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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
general
A high quality draft consensus sequence of the genome of a heterozygous grapevine variety
PLoS ONE, Volume 2, No. 12, Article e1326, Year 2007
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Description
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 Vitisspecific 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. © 2007 Velasco et al.
Authors & Co-Authors
Velasco, R.
Italy, San Michele All'adige
Fondazione Edmund Mach
Troggio, Michela
Italy, San Michele All'adige
Fondazione Edmund Mach
Cestaro, Alessandro
Italy, San Michele All'adige
Fondazione Edmund Mach
Pindo, Massimo
Italy, San Michele All'adige
Fondazione Edmund Mach
Vezzulli, Silvia
Italy, San Michele All'adige
Fondazione Edmund Mach
Malacarne, Giulia
Italy, San Michele All'adige
Fondazione Edmund Mach
Micheletti, Diego
Italy, San Michele All'adige
Fondazione Edmund Mach
Perazzolli, Michele
Italy, San Michele All'adige
Fondazione Edmund Mach
Gatto, Pamela
Italy, San Michele All'adige
Fondazione Edmund Mach
Moretto, Marco
Italy, San Michele All'adige
Fondazione Edmund Mach
Stefanini, Marco
Italy, San Michele All'adige
Fondazione Edmund Mach
Mraz, Amy
United States, Pullman
Amplicon Express
Costa, Fabrizio
Italy, San Michele All'adige
Fondazione Edmund Mach
Harkins, Timothy T.
United States, Indianapolis
Roche Diagnostics Corporation
Stella, Alessandra
Unknown Affiliation
Solovyev, Victor V.
United Kingdom, Egham
Royal Holloway, University of London
Sterck, Lieven
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Vandepoele, Klaas
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Grando, Maria Stella
Italy, San Michele All'adige
Fondazione Edmund Mach
Moser, Claudio
Italy, San Michele All'adige
Fondazione Edmund Mach
Lanchbury, Jerry S.S.
Unknown Affiliation
Skolnick, Mark H.
Unknown Affiliation
Van de Peer, Y.
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Salamini, Francesco O.
Unknown Affiliation
Viola, Roberto E.
Italy, San Michele All'adige
Fondazione Edmund Mach
Statistics
Citations: 993
Authors: 25
Affiliations: 6
Identifiers
Doi:
10.1371/journal.pone.0001326
ISSN:
19326203
Research Areas
Genetics And Genomics