Comparative Analysis of Grapevine Whole-genome Gene Predictions, Functional Annotation, Categorization and Integration of the Predicted Gene Sequences

Authors

Jerome Grimplet, Universidad de La Rioja
John Van Hemert, Iowa State University
Pablo Carbonell-Bejerano, Universidad de La Rioja
Jose Diaz-Riquelme, Universidad de La Rioja
Julie Dickerson, Iowa State University
Anne Fennell Dr, South Dakota State UniversityFollow
Mario Pezzotti, University of Verona
Jose M. Martinez-Zapater, Universidad de La Rioja

Document Type

Article

Publication Date

2012

Keywords

VitisNet, Vitis vinifera, Grapevine Molecular Networks, grape genome

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.

Publication Title

BMC Research Notes

Volume

5

Issue

213

Format

application/pdf

DOI of Published Version

10.1186/1756-0500-5-213

Publisher

BioMed Central

Rights

Copyright © 2012 the Authors

Recommended Citation

Grimplet, Jerome; Van Hemert, John; Carbonell-Bejerano, Pablo; Diaz-Riquelme, Jose; Dickerson, Julie; Fennell, Anne Dr; Pezzotti, Mario; and Martinez-Zapater, Jose M., "Comparative Analysis of Grapevine Whole-genome Gene Predictions, Functional Annotation, Categorization and Integration of the Predicted Gene Sequences" (2012). Agronomy, Horticulture and Plant Science Faculty Publications. 54.
https://openprairie.sdstate.edu/plant_faculty_pubs/54

Comments

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.