DroSpeGe: rapid access database for new Drosophila species genomes

Abstract

The Drosophila species comparative genome database DroSpeGe (http://insects.eugenes.org/DroSpeGe/) provides genome researchers with rapid, usable access to 12 new and old Drosophila genomes, since its inception in 2004. Scientists can use, with minimal computing expertise, the wealth of new genome information for developing new insights into insect evolution. New genome assemblies provided by several sequencing centers have been annotated with known model organism gene homologies and gene predictions to provided basic comparative data. TeraGrid supplies the shared cyberinfrastructure for the primary computations. This genome database includes homologies to Drosophila melanogaster and eight other eukaryote model genomes, and gene predictions from several groups. BLAST searches of the newest assemblies are integrated with genome maps. GBrowse maps provide detailed views of cross-species aligned genomes. BioMart provides for data mining of annotations and sequences. Common chromosome maps identify major synteny among species. Potential gain and loss of genes is suggested by Gene Ontology groupings for genes of the new species. Summaries of essential genome statistics include sizes, genes found and predicted, homology among genomes, phylogenetic trees of species and comparisons of several gene predictions for sensitivity and specificity in finding new and known genes.

Figure 1

Drosophila species assemblies, showing assembly sizes and coverage of these by D.melanogaster genome DNA (top and middle lines, in megabases, left ordinate), and counts of chromosome segments inverted relative to Dmel (bottom line, right ordinate). Species on abscissa are taxonomically ordered with Dgri most distant from Dmel. This is summarized from .

Figure 2

Aligned genomes view of new D.melanogaster gene locations on X chromosome, on D.melanogaster, Drosophila simulans and Drosophila yakuba, identified with cross-species comparison of coding exons, from DroSpeGe/data/dmel-dspp/newgenes. Several gene predictors match these common coding exons. Additional evidence from EST, protein HSP matches and gene expression data corroborate the new genes. Genomes with orthologous gene predictions not shown, but viewable at DroSpeGe maps, include Dsec, Dere, Dana, Dpse and Dmoj.