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

  1. Grimplet, J. 4
  2. Van Hemert, John L. 1
  3. Carbonell-Bejerano, P. 24
  4. Díaz-Riquelme, J. 4
  5. Dickerson, J. 1
  6. Fennell, A. 5
  7. Pezzotti, M. 3
  8. Martínez-Zapater, J.M. 24
  1. 1 Iowa State University
    info

    Iowa State University

    Ames, Estados Unidos

    ROR https://ror.org/04rswrd78

  2. 2 Centro Nacional de Biotecnología
    info

    Centro Nacional de Biotecnología

    Madrid, España

    ROR https://ror.org/015w4v032

  3. 3 University of Verona
    info

    University of Verona

    Verona, Italia

    ROR https://ror.org/039bp8j42

  4. 4 Instituto de Ciencias de la Vid y del Vino
    info

    Instituto de Ciencias de la Vid y del Vino

    Logroño, España

    ROR https://ror.org/01rm2sw78

  5. 5 South Dakota State University
    info

    South Dakota State University

    Brookings, Estados Unidos

    ROR https://ror.org/015jmes13

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Revista:
BMC Research Notes

ISSN: 1756-0500

Año de publicación: 2012

Volumen: 5

Páginas: 1-10

Tipo: Artículo

DOI: 10.1186/1756-0500-5-213 PMID: 22554261 SCOPUS: 2-s2.0-84860375778 GOOGLE SCHOLAR lock_openAcceso abierto editor

Otras publicaciones en: BMC Research Notes

Repositorio institucional: lock_openAcceso abierto Editor

Resumen

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 (). © 2012 Grimplet et al.; licensee BioMed Central Ltd.