FB2014_05, released September 9th, 2014
 
 

A Database of Drosophila Genes & Genomes

The FB2008_02 release

Dear Colleagues,

The current FB2008_02 release embodies the first update containing a full set of gene records and annotations from the 12 fully sequenced Drosophila species. The sequences and annotations of these 12 genomes represent a community-wide effort, with the initial results published by the Drosophila 12 Genomes Consortium in Nature 450: 203-218 (FBrf0200326) and more than 40 companion papers.

In FB2008_02, the 11 non-melanogaster annotation sets correspond to the consensus GLEANR gene models used by the Drosophila 12 Genomes Consortium. The version 1.0 GLEANR annotations for 10 species (excluding D.melanogaster and D.pseudoobscura) were fully incorporated into FlyBase beginning with database release FB2008_01. The current version 2.1 GLEANR annotations of the D. pseudoobscura genome replace the previous version 2.0 annotation set and are newly presented in FB2008_02. Where the connection was obvious, the GLEANR gene models have been associated with pre-existing FlyBase genes. The D. melanogaster annotation set is continuously updated, with version 5.5 being current in FB2008_02. However, it should be noted that the initial analyses for the Drosophila 12 Genomes Consortium publications were based on comparisons with the version 4.3 D. melanogaster annotation set. This annotation set along with the current annotations of the other 11 species will be archived to allow continued reference to these canonical analysis sets.

Over the next several release cycles, we expect to update a small subset of annotations in non-melanogaster species. These are necessary to comply with GenBank requirements regarding annotation submissions which are currently in process. These changes will include merges of annotations that share coding sequences into a single multi-transcript gene model, removal or truncation of annotations that artifactually span sequence gaps, and elimination of spurious short annotations of less than 50 residues lacking orthology support. In the longer term, we will establish procedures for the research community to contribute modifications to these annotation sets.

We are excited with the unprecedented research opportunities that these new genomes represent.

Sincerely,

The FlyBase Consortium