FB2006_01 Release Notes

This release consists of a full update of FlyBase data which incorporates additions and changes to several classes of data including; the bibliography, genetic and molecular information curated from the literature, fly stocks and images, Drosophila melanogaster annotated gene models and reagent sets that have been mapped to the melanogaster genome sequence.

In addition, this update provides the ability to view the genome sequences and gene prediction sets of 10 newly sequenced Drosophila species via the gbrowse genome browser. As consensus annotation sets become available these will be fully incorporated into FlyBase.

Drosophila melanogaster Release 5.1 Annotation Update.

Release 5.1 annotations are available in FlyBase and from NCBI.

The release 5 sequence by BDGP (see the BDGP release notes) contains some major improvements to the assembly of the major chromosome arm scaffolds as well as improvements to the assembly of those portions of the centric heterochromatin that cannot currently be attached to the major arms. The improvements to the arms include the major differences noted below plus an additional 4.7 Mbp of heterochromatic sequence attached to the proximal ends of the arms. Further, Release_5 is the first non-redundant assembly of the D. melanogaster genome, unifying the previously separate assemblies of the largely euchromatic arm scaffolds and the heterochromatic scaffolds. The entire Release_5 assembly can be downloaded from the BDGP web site. Some features of the assembly are enumerated in Table 1.

TABLE 1: Release_5 Assembly (from BDGP) and Release_5.1 Accessions

Annotation Release_5.1 includes the full annotation of gene models for the six major chromosome arm scaffolds (X, 2L, 2R, 3L, 3R, 4), merging previously existing and revised annotations by FlyBase of the euchromatic regions of the arms with the revised annotations of the heterochromatic segments by the Drosophila Heterochromatin Genome Project (DHGP). The remainder of the heterochromatin is currently being annotated by the DHGP and should be integrated into FlyBase as part of Annotation Release_5.2, which is scheduled for the first quarter of 2007. In the interim, we recommend that users interested in the heterochromatin annotations continue to refer to the DHGP Release_3.2b heterochromatin assembly/annotation set.

TABLE 2: Known Gaps in the Release 5 Assembly

Release 5 of the euchromatic sequence contains eight (known) gaps. There are two gaps on the X that have estimates for their size and 6 other gaps in the genome which are not sized. (Gaps of unknown size are denoted by 100 N's in the fasta files.). The gap 21485539..21485638 of scaffold Arm2L is the Histone gene cluster which reputedly contains ca. 100 copies of a ca. 5kb repeat unit containing the His1, His2A, His2B, His3 and His4 genes.

Additional data missing from this annotation release includes the approximately 6000 repeat regions with homology to transposable elements that were located primarily near the ends of the release 4.3 arm sequences.

For details on new, split and merged gene models see the DROSOPHILA MELANOGASTER ANNOTATION STATISTICS (Release 5.1) section below.

There have been updates to the evidence tracks that inform the gene model annotation. This includes alignments of cDNAs and proteins submitted to genbank since the last update as well as a number of new homology based gene prediction tracks that were submitted to the AAA site and generated in conjunction with the collaborative effort to annotate 11 new Drosophila species genomes.