FlyBase: genomes by the dozen

Abstract

FlyBase (http://flybase.org/) is the primary database of genetic and genomic data for the insect family Drosophilidae. Historically, Drosophila melanogaster has been the most extensively studied species in this family, but recent determination of the genomic sequences of an additional 11 Drosophila species opens up new avenues of research for other Drosophila species. This extensive sequence resource, encompassing species with well-defined phylogenetic relationships, provides a model system for comparative genomic analyses. FlyBase has developed tools to facilitate access to and navigation through this invaluable new data collection.

Figure 1

A FlyBase gene report. The new FlyBase design allows the user to choose which sections and subsections to view. In this example, the table showing classical alleles has been opened.

Figure 2

The Muller element arm synteny table. The phylogenetic relationships of the 12 sequenced species are shown to the left, color-coded diagrammatic karyotypes and a table of syntenic relationships are shown to the right. There is not a simple one-to-one correspondence of arms to Muller elements for all of the species, due to fusion and inversion events relative to D.melanogaster in five of the species.

Figure 3

The FlyBase BLAST tool. ‘BLAST Database’ selection options are shown in the ‘BLAST database availability key’ and include the whole-genome assemblies, annotated transposons, protein sequences or intergenic sequences, as well as GenBank and UniProt datasets. The species for which data are available are shown in a hierarchical tree; clicking on any node in the tree selects all descendants of that node. Not all types of data are available for each of the featured species: an availability code (colored letters) is shown after each species listing. Advanced BLAST options (out of view at bottom of page) allow customization of BLAST parameters and output format; an ON/OFF toggle is provided for the ‘Low Complexity Filter’; the ‘Expect’ threshold parameter may be adjusted at the top of the page. The BLAST output includes a ‘BLAST HIT on Genome Map’ or ‘Feature on Genome Map’ link shown at the top of an aligned segment; this allows immediate access to a GBrowse view of the genomic region that corresponds to the BLAST hit, with the aligned region indicated by a gray panel.

Figure 4

A GBrowse view. The region of the D.ananassae genome homologous to the D.melanogaster HP1c gene has been accessed via a link from the FlyBase BLAST output. The region of BLAST alignment is indicated by a gray panel. The default selection of data includes alignments of D.melanogaster putative orthologs and the GLEANR consensus predictions; in this view, additional gene prediction tracks have been selected. The presentation of the data options may be customized further by using a ‘Configure tracks’ option (out of view at bottom of page). The species being viewed may be changed at any time by choosing from the ‘Data Source’ menu. Once viewing the species of choice, a particular region can be specified using sequence coordinates or a ‘landmark’. For the newly sequenced species, the initial set of landmarks consists of the gene predictions, identified by their alphanumeric designations, and the D.melanogaster putative orthologs. The options for downloading the data shown are listed in the menu ‘Reports and Analysis’; the FASTA output may be customized by using the ‘Configure’ option.