Drosophila melanogaster (Fruit fly) - GCA_000001215.4 [FlyBase annotation] Assembly and Gene Annotation

About Drosophila melanogaster

Drosophila melanogaster is a cosmopolitan species of fruitfly that has been used as a model organism for over a hundred years, particularly with respect to genetics and developmental biology. It was the second metazoan (the first being Caenorhabditis elegans) to have its genome sequenced [1], and was one of 12 fruitfly genomes included in a large comparative study [2]. Ensembl Genomes imports data from FlyBase, who also have much more information about the biology of Drosophila melanogaster, 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 assembly presented here has been imported from INSDC and is linked to the assembly accession [GCA_000001215.4].

The total length of the assembly is 143706478 bp contained within 1869 scaffolds. The scaffold N50 value is 25286936, the scaffold L50 value is 3. The GC% content of the assembly is 42.0%.

Annotation

Protein-coding and RNA genes were imported from FlyBase, release dmel_r6.54 (FB2023_05).

Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 222,250 Low complexity (Dust) features, covering 8 Mb (5.5% of the genome); 48,594 RepeatMasker features (with a custom library), covering 28 Mb (19.5% of the genome); 1425 RepeatMasker features (with the RepBase library), covering 0 Mb (0.1% of the genome); 72,624 Tandem repeats (TRF) features, covering 6 Mb (4.1% of the genome).

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

References

1. The genome sequence of Drosophila melanogaster.
   Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF et al. 2000. Science. 287:2185-2195.
2. 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.