Fruitfly assembly and gene annotation


Ensembl uses the Berkeley Drosophila Genome Project (BDGP) assembly release 6 (July 2014). In contrast to release 5, regions without a chromosome assignment are stored as distinct scaffolds, rather than on a single pseudo-chromosome, and heterochromatin regions are incorporated in the chromosomal arms.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000001215.4

Other assemblies

Gene annotation

Protein-coding and ncRNA annotations were imported from FlyBase, release 6.02 (FB2014_05, dated September 2014).

Variation Data

The Ensembl Fruitfly Drosophila melanogaster variation database has been produced using data from release 1.0 of the "50 genomes" data set from the Drosophila Population Genome Project. The data set contains over 6.7 million SNPs from two populations, one comprising 37 lines from north Carolina and the other comprising 15 lines from Malawi. The SNPs were originally generated with respect to assembly version BDGP5, and these were mapped to BDGP6 using the FlyBase converter tool; only 308 SNPs were unable to be mapped.

This species (and other invertebrates, including 11 other drosophilid species) are also available from our sister site, Ensembl Metazoa


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.
Science. 2000. 287(5461):2185-95

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.
Nature. 2007 Nov 8. 450(7167):203-18

More information

General information about this species can be found in Wikipedia.



AssemblyBDGP6, INSDC Assembly GCA_000001215.4, Jul 2014
Database version82.602
Base Pairs142,573,017
Golden Path Length143,725,995
Genebuild byFlyBase
Genebuild methodImport
Genebuild startedMay 2014
Genebuild releasedSep 2014
Genebuild last updated/patchedSep 2014

Gene counts

Coding genes13,918
Non coding genes3,384
Small non coding genes1,018
Long non coding genes2,366
Gene transcripts34,749


Snap gene prediction17,607
Genscan gene predictions18,548
Short Variants6,794,559