A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety

Abstract

BackgroundWorldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented.Principal FindingsWe estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitis-specific large scale duplication event concerning at least 10 chromosomes (duplication not reported before).ConclusionsSanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape.

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

“…An overall heterozygous rate of the occurrence of SNPs and short indels was estimated at approximately 1.0 polymorphism per kilobase, which was lower than that (2.6 per kilobase) of the poplar genome 11 and that (4.2 per kilobase) of the grape genome 12 .…”

The genome of the domesticated apple (Malus × domestica Borkh.)

“…Poplar and grape gene lists were as described 2 . Colinearity in the gene order was detected with i-ADHoRe 2.4 (ref.…”

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

“…Reciprocal pair-wise comparisons 20 of the 28,269 chickpea gene models with 230,161 gene models from four sequenced legumes (M. truncatula 13 , L. japonicus 21 , pigeonpea 14 , soybean 15 ) and two nonlegume species (A. thaliana 22 and grape 23 ) identified 15,441 orthologous groups (Supplementary Table 14). On the one hand, 5,940 of these orthologous groups contain only a single chickpea gene, suggestive of simple orthology (Supplementary Table 15 and Supplementary Fig.…”

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