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A high quality draft consensus sequence of the genome of a heterozygous grapevine variety

(2007) PLOS ONE. 2(12).
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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. Principal Findings. 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.
Keywords
GENETIC-LINKAGE MAP, VITIS-VINIFERA L., MADS-BOX GENE, DISEASE RESISTANCE GENES, QUANTITATIVE TRAIT LOCUS, ARABIDOPSIS-THALIANA, TRANSCRIPTION FACTOR, PROANTHOCYANIDIN SYNTHESIS, PHYLOGENETIC ANALYSIS, TRANSGENIC TOBACCO

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Chicago
Velasco, Riccardo, Andrey Zharkikh, Michela Troggio, Dustin A Cartwright, Alessandro Cestaro, Dmitry Pruss, Massimo Pindo, et al. 2007. “A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety.” Plos One 2 (12).
APA
Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D. A., Cestaro, A., Pruss, D., Pindo, M., et al. (2007). A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLOS ONE, 2(12).
Vancouver
1.
Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, et al. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLOS ONE. 2007;2(12).
MLA
Velasco, Riccardo, Andrey Zharkikh, Michela Troggio, et al. “A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety.” PLOS ONE 2.12 (2007): n. pag. Print.
@article{425557,
  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. Principal Findings. 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.},
  articleno    = {e1326},
  author       = {Velasco, Riccardo and Zharkikh, Andrey and Troggio, Michela and Cartwright, Dustin A and Cestaro, Alessandro and Pruss, Dmitry and Pindo, Massimo and FitzGerald, Lisa M and Vezzulli, Silvia and Reid, Julia and Malacarne, Giulia and Iliev, Diana and Coppola, Giuseppina and Wardell, Bryan and Micheletti, Diego and Macalma, Teresita and Facci, Marco and Mitchell, Jeff T and Perazzolli, Michele and Eldredge, Glenn and Gatto, Pamela and Oyzerski, Rozan and Moretto, Marco and Gutin, Natalia and Stefanini, Marco and Chen, Yang and Segala, Cinzia and Davenport, Christine and Dematte, Lorenzo and Mraz, Amy and Battilana, Juri and Stormo, Keith and Costa, Fabrizio and Tao, Quanzhou and Si-Ammour, Azeddine and Harkins, Tim and Lackey, Angie and Perbost, Clotilde and Taillon, Bruce and Stella, Alessandra and Solovyev, Victor and Fawcett, Jeffrey and Sterck, Lieven and Vandepoele, Klaas and Grando, Stella M and Toppo, Stefano and Moser, Claudio and Lanchbury, Jerry and Bogden, Robert and Skolnick, Mark and Sgaramella, Vittorio and Bhatnagar, Satish K and Fontana, Paolo and Gutin, Alexander and Van de Peer, Yves and Salamini, Francesco and Viola, Roberto},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  language     = {eng},
  number       = {12},
  pages        = {17},
  title        = {A high quality draft consensus sequence of the genome of a heterozygous grapevine variety},
  url          = {http://dx.doi.org/10.1371/journal.pone.0001326},
  volume       = {2},
  year         = {2007},
}

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