Genome Sequencing

grape in hands

The Grapevine Reference Genome Sequence

A first 8X version of the Vitis vinifera genome sequence was obtained by shotgun sequencing of a nearly homozygous genotype (PN40024) by a french italian public consortium (Jaillon et al 2007).

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A 12X.0 version of the assembly has been realeased at NCBI in November 2009 with the V0 version of the gene annotation and is briefly described in Adam-Blondon et al 2011. A new version of annotation, the V1, has been implemented by CRIBI. The sequence and its annotations can also be retrieved or browsed on the INRA platform for plant and crop pathogens bioinformatics (URGI).

New versions of the reference genome assembly and of its annotation are in progress.

Other useful sites to browse the reference genome are Gramene, Phytosome and FlagDB++.

​​ References

Jaillon O, Aury J-M, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pé E, Valle G, Morgante M, Caboche M, Adam-Blondon A-F, Weissenbach J, Quétier F, Wincker P (2007). The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449:463-468

Adam-Blondon A-F, Jaillon O, Vezzulli S, Zharkikh A, Troggio M, Velasco R (2011) Genome Sequence Initiatives. in: A-F Adam-Blondon, JM Martinez-Zapater, Chittaranjan Kole (eds) Genetics, Genomics and Breeding of Grapes. Science Publishers and CRC Press. pp 211-234

Deciphering genome polymorphism in grapevine

Deciphering genome polymorphism in grapevine
  • A 18K Infinium genotyping chip for grapevine has been developed in the frame of a EU project ([1]) and resources are provided at [2]
  • Many other project are in progress to re-sequence genotypes from the Vitis genus: see for instance Da Silva et al 2013.
  • A first genome wide SNP discovery project was carried out by Myles et al (2010).
  • A de novo assembly of the sequence of the highly heterozygous V. vinifera cv Pinot Noir genome was obtained by Velasco et al (2007) and can be browsed at IASMA.