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 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 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.

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, E.A.; Gouzy, J.; Jasper, D.; Rees, G.; Guérif, P.; Muranty, H.; Durel, C.E.; 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, 49 (7): 1099-1106. doi: 10.1038/ng.3886 handle: http://hdl.handle.net/10449/42064

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

Linsmith, Gareth;Bianco, L.;Micheletti, D.;Velasco, R.;Di Pierro, E. A.
Primo
;
Troggio, M.;
2017-01-01

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 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 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.
Settore BIO/11 - BIOLOGIA MOLECOLARE
2017
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, E.A.; Gouzy, J.; Jasper, D.; Rees, G.; Guérif, P.; Muranty, H.; Durel, C.E.; 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, 49 (7): 1099-1106. doi: 10.1038/ng.3886 handle: http://hdl.handle.net/10449/42064
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