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

Publication Overview
TitleHigh-quality de novo assembly of the apple genome and methylome dynamics of early fruit development
AuthorsDaccord N, Celton JM, 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
TypeJournal Article
Journal NameNature Genetics
Volume49
Issue7
Year2017
Page(s)1099-1106
CitationDaccord N, Celton JM, 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. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nature Genetics. 2017 Jun 05; 49(7):1099-1106.

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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Additional details for this publication include:
Property NameValue
Publication TypeJournal Article
URLhttps://www.nature.com/articles/ng.3886
DOI10.1038/ng.3886
eISSN1546-1718
ISSN1546-1718
Journal AbbreviationNat. Genet.
Journal CountryUnited States
LanguageEnglish
Language Abbreng
Publication Date2017 Jun 05
Publication ModelPrint-Electronic
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PMID: PubMedPMID:28581499