title: A high quality draft consensus sequence of the genome of a heterozygous grapevine variety.
abstract: BACKGROUND
  Worldwide, 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.
  
  
  RESULTS
  We 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).
  
  
  CONCLUSIONS
  Sanger 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.
authors: IASMA Research Center, San Michele all'Adige, Trento, Italy. riccardo.velasco@iasma.it
authors: Riccardo
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authors: Velasco
authors: Andrey
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authors: Zharkikh
authors: Michela
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authors: Troggio
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authors: Cartwright
authors: Alessandro
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authors: Cestaro
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authors: Lisa M
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authors: Vezzulli
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authors: Malacarne
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authors: Iliev
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authors: Wardell
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authors: Micheletti
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authors: Macalma
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authors: Facci
authors: Jeff T
authors: JT
authors: Mitchell
authors: Michele
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authors: Perazzolli
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authors: Gatto
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authors: Oyzerski
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authors: Moretto
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authors: Gutin
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authors: Stefanini
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authors: Chen
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authors: Segala
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authors: Davenport
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authors: Demattè
authors: Amy
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authors: Mraz
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authors: Battilana
authors: Keith
authors: K
authors: Stormo
authors: Fabrizio
authors: F
authors: Costa
authors: Quanzhou
authors: Q
authors: Tao
authors: Azeddine
authors: A
authors: Si-Ammour
authors: Tim
authors: T
authors: Harkins
authors: Angie
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authors: Lackey
authors: Clotilde
authors: C
authors: Perbost
authors: Bruce
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authors: Taillon
authors: Alessandra
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authors: Stella
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authors: Solovyev
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authors: JA
authors: Fawcett
authors: Lieven
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authors: Sterck
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authors: Vandepoele
authors: Stella M
authors: SM
authors: Grando
authors: Stefano
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authors: Toppo
authors: Claudio
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authors: Moser
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authors: Lanchbury
authors: Robert
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authors: Bogden
authors: Mark
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authors: Skolnick
authors: Vittorio
authors: V
authors: Sgaramella
authors: Satish K
authors: SK
authors: Bhatnagar
authors: Paolo
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authors: Fontana
authors: Alexander
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authors: Gutin
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authors: Van de Peer
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authors: Salamini
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authors: Viola
mesh_terms: D032461:Chromosomes, Plant; D016384:Consensus Sequence; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D018745:Genome, Plant; D006579:Heterozygote; D010636:Phenols / Q000378:metabolism; D010935:Plant Diseases / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D013729:Terpenes / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism; D027843:Vitis / Q000235:genetics* / Q000378:metabolism
chemical_list: D018744:DNA, Plant; D010636:Phenols; D013729:Terpenes; D014157:Transcription Factors