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

Citations Over TimeTop 1% of 2017 papers

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.

Related Papers

• → Heat shock transcriptional factors in Malus domestica: identification, classification and expression analysis(2012)109 cited
• → A computational study of the dynamics of LTR retrotransposons in the Populus trichocarpa genome(2011)48 cited
• → A survey of Gypsy and Copia LTR-retrotransposon superfamilies and lineages and their distinct dynamics in the Populus trichocarpa (L.) genome(2015)33 cited
• → A comparison of methods for LTR-retrotransposon insertion time profiling in the Populus trichocarpa genome(2018)17 cited
• → A Model-Driven Quantitative Analysis of Retrotransposon Distributions in the Human Genome(2020)3 cited