| Analysis Name | Malus domestica ASM211411v1 Assembly & Annotation |
| Sequencing technology | Illumina; PacBio; BioNano |
| Assembly method | DBG2OLC v. May-2016; SOAPdenovo2 v. May-2016; BESST v. May-2016; BioNano hybrid assembly v. May-2016 |
| Release Date | 2017-05-03 |
Daccord 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. Nat Genet. 2017 Jul;49(7):1099-1106. doi: 10.1038/ng.3886.
AbstractUsing 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.
Assembly statistics
| Genome size | 703 Mb |
| Total ungapped length | 625.3 Mb |
| Number of chromosomes | 17 |
| Number of scaffolds | 806 |
| Scaffold N50 | 37.6 Mb |
| Scaffold L50 | 9 |
| Number of contigs | 7,496 |
| Contig N50 | 588.9 kb |
| Contig L50 | 329 |
| GC percent | 38 |
| Genome coverage | 700.0x |
| Assembly level | Chromosome |
The Malus domestica ASM211411v1 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GCA_002114115.1_ASM211411v1_genomic.fna.gz |
The Malus domestica ASM211411v1 genome gene prediction files are not available.
Downloads
| Genes (GFF3 file) | - |
Functional annotation for the Malus domestica ASM211411v1 is not available.
Downloads
| Domain from InterProScan | - |
Malus S genes Nucleotide
Malus S genes Protein