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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.

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Features of the Pinot Noir heterozygous genome.A) Comparison of constrasting haplotypes (a and b) co-mapping at two almost contigous regions in metacontig 32,921 of chromosome 1. Above: the 188 kb region; below: the 215 kb region. I from contig groups 1030-H15, 1079-G03, 2068-K04, 1034-C17 and II 2010-J07, 2044-L11, 1030-N10. In the genetic map the two regions are positioned at 60.1 cM: see preliminary experiment in Text S1. TE elements are labeled as follows: c: Copia; g: Gypsy/gypsy; a: Gypsy/athila; d: hAT/Dart; k: Karma; h: hAT; m: Mutator. B) SNP profiles of the 19 LGs of V. vinifera. Left and right of the figure correspond respectively to top and bottom of LGs of Troggio et al. [15]. The SNP values reported do not consider gaps in and among metacontigs. C) SNPs in exons and non-coding DNA and percentage of anchored genes tagged with SNPs. In parts B to E of this figure, gene prediction and annotation and the exon-intron boundaries were based on the methods described in Solovyev et al. [114]; Korf et al. [101]; Majoros et al. [115]; Altschul et al. [116]; Huang and Madan [117]. D) Relative age of grape duplicated genes estimated from the number of synonymous substitutions per synonymous sites (KS values). The peak between 0.6 and 1.2 KS supports a relatively large scale duplication event. Paralog genes were identified as in Li et al. [120] and KS distributions were calculated as in Maere et al. [105]. E) The same as in D for genes present in duplicated chromosome segments.
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pone-0001326-g007: Features of the Pinot Noir heterozygous genome.A) Comparison of constrasting haplotypes (a and b) co-mapping at two almost contigous regions in metacontig 32,921 of chromosome 1. Above: the 188 kb region; below: the 215 kb region. I from contig groups 1030-H15, 1079-G03, 2068-K04, 1034-C17 and II 2010-J07, 2044-L11, 1030-N10. In the genetic map the two regions are positioned at 60.1 cM: see preliminary experiment in Text S1. TE elements are labeled as follows: c: Copia; g: Gypsy/gypsy; a: Gypsy/athila; d: hAT/Dart; k: Karma; h: hAT; m: Mutator. B) SNP profiles of the 19 LGs of V. vinifera. Left and right of the figure correspond respectively to top and bottom of LGs of Troggio et al. [15]. The SNP values reported do not consider gaps in and among metacontigs. C) SNPs in exons and non-coding DNA and percentage of anchored genes tagged with SNPs. In parts B to E of this figure, gene prediction and annotation and the exon-intron boundaries were based on the methods described in Solovyev et al. [114]; Korf et al. [101]; Majoros et al. [115]; Altschul et al. [116]; Huang and Madan [117]. D) Relative age of grape duplicated genes estimated from the number of synonymous substitutions per synonymous sites (KS values). The peak between 0.6 and 1.2 KS supports a relatively large scale duplication event. Paralog genes were identified as in Li et al. [120] and KS distributions were calculated as in Maere et al. [105]. E) The same as in D for genes present in duplicated chromosome segments.

Mentions: The genomic region represented in Figure 7A highlights the differences which exist between homologous haplotypes. Notable differences in this region concern the presence of gaps and the number of copies of TE.


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)

Features of the Pinot Noir heterozygous genome.A) Comparison of constrasting haplotypes (a and b) co-mapping at two almost contigous regions in metacontig 32,921 of chromosome 1. Above: the 188 kb region; below: the 215 kb region. I from contig groups 1030-H15, 1079-G03, 2068-K04, 1034-C17 and II 2010-J07, 2044-L11, 1030-N10. In the genetic map the two regions are positioned at 60.1 cM: see preliminary experiment in Text S1. TE elements are labeled as follows: c: Copia; g: Gypsy/gypsy; a: Gypsy/athila; d: hAT/Dart; k: Karma; h: hAT; m: Mutator. B) SNP profiles of the 19 LGs of V. vinifera. Left and right of the figure correspond respectively to top and bottom of LGs of Troggio et al. [15]. The SNP values reported do not consider gaps in and among metacontigs. C) SNPs in exons and non-coding DNA and percentage of anchored genes tagged with SNPs. In parts B to E of this figure, gene prediction and annotation and the exon-intron boundaries were based on the methods described in Solovyev et al. [114]; Korf et al. [101]; Majoros et al. [115]; Altschul et al. [116]; Huang and Madan [117]. D) Relative age of grape duplicated genes estimated from the number of synonymous substitutions per synonymous sites (KS values). The peak between 0.6 and 1.2 KS supports a relatively large scale duplication event. Paralog genes were identified as in Li et al. [120] and KS distributions were calculated as in Maere et al. [105]. E) The same as in D for genes present in duplicated chromosome segments.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0001326-g007: Features of the Pinot Noir heterozygous genome.A) Comparison of constrasting haplotypes (a and b) co-mapping at two almost contigous regions in metacontig 32,921 of chromosome 1. Above: the 188 kb region; below: the 215 kb region. I from contig groups 1030-H15, 1079-G03, 2068-K04, 1034-C17 and II 2010-J07, 2044-L11, 1030-N10. In the genetic map the two regions are positioned at 60.1 cM: see preliminary experiment in Text S1. TE elements are labeled as follows: c: Copia; g: Gypsy/gypsy; a: Gypsy/athila; d: hAT/Dart; k: Karma; h: hAT; m: Mutator. B) SNP profiles of the 19 LGs of V. vinifera. Left and right of the figure correspond respectively to top and bottom of LGs of Troggio et al. [15]. The SNP values reported do not consider gaps in and among metacontigs. C) SNPs in exons and non-coding DNA and percentage of anchored genes tagged with SNPs. In parts B to E of this figure, gene prediction and annotation and the exon-intron boundaries were based on the methods described in Solovyev et al. [114]; Korf et al. [101]; Majoros et al. [115]; Altschul et al. [116]; Huang and Madan [117]. D) Relative age of grape duplicated genes estimated from the number of synonymous substitutions per synonymous sites (KS values). The peak between 0.6 and 1.2 KS supports a relatively large scale duplication event. Paralog genes were identified as in Li et al. [120] and KS distributions were calculated as in Maere et al. [105]. E) The same as in D for genes present in duplicated chromosome segments.
Mentions: The genomic region represented in Figure 7A highlights the differences which exist between homologous haplotypes. Notable differences in this region concern the presence of gaps and the number of copies of TE.

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