Genome Sequencing

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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).

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

  • 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.


References

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 (2007). A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2:e1326

Myles S, Chia J-M, Hurwitz B, Simon C, Zhong GY, Buckler E, Ware D (2010) Rapid Genomic Characterization of the Genus Vitis. PLOS ONE , 5: e8219

Da Silva C, Zamperin G, Ferrarini A, Minio A, Dal Molin A, Venturini L, Buson G, Tononi P, Avanzato C, Zago E, Boido E, Dellacassa E, Gaggero C, Pezzotti M, Carrau F, Delledonne M (2013) The High Polyphenol Content of Grapevine Cultivar Tannat Berries Is Conferred Primarily by Genes That Are Not Shared with the Reference Genome. Plant Cell. 2013 Dec 6


BAC libraries & BAC-end Sequencing

  • BAC end sequences obtained from Cabernet Sauvignon, Pinot Noir and PN40024 BAC clones and have been submitted to GenBank. The BES collections can also be retrieved at URGI


References

Tomkins JP, Peterson DG, Yang TJ, Ablett ER, Henry RJ, Lee LS, Holton TA, Waters D, Wing RA (2001). Grape (Vitis vinifera L;) BAC library construction, preliminary STC analysis, and identification of clones associated with flavonoid and stilbene biosynthesis. AM Am J Enol Vitic, 52 : 287-291

Adam-Blondon A-F, Bernole A, Faes G, Lamoureux D, Pateyron S, Grando MS, Caboche M, Velasco R, Chalhoub B (2005) Construction and characterization of BAC libraries from major grapevine cultivars. Theor Appl Genet 110:1363-1371

Lamoureux D, Bernole A, Le Clainche I, Tual, S, Thareau V, Paillard S, Legeai F, Dossat C, Wincker P, Oswald M, Merdinoglu D, Vignault C, Delrot S, Caboche M, Chalhoub B, Adam-Blondon A-F (2006). Anchoring a large set of markers onto a BAC library for the development of a draft physical map of the grapevine genome. Theor Appl Genet 113:344-356

This page is maintained by Anne-Françoise Adam-Blondon (email)

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