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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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Chromosomal organization of disease resistance genes of V. vinifera.A) Phylogenetic analysis of NBS-LRR protein sequences of V. vinifera present in Pinot Noir. The phylogeny of these genes is based on a distance-matrix neighbour-joining analysis (Clustal X, [124]; bootstrap of 1000) after alignment of sequences by TCoffee (version 5.05, [125]). The phylogenetic clades, in general, correspond to the classification based on protein domains (however, see text and Table S3). B) Genes assigned to LGs are represented by dots. Their gene number is specified in LG-specific insets and in Table S3. NBS clades (see A above) contain mainly genes of the following classes: (1) TIR-NBS-LRR in blue; (2) CC-NBS-LRRa in green; (3) CC-NBS-LRRb in yellow; (4) NBS-LRR in cyan; (5) CC-NBS-LRR in red. Other resistance genes, belonging to NBS and TIR-NBS groups, are represented by the open and filled dots, respectively. Resistance-related genes different from NBS genes are shown in black. The size of each LG is given in Mb (on the right), whereas markers of the genetic map ([15] and http://genomics.research.iasma.it) are shown on the left, together with the interval in cM between the two closest markers in each gene cluster.
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pone-0001326-g003: Chromosomal organization of disease resistance genes of V. vinifera.A) Phylogenetic analysis of NBS-LRR protein sequences of V. vinifera present in Pinot Noir. The phylogeny of these genes is based on a distance-matrix neighbour-joining analysis (Clustal X, [124]; bootstrap of 1000) after alignment of sequences by TCoffee (version 5.05, [125]). The phylogenetic clades, in general, correspond to the classification based on protein domains (however, see text and Table S3). B) Genes assigned to LGs are represented by dots. Their gene number is specified in LG-specific insets and in Table S3. NBS clades (see A above) contain mainly genes of the following classes: (1) TIR-NBS-LRR in blue; (2) CC-NBS-LRRa in green; (3) CC-NBS-LRRb in yellow; (4) NBS-LRR in cyan; (5) CC-NBS-LRR in red. Other resistance genes, belonging to NBS and TIR-NBS groups, are represented by the open and filled dots, respectively. Resistance-related genes different from NBS genes are shown in black. The size of each LG is given in Mb (on the right), whereas markers of the genetic map ([15] and http://genomics.research.iasma.it) are shown on the left, together with the interval in cM between the two closest markers in each gene cluster.

Mentions: Based on resistance domain analyses, the grape genome was found to contain 341 NBS genes (Figure 3 and Table S3), whereas 207 were found in Arabidopsis [21] and 398 in poplar [12]. The 233 NBS genes which contain the LRR domain can be grouped in 5 major clades (1 to 5 in Figure 3A). The clades were comprised of CC-NBS-LRR, the dictot-specific TIR-NBS-LRR and their truncated structures as follows: (1) mainly TIR-NBS-LRR; (2) and (3) mainly CC-NBS-LRR; (4) mainly NBS-LRR; and (5) CC-NBS-LRR. The CC-NBS-LRR group included 84 genes in grape, 51 in Arabidopsis and 119 in poplar, while the TIR-NBS-LRR group included 37 genes in grape, 64 in poplar and 83 in Arabidopsis. In addition, the grape NBS gene family included 5 truncated TIR-NBS genes, 112 truncated NBS-LRR genes and 103 genes characterized only by the NBS domain (Table S3).


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)

Chromosomal organization of disease resistance genes of V. vinifera.A) Phylogenetic analysis of NBS-LRR protein sequences of V. vinifera present in Pinot Noir. The phylogeny of these genes is based on a distance-matrix neighbour-joining analysis (Clustal X, [124]; bootstrap of 1000) after alignment of sequences by TCoffee (version 5.05, [125]). The phylogenetic clades, in general, correspond to the classification based on protein domains (however, see text and Table S3). B) Genes assigned to LGs are represented by dots. Their gene number is specified in LG-specific insets and in Table S3. NBS clades (see A above) contain mainly genes of the following classes: (1) TIR-NBS-LRR in blue; (2) CC-NBS-LRRa in green; (3) CC-NBS-LRRb in yellow; (4) NBS-LRR in cyan; (5) CC-NBS-LRR in red. Other resistance genes, belonging to NBS and TIR-NBS groups, are represented by the open and filled dots, respectively. Resistance-related genes different from NBS genes are shown in black. The size of each LG is given in Mb (on the right), whereas markers of the genetic map ([15] and http://genomics.research.iasma.it) are shown on the left, together with the interval in cM between the two closest markers in each gene cluster.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0001326-g003: Chromosomal organization of disease resistance genes of V. vinifera.A) Phylogenetic analysis of NBS-LRR protein sequences of V. vinifera present in Pinot Noir. The phylogeny of these genes is based on a distance-matrix neighbour-joining analysis (Clustal X, [124]; bootstrap of 1000) after alignment of sequences by TCoffee (version 5.05, [125]). The phylogenetic clades, in general, correspond to the classification based on protein domains (however, see text and Table S3). B) Genes assigned to LGs are represented by dots. Their gene number is specified in LG-specific insets and in Table S3. NBS clades (see A above) contain mainly genes of the following classes: (1) TIR-NBS-LRR in blue; (2) CC-NBS-LRRa in green; (3) CC-NBS-LRRb in yellow; (4) NBS-LRR in cyan; (5) CC-NBS-LRR in red. Other resistance genes, belonging to NBS and TIR-NBS groups, are represented by the open and filled dots, respectively. Resistance-related genes different from NBS genes are shown in black. The size of each LG is given in Mb (on the right), whereas markers of the genetic map ([15] and http://genomics.research.iasma.it) are shown on the left, together with the interval in cM between the two closest markers in each gene cluster.
Mentions: Based on resistance domain analyses, the grape genome was found to contain 341 NBS genes (Figure 3 and Table S3), whereas 207 were found in Arabidopsis [21] and 398 in poplar [12]. The 233 NBS genes which contain the LRR domain can be grouped in 5 major clades (1 to 5 in Figure 3A). The clades were comprised of CC-NBS-LRR, the dictot-specific TIR-NBS-LRR and their truncated structures as follows: (1) mainly TIR-NBS-LRR; (2) and (3) mainly CC-NBS-LRR; (4) mainly NBS-LRR; and (5) CC-NBS-LRR. The CC-NBS-LRR group included 84 genes in grape, 51 in Arabidopsis and 119 in poplar, while the TIR-NBS-LRR group included 37 genes in grape, 64 in poplar and 83 in Arabidopsis. In addition, the grape NBS gene family included 5 truncated TIR-NBS genes, 112 truncated NBS-LRR genes and 103 genes characterized only by the NBS domain (Table S3).

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
Related in: MedlinePlus