Studies about the role of SD in Vitis vinifera and other plant genome evolution have followed classical assembly-based approaches of sequence alignment and comparison, thus ignoring the impact and contribution of highly similar SDs. More divergent duplications with 94%) are frequently collapsed. The inability to identify such duplications results in the merging of distinct duplicated loci into the same sequence. It is widely known that the identification and characterization of high-identity SDs is problematic in WGS-based sequencing. An example is the NBS-LRR gene family, whose evolution and expansion through duplication have been studied in the Arabidopsis thaliana genome. Notably in plants, previous studies have reported a large impact of SDs on the evolution of genes involved in disease resistance, berry development and the ripening process. The erroneous pairing between two non-allelic SDs leads, after crossover, to translocation, inversion, deletion or duplication. Highly similar SDs are regions of genome instability as they predispose chromosomes to rearrangements providing templates for non-allelic homologous recombination (NAHR) events. SDs are large blocks of genomic sequence at least 1 kb in size mapping to more than one location in a genome. In fact, gene duplication represents the primary source of new gene function origination. It was reported that during plant and animal genome evolution, whole-genome and segmental duplication (SD) events occurred leading to an increase in biological complexity and the origin of evolutionary novelties. A genotype originally derived from the Pinot Noir grape variety (PN40024) has recently been sequenced and assembled using a whole-genome shotgun (WGS) approach resulting in 12-fold coverage. The grapevine genome is diploid and organized in 38 chromosomes (n = 19), with a total size of ~487 Mb. Grape was shown to reduce the incidence of cardiovascular and other diseases due to the content of secondary metabolites such as resveratrol, quercetin and others polyphenols. The productivity is generally valuated only by phenotype observation, although it is largely influenced by genotype, environment and cultural techniques. Today, this species is widely cultivated and represents almost the 98% of grape vineyards subdivided into table, wine and raisin grapes. Grapevine ( Vitis vinifera) is one of the oldest (appeared approximately 65 million years ago) and most important fruit crops in the world. This study represents a step forward in the full characterization of duplicated genes important for grapevine cultural needs and human health. These 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. Further we showed that several duplicated genes take part in the biosynthesis of compounds involved in plant response to environmental stress. In particular, the nine highest copy number genes have a copy in either or both organelle genomes. We detected mitochondrial and plastid DNA and genes (10% of gene annotation) in segmentally duplicated regions of the nuclear genome. We 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). In this regard, we performed a genome-wide analysis of high-identity SDs on the sequenced grapevine ( Vitis vinifera) genome (PN40024). Although data is plentiful for mammals, not much was known about the representation of SDs in plant genomes. SDs play an important role in genome plasticity by creating new genes and modeling genome structure. 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. Segmental 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%.
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