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

被引：765

作者：

Velasco, Riccardo ^{[1
]}

Zharkikh, Andrey ^{[2
]}

Troggio, Michela ^{[1
]}

Cartwright, Dustin A. ^{[1
,2
]}

Cestaro, Alessandro ^{[1
]}

Pruss, Dmitry ^{[2
]}

Pindo, Massimo ^{[1
]}

FitzGerald, Lisa M. ^{[2
]}

Vezzulli, Silvia ^{[1
]}

Reid, Julia ^{[2
]}

Malacarne, Giulia ^{[1
]}

Iliev, Diana ^{[2
]}

Coppola, Giuseppina ^{[1
]}

Wardell, Bryan ^{[2
]}

Micheletti, Diego ^{[1
]}

Macalma, Teresita ^{[2
]}

Facci, Marco ^{[1
]}

Mitchell, Jeff T. ^{[2
]}

Perazzolli, Michele ^{[1
]}

Eldredge, Glenn ^{[2
]}

Gatto, Pamela ^{[1
]}

Oyzerski, Rozan ^{[2
]}

Moretto, Marco ^{[1
]}

Gutin, Natalia ^{[2
]}

Stefanini, Marco ^{[1
]}

Chen, Yang ^{[2
]}

Segala, Cinzia ^{[1
]}

Davenport, Christine ^{[2
]}

Dematte, Lorenzo ^{[1
]}

Mraz, Amy ^{[5
]}

Battilana, Juri ^{[1
]}

Stormo, Keith ^{[5
]}

Costa, Fabrizio ^{[1
]}

Tao, Quanzhou ^{[5
]}

Si-Ammour, Azeddine ^{[1
]}

Harkins, Tim ^{[4
]}

Lackey, Angie ^{[4
]}

Perbost, Clotilde ^{[3
]}

Taillon, Bruce ^{[3
]}

Stella, Alessandra ^{[9
]}

Solovyev, Victor ^{[8
]}

Fawcett, Jeffrey A. ^{[6
]}

Sterck, Lieven ^{[6
]}

Vandepoele, Klaas ^{[6
]}

Grando, Stella M. ^{[1
]}

Toppo, Stefano ^{[7
]}

Moser, Claudio ^{[1
]}

Lanchbury, Jerry ^{[2
]}

Bogden, Robert ^{[5
]}

Skolnick, Mark ^{[2
]}

机构：

[1] IASMA Res Ctr, San Michele All Adige, Trento, Italy

[2] Myriad Genet Inc, Salt Lake City, UT USA

[3] 454 Life Sci Corp, Branford, CT USA

[4] Roche Diagnost Corp, Roche Appl Sci, Indianapolis, IN USA

[5] Amplicon Express Inc, Pullman, WA USA

[6] Gent Univ VIB, Dept Plant Syst Biol, Ghent, Belgium

[7] Univ Padua, Dept Biol Chem, Padua, Italy

[8] Univ London, Dept Comp Sci, Egham, Surrey, England

[9] Technol Pk Lodi, Lodi, Italy

来源：

PLOS ONE | 2007年 / 2卷 / 12期

关键词：

D O I：

10.1371/journal.pone.0001326

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：18

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