Drosophila sechellia (Fruit fly, Rob3c) Assembly and Gene Annotation

About Drosophila sechellia

Drosophila sechellia is endemic to (some of) the Seychelles, and was one of 12 fruitfly genomes sequenced for a large comparative study [1]. D. sechellia is useful for research into speciation because mating with D. simulans produces fertile females and sterile males [2]. Ensembl Genomes imports data from FlyBase, who also have much more information about the biology of Drosophila sechellia, 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

This is the October 2005 genome assembly of Drosophila sechellia. The 4.9x whole-genome shotgun sequencing was performed and assembly provided by the Broad Institute.

Annotation

Protein-coding and RNA genes were imported from FlyBase, release dsec_r1.3 (FB2017_04).

Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 227,452 Low complexity (Dust) features, covering 18 Mb (10.6% of the genome); 59,336 RepeatMasker features (with the RepBase library), covering 28 Mb (16.8% of the genome); 77,058 Tandem repeats (TRF) features, covering 15 Mb (9.1% 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.