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

Ignazio Verde; Albert G. Abbott; Simone Scalabrin; Sook Jung; Shengqiang Shu; Fabio Marroni; Tatyana Zhebentyayeva; Maria Teresa Dettori; Jane Grimwood; Federica Cattonaro; Andrea Zuccolo; Laura Rossini; Jerry Jenkins; Elisa Vendramin; Lee A. Meisel; Veronique Decroocq; Bryon Sosinski; Simon Prochnik; Therese Mitros; Alberto Policriti; Guido Cipriani; Luca Dondini; Stephen Ficklin; David M. Goodstein; Pengfei Xuan; Cristian Del Fabbro; Valeria Aramini; Dario Copetti; Susana Gonzalez; David S. Horner; Rachele Falchi; Susan Lucas; Erica Mica; Jonathan Maldonado; Barbara Lazzari; Douglas Bielenberg; Raul Pirona; Mara Miculan; Abdelali Barakat; Raffaele Testolin; Alessandra Stella; Stefano Tartarini; Pietro Tonutti; Pere Arús; Ariel Orellana; Christina Wells; Dorrie Main; Giannina Vizzotto; Herman Silva; Francesco Salamini; Jeremy Schmutz; Michele Morgante; Daniel S. Rokhsar

doi:10.1038/ng.2586

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

Ignazio Verde, Albert G. Abbott, Simone Scalabrin, Sook Jung, Shengqiang Shu, Fabio Marroni, Tatyana Zhebentyayeva, Maria Teresa Dettori, Jane Grimwood, Federica Cattonaro, Andrea Zuccolo, Laura Rossini, Jerry Jenkins, Elisa Vendramin, Lee A. Meisel, Veronique Decroocq, Bryon Sosinski, Simon Prochnik, Therese Mitros, Alberto PolicritiGuido Cipriani, Luca Dondini, Stephen Ficklin, David M. Goodstein, Pengfei Xuan, Cristian Del Fabbro, Valeria Aramini, Dario Copetti, Susana Gonzalez, David S. Horner, Rachele Falchi, Susan Lucas, Erica Mica, Jonathan Maldonado, Barbara Lazzari, Douglas Bielenberg, Raul Pirona, Mara Miculan, Abdelali Barakat, Raffaele Testolin, Alessandra Stella, Stefano Tartarini, Pietro Tonutti, Pere Arús, Ariel Orellana, Christina Wells, Dorrie Main, Giannina Vizzotto, Herman Silva, Francesco Salamini, Jeremy Schmutz, Michele Morgante, Daniel S. Rokhsar

Life Sciences School

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915 Citations (Scopus)

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.

Original language	English
Pages (from-to)	487-494
Number of pages	8
Journal	Nature Genetics
Volume	45
Issue number	5
DOIs	https://doi.org/10.1038/ng.2586
Publication status	Published - May 2013

ASJC Scopus subject areas

Genetics

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10.1038/ng.2586

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Verde, I., Abbott, A. G., Scalabrin, S., Jung, S., Shu, S., Marroni, F., Zhebentyayeva, T., Dettori, M. T., Grimwood, J., Cattonaro, F., Zuccolo, A., Rossini, L., Jenkins, J., Vendramin, E., Meisel, L. A., Decroocq, V., Sosinski, B., Prochnik, S., Mitros, T., ... Rokhsar, D. S. (2013). The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nature Genetics, 45(5), 487-494. https://doi.org/10.1038/ng.2586

