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Fruitfly assembly and gene annotation

Assembly

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 GCA_000001215.4

Gene annotation

Protein-coding and ncRNA annotations were imported from FlyBase, release dmel_6.17 (FB2017_04).

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

References

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.

Statistics

Summary

AssemblyBDGP6, INSDC Assembly GCA_000001215.4, Jul 2014
Base Pairs142,573,017
Golden Path Length143,725,995
Annotation providerFlyBase
Annotation methodImport
Genebuild startedAug 2017
Genebuild releasedSep 2014
Genebuild last updated/patched
Database version94.6

Gene counts

Coding genes13,931
Non coding genes3,497
Small non coding genes3,497
Pseudogenes309
Gene transcripts34,776

Other

Short Variants6,794,559

About this species