), C/Madre de Dios 51, Logroño, España, 26006, Vietnam , Logroño (Vietnam)
  • 2 Iowa State University, Bioinformatics and Computational Biology Department, Ames, IA, 50011, USA , Ames (United States)
  • 3 Centro Nacional de Biotecnología, Departamento de Genética Molecular de Plantas, (CNB-CSIC), C/Darwin 3, Madrid, España, 28049, Vietnam , Madrid (Vietnam)
  • 4 South Dakota State University, Plant Science Department, Brookings, SD, 57007, USA , Brookings (United States)
  • 5 University of Verona, Department of Biotechnology, Strada le Grazie 15, Verona, 37134, Italy , Verona (Italy)
Type
Published Article
Journal
BMC Research Notes
Publisher
Springer (Biomed Central Ltd.)
Publication Date
May 03, 2012
Volume
5
Issue
1
Identifiers
DOI: 10.1186/1756-0500-5-213
Source
Springer Nature
Keywords
License
Green

Abstract

BackgroundThe 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.ResultsIn 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.ConclusionsThe 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).

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