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

Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, Fitzgerald LM, Vezzulli S, Reid J, Malacarne G, Iliev D, Coppola G, Wardell B, Micheletti D, Macalma T, Facci M, Mitchell JT, Perazzolli M, Eldredge G, Gatto P, Oyzerski R, Moretto M, Gutin N, Stefanini M, Chen Y, Segala C, Davenport C, Demattè L, Mraz A, Battilana J, Stormo K, Costa F, Tao Q, Si-Ammour A, Harkins T, Lackey A, Perbost C, Taillon B, Stella A, Solovyev V, Fawcett JA, Sterck L, Vandepoele K, Grando SM, Toppo S, Moser C, Lanchbury J, Bogden R, Skolnick M, Sgaramella V, Bhatnagar SK, Fontana P, Gutin A, Van de Peer Y, Salamini F, Viola R - PLoS ONE (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: IASMA Research Center, San Michele all'Adige, Trento, Italy. riccardo.velasco@iasma.it

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.

Show MeSH
Scenario of angiosperm genome evolution.Alternative scenario to the one proposed by Jaillon et al. [7] to explain angiosperm genome evolution. Our analyses seem to suggest that there has been a large-scale duplication event, likely a hybridization event, in the Vitis lineage, rather than before the split of Vitis and other dicots. See text for details.
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pone-0001326-g008: Scenario of angiosperm genome evolution.Alternative scenario to the one proposed by Jaillon et al. [7] to explain angiosperm genome evolution. Our analyses seem to suggest that there has been a large-scale duplication event, likely a hybridization event, in the Vitis lineage, rather than before the split of Vitis and other dicots. See text for details.

Mentions: The fact that there is substantial ambiguity in the dating of the duplicates in duplicated segments suggests that the most recent large-scale duplication event reported here for Vitis might have occurred in close proximity to the Vitis speciation event. Therefore, an alternative scenario than the one presented by Jaillon et al. [7] that we would like to put forward is shown in Figure 8. We assume three genome duplications to have occurred in both poplar and Arabidopsis, as proposed earlier [12], [98], [105], one of which has been shared by all dicots (and possible also by the monocots, see [98]), one that has been shared by Arabidopsis and poplar, but not Vitis, and one that has been specific to Arabidopsis [98], [105] and poplar [12], respectively. Since many regions of the Vitis genome appear in triplicate in both Jaillon et al. [7] and our own analyses (not shown), the genome duplication shared by all dicots might have been followed by a hybridization event in Vitis, shortly after its divergence from the lineage leading to poplar and Arabidopsis (see Figure 8).


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

Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, Fitzgerald LM, Vezzulli S, Reid J, Malacarne G, Iliev D, Coppola G, Wardell B, Micheletti D, Macalma T, Facci M, Mitchell JT, Perazzolli M, Eldredge G, Gatto P, Oyzerski R, Moretto M, Gutin N, Stefanini M, Chen Y, Segala C, Davenport C, Demattè L, Mraz A, Battilana J, Stormo K, Costa F, Tao Q, Si-Ammour A, Harkins T, Lackey A, Perbost C, Taillon B, Stella A, Solovyev V, Fawcett JA, Sterck L, Vandepoele K, Grando SM, Toppo S, Moser C, Lanchbury J, Bogden R, Skolnick M, Sgaramella V, Bhatnagar SK, Fontana P, Gutin A, Van de Peer Y, Salamini F, Viola R - PLoS ONE (2007)

Scenario of angiosperm genome evolution.Alternative scenario to the one proposed by Jaillon et al. [7] to explain angiosperm genome evolution. Our analyses seem to suggest that there has been a large-scale duplication event, likely a hybridization event, in the Vitis lineage, rather than before the split of Vitis and other dicots. See text for details.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2147077&req=5

pone-0001326-g008: Scenario of angiosperm genome evolution.Alternative scenario to the one proposed by Jaillon et al. [7] to explain angiosperm genome evolution. Our analyses seem to suggest that there has been a large-scale duplication event, likely a hybridization event, in the Vitis lineage, rather than before the split of Vitis and other dicots. See text for details.
Mentions: The fact that there is substantial ambiguity in the dating of the duplicates in duplicated segments suggests that the most recent large-scale duplication event reported here for Vitis might have occurred in close proximity to the Vitis speciation event. Therefore, an alternative scenario than the one presented by Jaillon et al. [7] that we would like to put forward is shown in Figure 8. We assume three genome duplications to have occurred in both poplar and Arabidopsis, as proposed earlier [12], [98], [105], one of which has been shared by all dicots (and possible also by the monocots, see [98]), one that has been shared by Arabidopsis and poplar, but not Vitis, and one that has been specific to Arabidopsis [98], [105] and poplar [12], respectively. Since many regions of the Vitis genome appear in triplicate in both Jaillon et al. [7] and our own analyses (not shown), the genome duplication shared by all dicots might have been followed by a hybridization event in Vitis, shortly after its divergence from the lineage leading to poplar and Arabidopsis (see Figure 8).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: IASMA Research Center, San Michele all'Adige, Trento, Italy. riccardo.velasco@iasma.it

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.

Show MeSH