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 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

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
Database version79.602
Base Pairs142,573,017
Golden Path Length

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

143,725,995
Genebuild byFlyBase
Genebuild methodImport
Genebuild startedMay 2014
Genebuild releasedSep 2014
Genebuild last updated/patchedSep 2014

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

13,918
Non coding genes3,384
Small non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

1,018
Long non coding genes

Long non coding genes are usually greater than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as long non coding genes: 3prime_overlapping_ncrna, ambiguous_orf, antisense, antisense_RNA, lincRNA, ncrna_host, non_coding, non_stop_decay, processed_transcript, retained_intron, sense_intronic, sense_overlapping. The majority of the long non coding genes in Ensembl are annotated manually by HAVANA.

2,366
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

257
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.34,749

Other

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