The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution
The International Peach Genome Initiative: et al. ; 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. ; 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. ; Peer reviewed