@article{e1ae7f31f7a74fe7a789e21694998567,

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.",

author = "Ignazio Verde and Abbott, {Albert G.} and Simone Scalabrin and Sook Jung and Shengqiang Shu and Fabio Marroni and Tatyana Zhebentyayeva and Dettori, {Maria Teresa} and Jane Grimwood and Federica Cattonaro and Andrea Zuccolo and Laura Rossini and Jerry Jenkins and Elisa Vendramin and Meisel, {Lee A.} and Veronique Decroocq and Bryon Sosinski and Simon Prochnik and Therese Mitros and Alberto Policriti and Guido Cipriani and Luca Dondini and Stephen Ficklin and Goodstein, {David M.} and Pengfei Xuan and {Del Fabbro}, Cristian and Valeria Aramini and Dario Copetti and Susana Gonzalez and Horner, {David S.} and Rachele Falchi and Susan Lucas and Erica Mica and Jonathan Maldonado and Barbara Lazzari and Douglas Bielenberg and Raul Pirona and Mara Miculan and Abdelali Barakat and Raffaele Testolin and Alessandra Stella and Stefano Tartarini and Pietro Tonutti and Pere Ar{\'u}s and Ariel Orellana and Christina Wells and Dorrie Main and Giannina Vizzotto and Herman Silva and Francesco Salamini and Jeremy Schmutz and Michele Morgante and Rokhsar, {Daniel S.}",

note = "Funding Information: This work was jointly supported by the Office of Science of the US Department of Energy under contract number DE-AC02-05CH11231 and the Ministero delle Politiche Agricole Alimentari e Forestali–Italy (MiPAAF, http://www. politicheagricole.it) through the project {\textquoteleft}DRUPOMICS{\textquoteright} (grant DM14999/7303/08). We would also like to thank the US Department of Agriculture (USDA) for their support of the peach genomics program through USDA National Institute of Food and Agriculture (NIFA) Specialty Crop Research Initiative (SCRI) grant 2010-2010-03255, the Robert and Louis Coker Chair for Plant Molecular Genetics for their grant to Clemson University, the Chilean government for supporting this work through FDI G02P1001 (Chilean Genome Initiative), Basal ProgramPB-16 and FONDAP CRG15090007, the Consolider-Ingenio 2010 Program (CSD2007-00036) from the Spanish Ministry of Science and Innovation, the French National Research Agency (ANR) for supporting this work through Chex-ABRIWG ANR/ INRA 22000552, G. Reighard (Clemson University) for providing the leaf material of the Lovell double haploid, R. Quarta (Centro di Ricerca per la Frutticoltura di Roma (CRA-FRU)) and C. Pozzi (Fondazione Edmund Mach (FEM) S. Michele all{\textquoteright}Adige) for their efforts in the drafting of the DRUPOMICS proposal, T. Pascal (Institut National de la Recherche Agronomique (INRA) Avignon) for providing leaf material for the resequencing, T. Candresse (INRA Bordeaux) for his critical reading of the manuscript, M. Troggio (FEM S. Michele all{\textquoteright}Adige) for her help with the data analysis and G. Zhongshan (Zhejiang University) for the information provided about the Chinese peach accessions.",

year = "2013",

month = may,

doi = "10.1038/ng.2586",

language = "English",

volume = "45",

pages = "487--494",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Publishing Group",

number = "5",

}

Verde, I, Abbott, AG, Scalabrin, S, Jung, S, Shu, S, Marroni, F, Zhebentyayeva, T, Dettori, MT, Grimwood, J, Cattonaro, F, Zuccolo, A, Rossini, L, Jenkins, J, Vendramin, E, Meisel, LA, Decroocq, V, Sosinski, B, Prochnik, S, Mitros, T, Policriti, A, Cipriani, G, Dondini, L, Ficklin, S, Goodstein, DM, Xuan, P, Del Fabbro, C, Aramini, V, Copetti, D, Gonzalez, S, Horner, DS, Falchi, R, Lucas, S, Mica, E, Maldonado, J, Lazzari, B, Bielenberg, D, Pirona, R, Miculan, M, Barakat, A, Testolin, R, Stella, A, Tartarini, S, Tonutti, P, Arús, P, Orellana, A, Wells, C, Main, D, Vizzotto, G, Silva, H, Salamini, F, Schmutz, J, Morgante, M & Rokhsar, DS 2013, 'The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution', Nature Genetics, vol. 45, no. 5, pp. 487-494. https://doi.org/10.1038/ng.2586

TY - JOUR

T1 - The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

AU - Verde, Ignazio

AU - Abbott, Albert G.

