Recommended Conferences

Genetic Engineering and Gene Therapy

Paris, France

Human Genetics and Genetic Disorders

Miami, USA

Tissue Engineering and Regenerative Medicine

Chicago, USA
Related Subjects
 

A high quality draft consensus sequenceofthegenomeofaheterozygousgrapevinevariety

Author(s): Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, et al.

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.

Similar Articles

Emerging knowledge from genome sequencing of crop species

Author(s): Barabaschi D, Guerra D, Lacrima K, Laino P, Michelotti V, et al.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

Author(s): Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, et al.

Characterization of mango (Mangiferaindica L

Author(s): Azim KM, Khan IA, Zhang Y

The genome of the domesticatedapple (Malus x domesticaBorkh

Author(s): Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, et al.

The genome of pear (PyrusbretschneideriRehd)

Author(s): Wu J, WangZ, ShiZ, Zhang S, Ming R, et al.

The draft genomeof sweet orange (Citrus sinensis)

Author(s): Xu Q, Chen LL, Ruan X, Chen D, Zhu A, e t al.

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

Author(s): Al-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H,et al.

Genome sequence of the date palm Phoenix dactylifera L

Author(s): Ibrahim S, Al-MssallemSongnian H, Xiaowei Z, Qiang L, Wanfei L, et al.

The Draft Genome Sequence of European Pear (Pyruscommunis L

Author(s): Chagné D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, et al.