High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Nicolas Daccord, Jean-Marc Celton, Gareth Linsmith, Claude Becker, Nathalie Choisne, Elio Schijlen, Henri van de Geest, Luca Bianco, Diego Micheletti, Riccardo Velasco, Erica Adele Di Pierro, Jérôme Gouzy, D.J.G. Rees, Philippe Guérif, Hélène Muranty, Charles Eric Durel, François Laurens, Yves Lespinasse, Sylvain Gaillard, Sébastien Aubourg & 5 others Hadi Quesneville, Detlef Weigel, Eric van de Weg, Michela Troggio, Etienne Bucher

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164 Citations (Scopus)

Abstract

Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.
Original languageEnglish
Pages (from-to)1099-1106
JournalNature Genetics
Volume49
Issue number7
DOIs
Publication statusPublished - 2017

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Malus
Fruit
DNA Transposable Elements
Genome
Pyrus
Retroelements
Nucleic Acid Repetitive Sequences
DNA Methylation
Epigenomics
Technology

Cite this

Daccord, N., Celton, J-M., Linsmith, G., Becker, C., Choisne, N., Schijlen, E., ... Bucher, E. (2017). High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nature Genetics, 49(7), 1099-1106. https://doi.org/10.1038/ng.3886
Daccord, Nicolas ; Celton, Jean-Marc ; Linsmith, Gareth ; Becker, Claude ; Choisne, Nathalie ; Schijlen, Elio ; van de Geest, Henri ; Bianco, Luca ; Micheletti, Diego ; Velasco, Riccardo ; Di Pierro, Erica Adele ; Gouzy, Jérôme ; Rees, D.J.G. ; Guérif, Philippe ; Muranty, Hélène ; Durel, Charles Eric ; Laurens, François ; Lespinasse, Yves ; Gaillard, Sylvain ; Aubourg, Sébastien ; Quesneville, Hadi ; Weigel, Detlef ; van de Weg, Eric ; Troggio, Michela ; Bucher, Etienne. / High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. In: Nature Genetics. 2017 ; Vol. 49, No. 7. pp. 1099-1106.
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abstract = "Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.",
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Daccord, N, Celton, J-M, Linsmith, G, Becker, C, Choisne, N, Schijlen, E, van de Geest, H, Bianco, L, Micheletti, D, Velasco, R, Di Pierro, EA, Gouzy, J, Rees, DJG, Guérif, P, Muranty, H, Durel, CE, Laurens, F, Lespinasse, Y, Gaillard, S, Aubourg, S, Quesneville, H, Weigel, D, van de Weg, E, Troggio, M & Bucher, E 2017, 'High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development', Nature Genetics, vol. 49, no. 7, pp. 1099-1106. https://doi.org/10.1038/ng.3886

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. / Daccord, Nicolas; Celton, Jean-Marc; Linsmith, Gareth; Becker, Claude; Choisne, Nathalie; Schijlen, Elio; van de Geest, Henri; Bianco, Luca; Micheletti, Diego; Velasco, Riccardo; Di Pierro, Erica Adele; Gouzy, Jérôme; Rees, D.J.G.; Guérif, Philippe; Muranty, Hélène; Durel, Charles Eric; Laurens, François; Lespinasse, Yves; Gaillard, Sylvain; Aubourg, Sébastien; Quesneville, Hadi; Weigel, Detlef; van de Weg, Eric; Troggio, Michela; Bucher, Etienne.

In: Nature Genetics, Vol. 49, No. 7, 2017, p. 1099-1106.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - Daccord, Nicolas

AU - Celton, Jean-Marc

AU - Linsmith, Gareth

AU - Becker, Claude

AU - Choisne, Nathalie

AU - Schijlen, Elio

AU - van de Geest, Henri

AU - Bianco, Luca

AU - Micheletti, Diego

AU - Velasco, Riccardo

AU - Di Pierro, Erica Adele

AU - Gouzy, Jérôme

AU - Rees, D.J.G.

AU - Guérif, Philippe

AU - Muranty, Hélène

AU - Durel, Charles Eric

AU - Laurens, François

AU - Lespinasse, Yves

AU - Gaillard, Sylvain

AU - Aubourg, Sébastien

AU - Quesneville, Hadi

AU - Weigel, Detlef

AU - van de Weg, Eric

AU - Troggio, Michela

AU - Bucher, Etienne

PY - 2017

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AB - Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.

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