Analysis of high-identity segmental duplications in the grapevine genome

Abstract

BackgroundSegmental duplications (SDs) are blocks of genomic sequence of 1-200 kb that map to different loci in a genome and share a sequence identity > 90%. SDs show at the sequence level the same characteristics as other regions of the human genome: they contain both high-copy repeats and gene sequences. SDs play an important role in genome plasticity by creating new genes and modeling genome structure. Although data is plentiful for mammals, not much was known about the representation of SDs in plant genomes. In this regard, we performed a genome-wide analysis of high-identity SDs on the sequenced grapevine (Vitis vinifera) genome (PN40024).ResultsWe demonstrate that recent SDs (> 94% identity and >= 10 kb in size) are a relevant component of the grapevine genome (85 Mb, 17% of the genome sequence). We detected mitochondrial and plastid DNA and genes (10% of gene annotation) in segmentally duplicated regions of the nuclear genome. In particular, the nine highest copy number genes have a copy in either or both organelle genomes. Further we showed that several duplicated genes take part in the biosynthesis of compounds involved in plant response to environmental stress.ConclusionsThese data show the great influence of SDs and organelle DNA transfers in modeling the Vitis vinifera nuclear DNA structure as well as the impact of SDs in contributing to the adaptive capacity of grapevine and the nutritional content of grape products through genome variation. This study represents a step forward in the full characterization of duplicated genes important for grapevine cultural needs and human health.

The Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program

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Genome-wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress-responsive and development-related members

“…Whole-genome duplication and segmental duplication events are the primary origin of new gene functions during the evolution of plants, allowing an increase in biological complexity56. Accordingly, several of the grapevine ATL genes appear to originate from tandem duplication events and others from whole-genome duplication, and the retention of the duplicated genes probably reflects the fixation of adaptive mutations that have diversified the corresponding protein functions (subfunctionalisation).…”

A UDP-Glucose:Monoterpenol Glucosyltransferase Adds to the Chemical Diversity of the Grapevine Metabolome

“…The highly similar genes may be merged into the same sequence during genome assembly, even if Sanger technology with its long read was used. That is especially true for the polyploidized genome of grape, where three ancestral genomes contribute to the haploid content (Jaillon et al, 2007;Velasco et al, 2007;Giannuzzi et al, 2011). The estimated number of grape genes is about 30,000, but EST records showed that a minimum of about 40,000 genes are present in Vitis spp.…”