Drosophila simulans (Fruit fly, w501) Assembly and Gene Annotation

About Drosophila simulans

Drosophila simulans is, in evolutionary terms, closely related to D. melanogaster, and was one of 12 fruitfly genomes sequenced for a large comparative study [1]. In addition to comparison with the exceptionally well-studied D. melanogaster, D. simulans is useful for research into speciation due to its close relationship with D. sechellia and D. mauritiana [2]. Ensembl Genomes imports data from FlyBase, who also have much more information about the biology of Drosophila simulans, and a phylogeny of the 12 sequenced fruitfly species.

Picture credit (Creative Commons BY-NC-SA 2.0 FR): Nicolas Gompel 2008. Image shows a female fly.

Assembly

The ASM75419v3 assembly of Drosophila simulans is a chromosome-level assembly with a genome size of ~125Mb [3].

Annotation

Protein-coding and RNA genes, which were annotated with the NCBI eukaryotic genome annotation pipeline, were imported from FlyBase, release dsim_r2.02 (FB2017_04).

Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 180,460 Low complexity (Dust) features, covering 6 Mb (4.6% of the genome); 31,441 RepeatMasker features (with the RepBase library), covering 9 Mb (7.2% of the genome); 60,487 Tandem repeats (TRF) features, covering 3 Mb (2.5% of the genome).

Protein domains were annotated with the Ensembl Genomes protein feature pipeline.

References

1. Evolution of genes and genomes on the Drosophila phylogeny.
   Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W et al. 2007. Nature. 450:203-218.
2. The reproductive relationships of Drosophila sechellia with D. mauritiana, D. simulans, and D. melanogaster from the afrotropical region.
   Lachaise D, David JR, Lemeunier F, Tsacas L, Ashburner M. 1986. Evolution. 40(2):262-271.
3. A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.
   Hu TT, Eisen MB, Thornton KR, Andolfatto P . 2012. Genome Research. 23:89-98.