Journal Article

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

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

2017

Overview

Etienne Bucher and colleagues use a combination of short- and long-read sequencing, along with optical mapping technologies, to produce the high-quality de novo assembly of the apple genome. They identify a new repetitive retrotransposon sequence and analyze DNA methylation data in relation to important agronomic traits. 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.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 38/23 / 45/91 / 631/208/212/177 / 631/449/2491 / Agricultural sciences / Agriculture / Agronomy / Animal Genetics and Genomics / Annotations / Apples / Assembly / Bioinformatics / Biomedicine / BIOS Applied Bioinformatics / Cancer Research / Chromosomes, Plant - genetics / Deoxyribonucleic acid / Divergence / DNA / DNA Methylation / DNA Transposable Elements / DNA, Plant - chemistry / DNA, Plant - genetics / Epigenetics / EPS / Fruit - growth & development / Fruits / Gene expression / Gene Function / Gene mapping / Gene sequencing / Genes, Plant / Genetic aspects / Genetic research / Genome, Plant / Genomes / Genotype / Human Genetics / Life Sciences / Linkage Disequilibrium / Malus - genetics / Malus - growth & development / Molecular Sequence Annotation / Mountains / Nucleotide sequence / PBR Biodiversiteit en Genetische Variatie / PBR Biodiversity and genetic variation / PE&RC / Plant development / PRI BIOS Applied Bioinformatics / Properties / Sequence Analysis, DNA / Studies / Synteny / Transfer RNA / Transposons / Uplift / Vegetal Biology / WUR PB Biodiversiteit en Genetische Variatie