The genome of the domesticated apple (Malus × domestica Borkh.)

Riccardo Velasco, Andrey Zharkikh, Jason Affourtit, Amit Dhingra, Alessandro Cestaro, Ananth Kalyanaraman, Paolo Fontana, Satish K. Bhatnagar, Michela Troggio, Dmitry Pruss, Silvio Salvi, Massimo Pindo, Paolo Baldi, Sara Castelletti, Marina Cavaiuolo, Giuseppina Coppola, Fabrizio Costa, Valentina Cova, Antonio Dal Ri, Vadim Goremykin & 66 others Matteo Komjanc, Sara Longhi, Pierluigi Magnago, Giulia Malacarne, Mickael Malnoy, Diego Micheletti, Marco Moretto, Michele Perazzolli, Azeddine Si-Ammour, Silvia Vezzulli, Elena Zini, Glenn Eldredge, Lisa M. Fitzgerald, Natalia Gutin, Jerry Lanchbury, Teresita MacAlma, Jeff T. Mitchell, Julia Reid, Bryan Wardell, Chinnappa Kodira, Zhoutao Chen, Brian Desany, Faheem Niazi, Melinda Palmer, Tyson Koepke, Derick Jiwan, Scott Schaeffer, Vandhana Krishnan, Changjun Wu, Vu T. Chu, Stephen T. King, Jessica Vick, Quanzhou Tao, Amy Mraz, Aimee Stormo, Keith Stormo, Robert Bogden, Davide Ederle, Alessandra Stella, Alberto Vecchietti, Martin M. Kater, Simona Masiero, Pauline Lasserre, Yves Lespinasse, Andrew C. Allan, Vincent Bus, David Chagné, Ross N. Crowhurst, Andrew P. Gleave, Enrico Lavezzo, Jeffrey A. Fawcett, Sebastian Proost, Pierre Rouzé, Lieven Sterck, Stefano Toppo, Barbara Lazzari, Roger P. Hellens, Charles Eric Durel, Alexander Gutin, Roger E. Bumgarner, Susan E. Gardiner, Mark Skolnick, Michael Egholm, Yves Van De Peer, Francesco Salamini, Roberto Viola

  • 753 Citations

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. © 2010 Nature America, Inc. All rights reserved.

Original languageEnglish
Pages (from-to)833-839
Number of pages7
JournalNature Genetics
Volume42
Issue number10
DOIs
StatePublished - Oct 2010
Externally publishedYes

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Malus
Genome
Fruit
Genes
Rosaceae
Chromosomes, Human, Pair 17
Sorbitol
Chromosomes

ASJC Scopus subject areas

  • Genetics
  • Medicine(all)

Cite this

Velasco, R., Zharkikh, A., Affourtit, J., Dhingra, A., Cestaro, A., Kalyanaraman, A., ... Viola, R. (2010). The genome of the domesticated apple (Malus × domestica Borkh.). Nature Genetics, 42(10), 833-839. DOI: 10.1038/ng.654

The genome of the domesticated apple (Malus × domestica Borkh.). / Velasco, Riccardo; Zharkikh, Andrey; Affourtit, Jason; Dhingra, Amit; Cestaro, Alessandro; Kalyanaraman, Ananth; Fontana, Paolo; Bhatnagar, Satish K.; Troggio, Michela; Pruss, Dmitry; Salvi, Silvio; Pindo, Massimo; Baldi, Paolo; Castelletti, Sara; Cavaiuolo, Marina; Coppola, Giuseppina; Costa, Fabrizio; Cova, Valentina; Dal Ri, Antonio; Goremykin, Vadim; Komjanc, Matteo; Longhi, Sara; Magnago, Pierluigi; Malacarne, Giulia; Malnoy, Mickael; Micheletti, Diego; Moretto, Marco; Perazzolli, Michele; Si-Ammour, Azeddine; Vezzulli, Silvia; Zini, Elena; Eldredge, Glenn; Fitzgerald, Lisa M.; Gutin, Natalia; Lanchbury, Jerry; MacAlma, Teresita; Mitchell, Jeff T.; Reid, Julia; Wardell, Bryan; Kodira, Chinnappa; Chen, Zhoutao; Desany, Brian; Niazi, Faheem; Palmer, Melinda; Koepke, Tyson; Jiwan, Derick; Schaeffer, Scott; Krishnan, Vandhana; Wu, Changjun; Chu, Vu T.; King, Stephen T.; Vick, Jessica; Tao, Quanzhou; Mraz, Amy; Stormo, Aimee; Stormo, Keith; Bogden, Robert; Ederle, Davide; Stella, Alessandra; Vecchietti, Alberto; Kater, Martin M.; Masiero, Simona; Lasserre, Pauline; Lespinasse, Yves; Allan, Andrew C.; Bus, Vincent; Chagné, David; Crowhurst, Ross N.; Gleave, Andrew P.; Lavezzo, Enrico; Fawcett, Jeffrey A.; Proost, Sebastian; Rouzé, Pierre; Sterck, Lieven; Toppo, Stefano; Lazzari, Barbara; Hellens, Roger P.; Durel, Charles Eric; Gutin, Alexander; Bumgarner, Roger E.; Gardiner, Susan E.; Skolnick, Mark; Egholm, Michael; Van De Peer, Yves; Salamini, Francesco; Viola, Roberto.

