title: The genome of the domesticated apple (Malus × domestica Borkh.).
abstract: 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.
authors.affiliation: Istituto Agrario San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, Trento, Italy. riccardo.velasco@iasma.it
authors.forename: Riccardo
authors.initials: R
authors.lastname: Velasco
authors.forename: Andrey
authors.initials: A
authors.lastname: Zharkikh
authors.forename: Jason
authors.initials: J
authors.lastname: Affourtit
authors.forename: Amit
authors.initials: A
authors.lastname: Dhingra
authors.forename: Alessandro
authors.initials: A
authors.lastname: Cestaro
authors.forename: Ananth
authors.initials: A
authors.lastname: Kalyanaraman
authors.forename: Paolo
authors.initials: P
authors.lastname: Fontana
authors.forename: Satish K
authors.initials: SK
authors.lastname: Bhatnagar
authors.forename: Michela
authors.initials: M
authors.lastname: Troggio
authors.forename: Dmitry
authors.initials: D
authors.lastname: Pruss
authors.forename: Silvio
authors.initials: S
authors.lastname: Salvi
authors.forename: Massimo
authors.initials: M
authors.lastname: Pindo
authors.forename: Paolo
authors.initials: P
authors.lastname: Baldi
authors.forename: Sara
authors.initials: S
authors.lastname: Castelletti
authors.forename: Marina
authors.initials: M
authors.lastname: Cavaiuolo
authors.forename: Giuseppina
authors.initials: G
authors.lastname: Coppola
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Costa
authors.forename: Valentina
authors.initials: V
authors.lastname: Cova
authors.forename: Antonio
authors.initials: A
authors.lastname: Dal Ri
authors.forename: Vadim
authors.initials: V
authors.lastname: Goremykin
authors.forename: Matteo
authors.initials: M
authors.lastname: Komjanc
authors.forename: Sara
authors.initials: S
authors.lastname: Longhi
authors.forename: Pierluigi
authors.initials: P
authors.lastname: Magnago
authors.forename: Giulia
authors.initials: G
authors.lastname: Malacarne
authors.forename: Mickael
authors.initials: M
authors.lastname: Malnoy
authors.forename: Diego
authors.initials: D
authors.lastname: Micheletti
authors.forename: Marco
authors.initials: M
authors.lastname: Moretto
authors.forename: Michele
authors.initials: M
authors.lastname: Perazzolli
authors.forename: Azeddine
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authors.lastname: Si-Ammour
authors.forename: Silvia
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authors.lastname: Vezzulli
authors.forename: Elena
authors.initials: E
authors.lastname: Zini
authors.forename: Glenn
authors.initials: G
authors.lastname: Eldredge
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Fitzgerald
authors.forename: Natalia
authors.initials: N
authors.lastname: Gutin
authors.forename: Jerry
authors.initials: J
authors.lastname: Lanchbury
authors.forename: Teresita
authors.initials: T
authors.lastname: Macalma
authors.forename: Jeff T
authors.initials: JT
authors.lastname: Mitchell
authors.forename: Julia
authors.initials: J
authors.lastname: Reid
authors.forename: Bryan
authors.initials: B
authors.lastname: Wardell
authors.forename: Chinnappa
authors.initials: C
authors.lastname: Kodira
authors.forename: Zhoutao
authors.initials: Z
authors.lastname: Chen
authors.forename: Brian
authors.initials: B
authors.lastname: Desany
authors.forename: Faheem
authors.initials: F
authors.lastname: Niazi
authors.forename: Melinda
authors.initials: M
authors.lastname: Palmer
authors.forename: Tyson
authors.initials: T
authors.lastname: Koepke
authors.forename: Derick
authors.initials: D
authors.lastname: Jiwan
authors.forename: Scott
authors.initials: S
authors.lastname: Schaeffer
authors.forename: Vandhana
authors.initials: V
authors.lastname: Krishnan
authors.forename: Changjun
authors.initials: C
authors.lastname: Wu
authors.forename: Vu T
authors.initials: VT
authors.lastname: Chu
authors.forename: Stephen T
authors.initials: ST
authors.lastname: King
authors.forename: Jessica
authors.initials: J
authors.lastname: Vick
authors.forename: Quanzhou
authors.initials: Q
authors.lastname: Tao
authors.forename: Amy
authors.initials: A
authors.lastname: Mraz
authors.forename: Aimee
authors.initials: A
authors.lastname: Stormo
authors.forename: Keith
authors.initials: K
authors.lastname: Stormo
authors.forename: Robert
authors.initials: R
authors.lastname: Bogden
authors.forename: Davide
authors.initials: D
authors.lastname: Ederle
authors.forename: Alessandra
authors.initials: A
authors.lastname: Stella
authors.forename: Alberto
authors.initials: A
authors.lastname: Vecchietti
authors.forename: Martin M
authors.initials: MM
authors.lastname: Kater
authors.forename: Simona
authors.initials: S
authors.lastname: Masiero
authors.forename: Pauline
authors.initials: P
authors.lastname: Lasserre
authors.forename: Yves
authors.initials: Y
authors.lastname: Lespinasse
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Allan
authors.forename: Vincent
authors.initials: V
authors.lastname: Bus
authors.forename: David
authors.initials: D
authors.lastname: Chagné
authors.forename: Ross N
authors.initials: RN
authors.lastname: Crowhurst
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Gleave
authors.forename: Enrico
authors.initials: E
authors.lastname: Lavezzo
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Fawcett
authors.forename: Sebastian
authors.initials: S
authors.lastname: Proost
authors.forename: Pierre
authors.initials: P
authors.lastname: Rouzé
authors.forename: Lieven
authors.initials: L
authors.lastname: Sterck
authors.forename: Stefano
authors.initials: S
authors.lastname: Toppo
authors.forename: Barbara
authors.initials: B
authors.lastname: Lazzari
authors.forename: Roger P
authors.initials: RP
authors.lastname: Hellens
authors.forename: Charles-Eric
authors.initials: CE
authors.lastname: Durel
authors.forename: Alexander
authors.initials: A
authors.lastname: Gutin
authors.forename: Roger E
authors.initials: RE
authors.lastname: Bumgarner
authors.forename: Susan E
authors.initials: SE
authors.lastname: Gardiner
authors.forename: Mark
authors.initials: M
authors.lastname: Skolnick
authors.forename: Michael
authors.initials: M
authors.lastname: Egholm
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.forename: Francesco
authors.initials: F
authors.lastname: Salamini
authors.forename: Roberto
authors.initials: R
authors.lastname: Viola
mesh_terms: 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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