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

Research output: Contribution to journalArticle

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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 languageEnglish (US)
Pages (from-to)487-494
Number of pages8
JournalNature Genetics
Volume45
Issue number5
DOIs
StatePublished - May 1 2013

All Science Journal Classification (ASJC) codes

  • Genetics

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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