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

Published in:

Nat Genet 45(5) , 487-94 (May 2013)

Author(s):

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., Policriti, A., Cipriani, G., Dondini, L., Ficklin, S., Goodstein, D. M., Xuan, P., Del Fabbro, C., Aramini, V., Copetti, D., Gonzalez, S., Horner, D. S., 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., Arus, P., Orellana, A., Wells, C., Main, D., Vizzotto, G., Silva, H., Salamini, F., Schmutz, J., Morgante, M., Rokhsar, D. S.

DOI:

10.1038/ng.2586

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.

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