title: The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.
abstract: Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.
authors.affiliation: Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA)-Centro di Ricerca per la Frutticoltura, Rome, Italy. ignazio.verde@entecra.it
authors.forename: Ignazio
authors.initials: I
authors.lastname: Verde
authors.forename: Albert G
authors.initials: AG
authors.lastname: Abbott
authors.forename: Simone
authors.initials: S
authors.lastname: Scalabrin
authors.forename: Sook
authors.initials: S
authors.lastname: Jung
authors.forename: Shengqiang
authors.initials: S
authors.lastname: Shu
authors.forename: Fabio
authors.initials: F
authors.lastname: Marroni
authors.forename: Tatyana
authors.initials: T
authors.lastname: Zhebentyayeva
authors.forename: Maria Teresa
authors.initials: MT
authors.lastname: Dettori
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.forename: Federica
authors.initials: F
authors.lastname: Cattonaro
authors.forename: Andrea
authors.initials: A
authors.lastname: Zuccolo
authors.forename: Laura
authors.initials: L
authors.lastname: Rossini
authors.forename: Jerry
authors.initials: J
authors.lastname: Jenkins
authors.forename: Elisa
authors.initials: E
authors.lastname: Vendramin
authors.forename: Lee A
authors.initials: LA
authors.lastname: Meisel
authors.forename: Veronique
authors.initials: V
authors.lastname: Decroocq
authors.forename: Bryon
authors.initials: B
authors.lastname: Sosinski
authors.forename: Simon
authors.initials: S
authors.lastname: Prochnik
authors.forename: Therese
authors.initials: T
authors.lastname: Mitros
authors.forename: Alberto
authors.initials: A
authors.lastname: Policriti
authors.forename: Guido
authors.initials: G
authors.lastname: Cipriani
authors.forename: Luca
authors.initials: L
authors.lastname: Dondini
authors.forename: Stephen
authors.initials: S
authors.lastname: Ficklin
authors.forename: David M
authors.initials: DM
authors.lastname: Goodstein
authors.forename: Pengfei
authors.initials: P
authors.lastname: Xuan
authors.forename: Cristian
authors.initials: C
authors.lastname: Del Fabbro
authors.forename: Valeria
authors.initials: V
authors.lastname: Aramini
authors.forename: Dario
authors.initials: D
authors.lastname: Copetti
authors.forename: Susana
authors.initials: S
authors.lastname: Gonzalez
authors.forename: David S
authors.initials: DS
authors.lastname: Horner
authors.forename: Rachele
authors.initials: R
authors.lastname: Falchi
authors.forename: Susan
authors.initials: S
authors.lastname: Lucas
authors.forename: Erica
authors.initials: E
authors.lastname: Mica
authors.forename: Jonathan
authors.initials: J
authors.lastname: Maldonado
authors.forename: Barbara
authors.initials: B
authors.lastname: Lazzari
authors.forename: Douglas
authors.initials: D
authors.lastname: Bielenberg
authors.forename: Raul
authors.initials: R
authors.lastname: Pirona
authors.forename: Mara
authors.initials: M
authors.lastname: Miculan
authors.forename: Abdelali
authors.initials: A
authors.lastname: Barakat
authors.forename: Raffaele
authors.initials: R
authors.lastname: Testolin
authors.forename: Alessandra
authors.initials: A
authors.lastname: Stella
authors.forename: Stefano
authors.initials: S
authors.lastname: Tartarini
authors.forename: Pietro
authors.initials: P
authors.lastname: Tonutti
authors.forename: Pere
authors.initials: P
authors.lastname: Arús
authors.forename: Ariel
authors.initials: A
authors.lastname: Orellana
authors.forename: Christina
authors.initials: C
authors.lastname: Wells
authors.forename: Dorrie
authors.initials: D
authors.lastname: Main
authors.forename: Giannina
authors.initials: G
authors.lastname: Vizzotto
authors.forename: Herman
authors.initials: H
authors.lastname: Silva
authors.forename: Francesco
authors.initials: F
authors.lastname: Salamini
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.forename: Michele
authors.initials: M
authors.lastname: Morgante
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Rokhsar
mesh_terms: D000383:Agriculture; D005075:Biological Evolution; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D011108:Polymers / Q000378:metabolism; D020005:Propanols / Q000378:metabolism; D027861:Prunus / Q000145:classification / Q000235:genetics*
chemical_list: D011108:Polymers; D020005:Propanols; C024617:polyol; C439395:1-phenylpropanol