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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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Comparison of four plant genomes based on gene homology.All genes were compared each other as all-vs-all similarity searches using BLAST. Genes predicted for poplar, Arabidopsis and rice are respectively from www.genome.jgi-psf.org; www.arabidopsis.org; www.tigr.org. Grape gene estimates have been carried out on 58,611 assembled contigs. Genes of similar length with over 60% of similarity alignments at protein level were considered homologous using BLOSUM62 matrix [123]. The frequencies of sequences shared among species are reported on the right.
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pone-0001326-g002: Comparison of four plant genomes based on gene homology.All genes were compared each other as all-vs-all similarity searches using BLAST. Genes predicted for poplar, Arabidopsis and rice are respectively from www.genome.jgi-psf.org; www.arabidopsis.org; www.tigr.org. Grape gene estimates have been carried out on 58,611 assembled contigs. Genes of similar length with over 60% of similarity alignments at protein level were considered homologous using BLOSUM62 matrix [123]. The frequencies of sequences shared among species are reported on the right.

Mentions: Gene annotation followed a consensus approach. More than 79% of the genes predicted for the grape genome were annotated. Conserved putative grape genes were searched by the BLAST program with rice, poplar and Arabidopsis as references. A decision tree was implemented and used to carry this out. Sets of gene clusters with different levels of similarities among species as well as unique and putative species-specific genes were built. Using strict rules for homology determination, the subset of grape specific genes amounted to 16,859 (Figure 2).


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)

Comparison of four plant genomes based on gene homology.All genes were compared each other as all-vs-all similarity searches using BLAST. Genes predicted for poplar, Arabidopsis and rice are respectively from www.genome.jgi-psf.org; www.arabidopsis.org; www.tigr.org. Grape gene estimates have been carried out on 58,611 assembled contigs. Genes of similar length with over 60% of similarity alignments at protein level were considered homologous using BLOSUM62 matrix [123]. The frequencies of sequences shared among species are reported on the right.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0001326-g002: Comparison of four plant genomes based on gene homology.All genes were compared each other as all-vs-all similarity searches using BLAST. Genes predicted for poplar, Arabidopsis and rice are respectively from www.genome.jgi-psf.org; www.arabidopsis.org; www.tigr.org. Grape gene estimates have been carried out on 58,611 assembled contigs. Genes of similar length with over 60% of similarity alignments at protein level were considered homologous using BLOSUM62 matrix [123]. The frequencies of sequences shared among species are reported on the right.
Mentions: Gene annotation followed a consensus approach. More than 79% of the genes predicted for the grape genome were annotated. Conserved putative grape genes were searched by the BLAST program with rice, poplar and Arabidopsis as references. A decision tree was implemented and used to carry this out. Sets of gene clusters with different levels of similarities among species as well as unique and putative species-specific genes were built. Using strict rules for homology determination, the subset of grape specific genes amounted to 16,859 (Figure 2).

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