Drosophila yakuba (dyak_caf1)

Drosophila yakuba Assembly and Gene Annotation

About Drosophila yakuba

Drosophila yakuba is an African fruitfly that is predominantly found in open savanna, and was one of 12 fruitfly genomes sequenced for a large comparative study [1]. Ensembl Genomes imports data from FlyBase, who also have more information about the biology of Drosophila yakuba, 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.


This is the November 2005 genome assembly 2.0 of Drosophila yakuba. The 9.1x whole-genome shotgun sequencing was performed and assembly provided by the Genome Sequencing Center, Washington University School of Medicine in St. Louis (WUGSC).

The data were assembled using PCAP [2] followed by two rounds of primer-directed sequence improvement targeted at improving regions of low-quality sequence and closing gaps. The data was re-assembled and supercontigs were assigned to chromosomes based on their alignment to the D. melanogaster genome. Inversions based on the D. yakuba assembly were then introduced and checked against polytene chromosome banding data.


Protein-coding and RNA genes, which were annotated with the NCBI eukaryotic genome annotation pipeline, were imported from FlyBase, release dyak_r1.05 (FB2017_04).

Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 254,353 Low complexity (Dust) features, covering 11 Mb (6.6% of the genome); 75,581 RepeatMasker features (with the RepBase library), covering 33 Mb (20.0% of the genome); 122,416 Tandem repeats (TRF) features, covering 9 Mb (5.5% of the genome).

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

EST Alignments

Drosophila yakuba ESTs from dbEST were mapped onto the genome using Exonerate.


  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. PCAP: a whole-genome assembly program.
    Huang X, Wang J, Aluru S, Yang SP, Hillier L. 2003. Genome Research. 13:2164-2170.

More information

General information about this species can be found in Wikipedia.



Assemblydyak_caf1, INSDC Assembly GCA_000005975.1, Nov 2008
Database version100.1
Base Pairs162,582,000
Golden Path Length165,693,946
Genebuild byFlyBase
Genebuild methodImport
Data sourceFlyBase

Gene counts

Coding genes14,824
Non coding genes1,100
Small non coding genes1,100
Gene transcripts25,216

About this species