A high quality draft consensus sequence of the genome of a heterozygous grapevine variety.
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.


RESULTS
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.
Velasco
Riccardo
R
IASMA Research Center, San Michele all'Adige, Trento, Italy. riccardo.velasco@iasma.it
Zharkikh
Andrey
A
Troggio
Michela
M
Cartwright
Dustin A
DA
Cestaro
Alessandro
A
Pruss
Dmitry
D
Pindo
Massimo
M
Fitzgerald
Lisa M
LM
Vezzulli
Silvia
S
Reid
Julia
J
Malacarne
Giulia
G
Iliev
Diana
D
Coppola
Giuseppina
G
Wardell
Bryan
B
Micheletti
Diego
D
Macalma
Teresita
T
Facci
Marco
M
Mitchell
Jeff T
JT
Perazzolli
Michele
M
Eldredge
Glenn
G
Gatto
Pamela
P
Oyzerski
Rozan
R
Moretto
Marco
M
Gutin
Natalia
N
Stefanini
Marco
M
Chen
Yang
Y
Segala
Cinzia
C
Davenport
Christine
C
Demattè
Lorenzo
L
Mraz
Amy
A
Battilana
Juri
J
Stormo
Keith
K
Costa
Fabrizio
F
Tao
Quanzhou
Q
Si-Ammour
Azeddine
A
Harkins
Tim
T
Lackey
Angie
A
Perbost
Clotilde
C
Taillon
Bruce
B
Stella
Alessandra
A
Solovyev
Victor
V
Fawcett
Jeffrey A
JA
Sterck
Lieven
L
Vandepoele
Klaas
K
Grando
Stella M
SM
Toppo
Stefano
S
Moser
Claudio
C
Lanchbury
Jerry
J
Bogden
Robert
R
Skolnick
Mark
M
Sgaramella
Vittorio
V
Bhatnagar
Satish K
SK
Fontana
Paolo
P
Gutin
Alexander
A
Van de Peer
Yves
Y
Salamini
Francesco
F
Viola
Roberto
R
D032461:Chromosomes, Plant; D016384:Consensus Sequence; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D018745:Genome, Plant; D006579:Heterozygote; D010636:Phenols / Q000378:metabolism; D010935:Plant Diseases / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D013729:Terpenes / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism; D027843:Vitis / Q000235:genetics* / Q000378:metabolism
D018744:DNA, Plant; D010636:Phenols; D013729:Terpenes; D014157:Transcription Factors