AU - Scalabrin, Simone

AU - Jung, Sook

AU - Shu, Shengqiang

AU - Marroni, Fabio

AU - Zhebentyayeva, Tatyana

AU - Dettori, Maria Teresa

AU - Grimwood, Jane

AU - Cattonaro, Federica

AU - Zuccolo, Andrea

AU - Rossini, Laura

AU - Jenkins, Jerry

AU - Vendramin, Elisa

AU - Meisel, Lee A.

AU - Decroocq, Veronique

AU - Sosinski, Bryon

AU - Prochnik, Simon

AU - Mitros, Therese

AU - Policriti, Alberto

AU - Cipriani, Guido

AU - Dondini, Luca

AU - Ficklin, Stephen

AU - Goodstein, David M.

AU - Xuan, Pengfei

AU - Del Fabbro, Cristian

AU - Aramini, Valeria

AU - Copetti, Dario

AU - Gonzalez, Susana

AU - Horner, David S.

AU - Falchi, Rachele

AU - Lucas, Susan

AU - Mica, Erica

AU - Maldonado, Jonathan

AU - Lazzari, Barbara

AU - Bielenberg, Douglas

AU - Pirona, Raul

AU - Miculan, Mara

AU - Barakat, Abdelali

AU - Testolin, Raffaele

AU - Stella, Alessandra

AU - Tartarini, Stefano

AU - Tonutti, Pietro

AU - Arús, Pere

AU - Orellana, Ariel

AU - Wells, Christina

AU - Main, Dorrie

AU - Vizzotto, Giannina

AU - Silva, Herman

AU - Salamini, Francesco

AU - Schmutz, Jeremy

AU - Morgante, Michele

AU - Rokhsar, Daniel S.

N1 - Funding Information: This work was jointly supported by the Office of Science of the US Department of Energy under contract number DE-AC02-05CH11231 and the Ministero delle Politiche Agricole Alimentari e Forestali–Italy (MiPAAF, http://www. politicheagricole.it) through the project ‘DRUPOMICS’ (grant DM14999/7303/08). We would also like to thank the US Department of Agriculture (USDA) for their support of the peach genomics program through USDA National Institute of Food and Agriculture (NIFA) Specialty Crop Research Initiative (SCRI) grant 2010-2010-03255, the Robert and Louis Coker Chair for Plant Molecular Genetics for their grant to Clemson University, the Chilean government for supporting this work through FDI G02P1001 (Chilean Genome Initiative), Basal ProgramPB-16 and FONDAP CRG15090007, the Consolider-Ingenio 2010 Program (CSD2007-00036) from the Spanish Ministry of Science and Innovation, the French National Research Agency (ANR) for supporting this work through Chex-ABRIWG ANR/ INRA 22000552, G. Reighard (Clemson University) for providing the leaf material of the Lovell double haploid, R. Quarta (Centro di Ricerca per la Frutticoltura di Roma (CRA-FRU)) and C. Pozzi (Fondazione Edmund Mach (FEM) S. Michele all’Adige) for their efforts in the drafting of the DRUPOMICS proposal, T. Pascal (Institut National de la Recherche Agronomique (INRA) Avignon) for providing leaf material for the resequencing, T. Candresse (INRA Bordeaux) for his critical reading of the manuscript, M. Troggio (FEM S. Michele all’Adige) for her help with the data analysis and G. Zhongshan (Zhejiang University) for the information provided about the Chinese peach accessions.

PY - 2013/5

Y1 - 2013/5

N2 - 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.

AB - 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.

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U2 - 10.1038/ng.2586

DO - 10.1038/ng.2586

M3 - Article

C2 - 23525075

AN - SCOPUS:84878553926

SN - 1061-4036

VL - 45

SP - 487

EP - 494

JO - Nature Genetics

JF - Nature Genetics

IS - 5

ER -

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

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