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

By N. Daccord, J. Celton, G. Linsmith, C. Becker, N. Choisne, E. Schijlen, H. van de Geest, L. Bianco, D. Micheletti, R. Velasco and 15 more. Nature Genetics, 2017

806 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/14024c8d85bb72b0690e3525bfca190c602b2d9b

How researchers see this paper

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In Molecular Biology

1. S. Schmidt
2. M. Roach
3. A. Borneman

In Plant Science

1. Jill L. Wegrzyn
2. S. Schmidt
3. James McFerson
4. M. Roach
5. A. Borneman

Citations in the corpus

• Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies (2018, methodology): “They are used extensively for estimating the completeness, duplication and fragmentation of genome assemblies [1, 4, 31, 32].”
• 15 years of GDR: New data and functionality in the Genome Database for Rosaceae (2018, background): “For Malus × domestica, a de novo assembly of a ‘Golden Delicious’ doubled-haploid apple tree (GDDH13) with 17 pseudomolecules is now available (15) along with three versions of assemblies for the heterozygous apple genome (16).”