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

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).

The High Polyphenol Content of Grapevine Cultivar Tannat Berries Is Conferred Primarily by Genes That Are Not Shared with the Reference Genome

“…To report complex alleles consistently, we defined all variants against the 12x grapevine reference genome assembly (Grimplet et al, 2012). There were 2,087,275 single-base differences between Tannat and PN40024, as well as 240,355 (11.5%) ambiguous calls.…”

“…For genes transferred from the V1 annotation, we integrated the VitisNet annotations (Grimplet et al, 2012). Definitions could be assigned by homology searches to 20,170 of the genes (;58%).…”

“…Genes were functionally annotated by integrating the V1 manual annotation (Grimplet et al, 2012) and automatic annotations performed with Blast2GO (Conesa et al, 2005). Novel and varietal genes without assigned Enzyme Commission numbers were manually classified by BLAST using known polyphenol-related genes as reference sequences and discarding hits with an E-value >1*10 210 .…”

Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development

“…To provide an overview of their roles, the differentially expressed genes (DEGs) were classified on the basis of a manually improved functional annotation (Grimplet et al, 2012;Supplemental Data Set 2). The significantly overrepresented (P < 0.05) functional categories identified for downregulated and upregulated genes (Supplemental Figure 2 and Supplemental Data Set 2) showed that maturation involves the suppression of diverse metabolic processes, including photosynthesis, energy metabolism, carbohydrate metabolism, cellular component organization, and the cell cycle, which are related to vegetative growth.…”

The Phenylpropanoid Pathway Is Controlled at Different Branches by a Set of R2R3-MYB C2 Repressors in Grapevine

“…The transcriptomes of 35S:MYBC2-L3 and wild-type lines were analyzed using both a coexpression-based approach (Usadel et al, 2009) to identify genes showing negatively correlated profiles with respect to MYBC2-L3 and a twoclass unpaired comparison using significance analysis of microarray (SAM; Table I; Supplemental Data S2). All genes selected by these approaches were automatically annotated against the V1 gene prediction version of the grapevine genome (Grimplet et al, 2012) and manually improved where possible. Among the genes most negatively correlated to MYBC2-L3 expression, we found many structural genes related to phenylpropanoid, general flavonoid, or PA synthesis and transport (Table I; Supplemental Data S2).…”