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).
Highlights
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
The bioinformatics resources for the grapevine species has expanded in the past few years, with a variety of tools created for postgenomics era applications [7]
Other earlier microarray platforms have been widely popular within the grapevine research community, in particular the two Affymetrix microarray platforms, the Vitis vinifera GeneChipW [13] based on the EST sequences assembled into contigs corresponding to the DFCI gene index version 4 and the GrapeGen microarrays [14] based on the DFCI gene index version 5 complemented by the GrapeGen project EST sequences
Summary
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. Edu/tgi/cgi-bin/tgi/gimain.pl?gudb=grape) and the GrapeGen microarrays [14] based on the DFCI gene index version 5 complemented by the GrapeGen project EST sequences Within this context, the assessment of the correspondence between all the different sets of grapevine genes (8X and 12X genome sequence coverage and EST) has several interests: (i) to provide correspondence tables to the grapevine scientific community that relate identical genes with different names, which would allow work performed with the 8X genome gene IDs to be updated to the 12X gene IDs; (ii) to use the functional annotation performed on the 8X predicted genes and to implement it on the 12X genome; (iii) to update VitisNet, which was based on the 8X prediction [15], for the 12X genome and make it compatible with the NimbleGen array; and (iv) to allow comparison of results obtained from different high throughput platforms such as microarrays or proteomics studies
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