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

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

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.

Journal: Nature genetics
DOI: 10.1038/ng.3886
Year: 2017

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