Abstract
We report a high-quality draft genome sequence of the domesticated apple (Malus × domestica). We show that a relatively recent (>50 million years ago) genome-wide duplication (GWD) has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae. Traces of older GWDs partly support the monophyly of the ancestral paleohexaploidy of eudicots. Phylogenetic reconstruction of Pyreae and the genus Malus, relative to major Rosaceae taxa, identified the progenitor of the cultivated apple as M. sieversii. Expansion of gene families reported to be involved in fruit development may explain formation of the pome, a Pyreae-specific false fruit that develops by proliferation of the basal part of the sepals, the receptacle. In apple, a subclade of MADS-box genes, normally involved in flower and fruit development, is expanded to include 15 members, as are other gene families involved in Rosaceae-specific metabolism, such as transport and assimilation of sorbitol.
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Acknowledgements
The Italian apple genome project was supported by the research office of the Provincia Autonoma di Trento. The US apple genome project was supported by Washington State University Agriculture Research Center, Washington Tree Fruit Research Commission and US Department of Agriculture National Research Initiative (USDA-NRI) grant 2008 −35300-04676 to A.D., A.K. and R.E.B. V.K. and C.W. received support from the USDA-NRI grant. S. Schaeffer and T.K. were supported by the US National Institutes of Health Protein Biotechnology Training Program and an Achievement Rewards for College Scientists fellowship. A.C.A., V.B., D.C., A.P.G., S.E.G., R.P.H. and R.N.C. were partially supported by the New Zealand Foundation for Research Science and Technology, contract no. C06X0812. We thank S. Attiya, E. Buglione and C. Celone from 454 Life Sciences-Roche Company as well as E. Stefani, A. Castelli and E. Potenza for technical support and V. Sgaramella for critical reading of the manuscript. Fosmid and shotgun libraries were prepared following the method developed by R. Meilan (Oregon State University).
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R. Velasco, A.D., A.K., R.E.B., M.S., M.E., F.S. and R. Viola managed the project. R. Velasco, A.Z., J.A., A.D., A.C., A.K., P.F., S.K.B., M.T., D.P., S. Salvi, J.L., A.G., R.E.B., S.E.G., M.S., M.E., Y.V.d.P. and F.S. designed the analyses. J.A., S.K.B., D.P., M. Pindo, G.C., D.M., G.E., L.M.F., N.G., T.M., J.T.M., J.R., B.W., C.K., Z.C., B.D., F.N., M. Palmer, T.K., D.J., S. Schaeffer, V.T.C., S.T.K., J.V., Q.T., A.M., A. Stormo, K.S. and R.B. performed DNA preparation and sequencing. R. Velasco, A.Z., A.D., A.C., A.K., P.F., M.T., D.P., P.B., V.C., A.D.R., M.K., P.M., D.M., P.L., Y.L., V.B., D.C., R.N.C., S.T., C.-E.D., A.G., R.E.B. and S.E.G. contributed to sequence assembly and anchoring to chromosomes. A.Z., A.D., A.C., A.K., P.F., M.T., S. Salvi, M. Pindo, S.C., M.C., F.C., V.G., S.L., G.M., M. Malnoy, D.M., M. Moretto, M. Perazzolli, A.S.-A., S.V., E.Z., V.K., C.W., D.E., A. Stella, A.V., M.M.K., S.M., A.C.A., R.N.C., A.P.G., E.L., J.A.F., S.P., P.R., L.S., S.T., B.L., R.P.H., Y.V.d.P. and F.S. contributed to automatic and manual genome annotation, genome structure and evolution analyses. R. Velasco, A.Z., J.A., A.D., A.K., P.F., M.T., S. Salvi, F.C., M. Malnoy, A.S.-A., S.V., R.E.B., A.V., S.M., J.A.F., L.S., S.T., B.L. and F.S. wrote the paper. M.M.K., A.C.A., R.N.C., A.P.G., R.P.H., C.-E.D., A.G., R.E.B., S.E.G., M.S., Y.V.d.P. and R. Viola revised the paper. All authors read and approved the manuscript.
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Supplementary Note, Supplementary Tables 1–10 and 12–26 and Supplementary Figures 1–16 (PDF 10993 kb)
Supplementary Table 11
Resistance-related genes of Malus x domestica (XLS 197 kb)
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Velasco, R., Zharkikh, A., Affourtit, J. et al. The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42, 833–839 (2010). https://doi.org/10.1038/ng.654
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DOI: https://doi.org/10.1038/ng.654
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