Genome Sequencing
From IGGP
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 12.0X version of the assembly has been realeased at NCBI in November 2009 with the V0 version of the gene annotation.
The sequence can be retrieved or browsed at Genoscope and URGI. Other useful sites to browse the V0 version of the Pinot Noir genome are Gramene and Phytosome
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
Deciphering genome polymorphism in grapevine
- 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.
- A first genome wide SNP discovery project was carried out by Myles et al (2010).
- Many other project are in progress to re-sequence genotypes from the Vitis genus : Current Sequencing Projects
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
BAC libraries, Physical maps & BAC-end Sequencing
- BAC libraries have been developed from V. vinifera cv Cabernet Sauvignon, Pinot Noir, PN40024 and Syrah and are available at French Plant Genomic Resource Centreand CUGI.
- Physical maps have been constructed from the V. vinifera cv Cabernet Sauvignon and Pinot Noir and can be queries at URGI and IASMA.
- BAC end sequences obtained from Cabernet Sauvignon, Pinot Noir and PN40024 BAC clones and have been submitted to GenBank.
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
Moroldo M, Paillard S, Marconi R, Legeai F, Canaguier A, Cruaud C, De Berardinis V, Guichard C, Brunaud V, Le Clainche I, Scalabrin S, Testolin R, Di Gaspero G, Morgante M., Adam-Blondon A.F (2008). A physical map of the heterozygous grapevine ‘Cabernet Sauvignon’ allows mapping candidate genes for disease resistance. BMC Plant Biol, 8:66
Scalabrin S, Troggio M, Moroldo M, Pindo M, Felice N, Coppola G, Prete G, Malacarne G, Marconi R, Faes G, Jurman I, Grando S, Jesse T, Segala C, Valle G, Policriti A, Fontana P, Morgante M, Velasco R (2010) Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar BMC Genomics 11:204
This page is maintained by Anne-Françoise Adam-Blondon (email)
