The genome of the domesticated apple (Malus × domestica Borkh.).
We report a high-quality draft genome sequence of the domesticated apple (Malus × domestica). We show that a relatively recent (>50 million years ago) genome-wide duplication (GWD) has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae. Traces of older GWDs partly support the monophyly of the ancestral paleohexaploidy of eudicots. Phylogenetic reconstruction of Pyreae and the genus Malus, relative to major Rosaceae taxa, identified the progenitor of the cultivated apple as M. sieversii. Expansion of gene families reported to be involved in fruit development may explain formation of the pome, a Pyreae-specific false fruit that develops by proliferation of the basal part of the sepals, the receptacle. In apple, a subclade of MADS-box genes, normally involved in flower and fruit development, is expanded to include 15 members, as are other gene families involved in Rosaceae-specific metabolism, such as transport and assimilation of sorbitol.
Velasco
Riccardo
R
Istituto Agrario San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, Trento, Italy. riccardo.velasco@iasma.it
Zharkikh
Andrey
A
Affourtit
Jason
J
Dhingra
Amit
A
Cestaro
Alessandro
A
Kalyanaraman
Ananth
A
Fontana
Paolo
P
Bhatnagar
Satish K
SK
Troggio
Michela
M
Pruss
Dmitry
D
Salvi
Silvio
S
Pindo
Massimo
M
Baldi
Paolo
P
Castelletti
Sara
S
Cavaiuolo
Marina
M
Coppola
Giuseppina
G
Costa
Fabrizio
F
Cova
Valentina
V
Dal Ri
Antonio
A
Goremykin
Vadim
V
Komjanc
Matteo
M
Longhi
Sara
S
Magnago
Pierluigi
P
Malacarne
Giulia
G
Malnoy
Mickael
M
Micheletti
Diego
D
Moretto
Marco
M
Perazzolli
Michele
M
Si-Ammour
Azeddine
A
Vezzulli
Silvia
S
Zini
Elena
E
Eldredge
Glenn
G
Fitzgerald
Lisa M
LM
Gutin
Natalia
N
Lanchbury
Jerry
J
Macalma
Teresita
T
Mitchell
Jeff T
JT
Reid
Julia
J
Wardell
Bryan
B
Kodira
Chinnappa
C
Chen
Zhoutao
Z
Desany
Brian
B
Niazi
Faheem
F
Palmer
Melinda
M
Koepke
Tyson
T
Jiwan
Derick
D
Schaeffer
Scott
S
Krishnan
Vandhana
V
Wu
Changjun
C
Chu
Vu T
VT
King
Stephen T
ST
Vick
Jessica
J
Tao
Quanzhou
Q
Mraz
Amy
A
Stormo
Aimee
A
Stormo
Keith
K
Bogden
Robert
R
Ederle
Davide
D
Stella
Alessandra
A
Vecchietti
Alberto
A
Kater
Martin M
MM
Masiero
Simona
S
Lasserre
Pauline
P
Lespinasse
Yves
Y
Allan
Andrew C
AC
Bus
Vincent
V
Chagné
David
D
Crowhurst
Ross N
RN
Gleave
Andrew P
AP
Lavezzo
Enrico
E
Fawcett
Jeffrey A
JA
Proost
Sebastian
S
Rouzé
Pierre
P
Sterck
Lieven
L
Toppo
Stefano
S
Lazzari
Barbara
B
Hellens
Roger P
RP
Durel
Charles-Eric
CE
Gutin
Alexander
A
Bumgarner
Roger E
RE
Gardiner
Susan E
SE
Skolnick
Mark
M
Egholm
Michael
M
Van de Peer
Yves
Y
Salamini
Francesco
F
Viola
Roberto
R
D035264:Flowers / Q000235:genetics / Q000254:growth & development; D005638:Fruit / Q000235:genetics / Q000254:growth & development; D020440:Gene Duplication; D017343:Genes, Plant / Q000235:genetics*; D008040:Genetic Linkage; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D027845:Malus / Q000235:genetics* / Q000254:growth & development; D010802:Phylogeny
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