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Nat Genet. 2017 Jul;49(7):1099-1106. doi: 10.1038/ng.3886. Epub 2017 Jun 5.

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

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Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université Bretagne Loire, Angers, France.
Research and Innovation Center, Department of Genomics and Biology of Fruit Crops, Fondazione E Mach di San Michele all'Adige, Italy.
Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
UR1164 URGI, Research Unit in Genomics-Info, INRA, Université Paris-Saclay, Versailles, France.
Wageningen UR-Bioscience, Wageningen, the Netherlands.
Department of Biosciences, University of Milan, Milan, Italy.
LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France.
Agricultural Research Council, Biotechnology Platform, Onderstepoort, Pretoria, South Africa.
Wageningen UR-Plant Breeding, Wageningen, the Netherlands.


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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