In: Nature Genetics, Vol. 42, No. 10, 10.2010, p. 833-839.

Research output: Contribution to journalArticle

Velasco, R, Zharkikh, A, Affourtit, J, Dhingra, A, Cestaro, A, Kalyanaraman, A, Fontana, P, Bhatnagar, SK, Troggio, M, Pruss, D, Salvi, S, Pindo, M, Baldi, P, Castelletti, S, Cavaiuolo, M, Coppola, G, Costa, F, Cova, V, Dal Ri, A, Goremykin, V, Komjanc, M, Longhi, S, Magnago, P, Malacarne, G, Malnoy, M, Micheletti, D, Moretto, M, Perazzolli, M, Si-Ammour, A, Vezzulli, S, Zini, E, Eldredge, G, Fitzgerald, LM, Gutin, N, Lanchbury, J, MacAlma, T, Mitchell, JT, Reid, J, Wardell, B, Kodira, C, Chen, Z, Desany, B, Niazi, F, Palmer, M, Koepke, T, Jiwan, D, Schaeffer, S, Krishnan, V, Wu, C, Chu, VT, King, ST, Vick, J, Tao, Q, Mraz, A, Stormo, A, Stormo, K, Bogden, R, Ederle, D, Stella, A, Vecchietti, A, Kater, MM, Masiero, S, Lasserre, P, Lespinasse, Y, Allan, AC, Bus, V, Chagné, D, Crowhurst, RN, Gleave, AP, Lavezzo, E, Fawcett, JA, Proost, S, Rouzé, P, Sterck, L, Toppo, S, Lazzari, B, Hellens, RP, Durel, CE, Gutin, A, Bumgarner, RE, Gardiner, SE, Skolnick, M, Egholm, M, Van De Peer, Y, Salamini, F & Viola, R 2010, 'The genome of the domesticated apple (Malus × domestica Borkh.)' Nature Genetics, vol 42, no. 10, pp. 833-839. DOI: 10.1038/ng.654
Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A et al. The genome of the domesticated apple (Malus × domestica Borkh.). Nature Genetics. 2010 Oct;42(10):833-839. Available from, DOI: 10.1038/ng.654

Velasco, Riccardo; Zharkikh, Andrey; Affourtit, Jason; Dhingra, Amit; Cestaro, Alessandro; Kalyanaraman, Ananth; Fontana, Paolo; Bhatnagar, Satish K.; Troggio, Michela; Pruss, Dmitry; Salvi, Silvio; Pindo, Massimo; Baldi, Paolo; Castelletti, Sara; Cavaiuolo, Marina; Coppola, Giuseppina; Costa, Fabrizio; Cova, Valentina; Dal Ri, Antonio; Goremykin, Vadim; Komjanc, Matteo; Longhi, Sara; Magnago, Pierluigi; Malacarne, Giulia; Malnoy, Mickael; Micheletti, Diego; Moretto, Marco; Perazzolli, Michele; Si-Ammour, Azeddine; Vezzulli, Silvia; Zini, Elena; Eldredge, Glenn; Fitzgerald, Lisa M.; Gutin, Natalia; Lanchbury, Jerry; MacAlma, Teresita; Mitchell, Jeff T.; Reid, Julia; Wardell, Bryan; Kodira, Chinnappa; Chen, Zhoutao; Desany, Brian; Niazi, Faheem; Palmer, Melinda; Koepke, Tyson; Jiwan, Derick; Schaeffer, Scott; Krishnan, Vandhana; Wu, Changjun; Chu, Vu T.; King, Stephen T.; Vick, Jessica; Tao, Quanzhou; Mraz, Amy; Stormo, Aimee; Stormo, Keith; Bogden, Robert; Ederle, Davide; Stella, Alessandra; Vecchietti, Alberto; Kater, Martin M.; Masiero, Simona; Lasserre, Pauline; Lespinasse, Yves; Allan, Andrew C.; Bus, Vincent; Chagné, David; Crowhurst, Ross N.; Gleave, Andrew P.; Lavezzo, Enrico; Fawcett, Jeffrey A.; Proost, Sebastian; Rouzé, Pierre; Sterck, Lieven; Toppo, Stefano; Lazzari, Barbara; Hellens, Roger P.; Durel, Charles Eric; Gutin, Alexander; Bumgarner, Roger E.; Gardiner, Susan E.; Skolnick, Mark; Egholm, Michael; Van De Peer, Yves; Salamini, Francesco; Viola, Roberto / The genome of the domesticated apple (Malus × domestica Borkh.).

In: Nature Genetics, Vol. 42, No. 10, 10.2010, p. 833-839.

Research output: Contribution to journalArticle

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