The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

被引：906

作者：

Verde, Ignazio ^{[1
]}

Abbott, Albert G. ^{[2
,3
]}

Scalabrin, Simone ^{[4
]}

Jung, Sook ^{[5
]}

Shu, Shengqiang ^{[6
]}

Marroni, Fabio ^{[4
,7
]}

Zhebentyayeva, Tatyana ^{[2
]}

Dettori, Maria Teresa ^{[1
]}

Grimwood, Jane ^{[6
,8
]}

Cattonaro, Federica ^{[4
]}

Zuccolo, Andrea ^{[4
,9
]}

Rossini, Laura ^{[10
,11
]}

Jenkins, Jerry ^{[6
,8
]}

Vendramin, Elisa ^{[1
]}

Meisel, Lee A. ^{[12
,13
]}

Decroocq, Veronique ^{[3
]}

Sosinski, Bryon ^{[14
]}

Prochnik, Simon ^{[6
]}

Mitros, Therese ^{[15
]}

Policriti, Alberto ^{[4
,16
]}

Cipriani, Guido ^{[1
,7
]}

Dondini, Luca ^{[17
]}

Ficklin, Stephen ^{[5
]}

Goodstein, David M. ^{[6
]}

Xuan, Pengfei ^{[18
]}

Del Fabbro, Cristian ^{[4
]}

Aramini, Valeria ^{[1
]}

Copetti, Dario ^{[4
]}

Gonzalez, Susana ^{[19
]}

Horner, David S. ^{[20
]}

Falchi, Rachele ^{[7
]}

Lucas, Susan ^{[6
]}

Mica, Erica ^{[9
]}

Maldonado, Jonathan ^{[21
]}

Lazzari, Barbara ^{[10
]}

Bielenberg, Douglas ^{[22
]}

Pirona, Raul ^{[10
]}

Miculan, Mara ^{[4
]}

Barakat, Abdelali ^{[2
]}

Testolin, Raffaele ^{[4
,7
]}

Stella, Alessandra ^{[10
,23
]}

Tartarini, Stefano ^{[17
]}

Tonutti, Pietro ^{[9
]}

Arus, Pere ^{[24
]}

Orellana, Ariel ^{[19
]}

Wells, Christina ^{[22
]}

Main, Dorrie ^{[5
]}

Vizzotto, Giannina ^{[7
]}

Silva, Herman ^{[21
]}

Salamini, Francesco ^{[10
,25
]}

机构：

[1] Ctr Ric Frutticoltura, Consiglio Ric & Sperimentaz Agr CRA, Rome, Italy

[2] Clemson Univ, Dept Genet & Biochem, Clemson, SC USA

[3] Univ Bordeaux, INRA, UMR Biol Fruit & Pathol BFP 1332, Villenave Dornon, France

[4] IGA, Udine, Italy

[5] Washington State Univ, Dept Hort & Landscape Architecture, Pullman, WA 99164 USA

[6] US Dept Energy Joint Genome Inst, Walnut Creek, CA USA

[7] Univ Udine, Dipartimento Sci Agr & Ambientali, I-33100 Udine, Italy

[8] HudsonAlpha Inst Biotechnol, Huntsville, AL USA

[9] SSSA, Pisa, Italy

[10] Parco Tecnol Padano, Lodi, Italy

[11] Univ Milan, Dipartimento Sci Agr & Ambientali Prod, Milan, Italy

[12] Univ Chile, INTA, Santiago, Chile

[13] Univ Andres Bello, Fac Ciencias Biol, Ctr Biotecnol Vegetal, Santiago, Chile

[14] N Carolina State Univ, Dept Hort Sci, Raleigh, NC 27695 USA

[15] Univ Calif Berkeley, Energy Biosci Inst, Berkeley, CA 94720 USA

[16] Univ Udine, Dipartimento Matemat & Informat, I-33100 Udine, Italy

[17] Univ Bologna, Dept Fruit Tree & Woody Plant Sci, Bologna, Italy

[18] Clemson Univ, Sch Comp, Clemson, SC USA

[19] Univ Andres Bello, Fondo Invest Avanzada Areas Prioritarias FONDAP, Ctr Genome Regulat, Ctr Biotecnol Vegetal,Fac Ciencias Biol, Santiago, Chile

[20] Univ Milan, Dipartimento Sci Biomol & Biotecnol, Milan, Italy

[21] Univ Chile, Fac Ciencias Agron, Lab Genom Func & Bioinformat, La Pintana, Chile

[22] Clemson Univ, Sch Agr Forest & Environm Sci, Clemson, SC USA

[23] CNR, Ist Biol & Biotecnol Agr, Lodi, Italy

[24] Univ Barcelona, Univ Autonoma Barcelona, IRTA, Ctr Recerca Agrigenom,CSIC,IRTA, Barcelona, Spain

[25] Fdn Edmund Mach, IASMA, Res & Innovat Ctr, San Michele All Adige, Trento, Italy

[26] Univ Calif Berkeley, Ctr Integrat Genom, Berkeley, CA 94720 USA

来源：

NATURE GENETICS | 2013年 / 45卷 / 05期

基金：

美国食品与农业研究所;

关键词：

LINKAGE DISEQUILIBRIUM; SORBITOL TRANSPORTERS; NUCLEOTIDE DIVERSITY; WHOLE; CULTIVARS; PHLOEM; MODEL; FRUIT; RNA; METABOLISM;

D O I：

10.1038/ng.2586

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页码：487 / 494

页数：8

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