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

作者：Riccardo Velasco, Andrey Zharkikh, Michela Troggio, Dustin Cartwright, Alessandro Cestaro, Dmitry Pruss, Massimo Pindo, Lisa M. Fitzgerald, Silvia Vezzulli, Julia Reid, Giulia Malacarne, Diana Iliev, Giuseppina Coppola, Bryan B. Wardell, Diego Micheletti, Teresita Macalma, M. G. D. FACCI, Jeff T. Mitchell, Michele Perazzolli, Glenn Eldredge, Pamela Gatto, Rozan Oyzerski, Marco Moretto, Natalia Gutin, M. Stefanini, Yang Chen, Cinzia Segala, Christine Davenport, Lorenzo Demattè, Amy Mraz, Juri Battilana, Keith E. Stormo, Fabrizio Costa, Quanzhou Tao, Azeddine Si‐Ammour, Tim T. Harkins, Angie Lackey, Clotilde S. Perbost, Bruce E. Taillon, Alessandra Stella, Victor Solovyev, Jeffrey A. Fawcett, Lieven Sterck, Klaas Vandepoele, S. Grando, Stefano Toppo, Claudio Moser, Jerry S. S. Lanchbury, Robert Bogden, Mark H. Skolnick, V. Sgaramella, Satish K. Bhatnagar, Paolo Fontana, Alexander Gutin, Yves Van de Peer, Francesco Salamini, Roberto Viola · 发表于：PLoS ONE · 年份：2007 · DOI：10.1371/journal.pone.0001326 · 被引用次数：1106 · 研究领域：Horticultural and Viticultural Research、Fermentation and Sensory Analysis、Wine Industry and Tourism

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 e...