Drosophila species genome x D melanogaster gene averages

This is a chart of species genome-wide averages of D. melanogaster protein matches, showing protein similarity, alignment length, HSP count (an estimate of exons), gap size (an estimate of introns), duplicate gene (paralog) count, and distance to duplicate (tandem gene duplication distance).

Three outgroup genomes ( C. elegans:cele, crustacean Daphnia: dpulex, and insect Anopholes:agam) are included, and have obvious differences from Drosophila (Dmel to Dgri). There may be Drosophila species differences estimated for exon count and intron size, especially for Dmoj-Dvir-Dwil. Assembly quality could also be affecting these. One notable phylogenetic outlier is D.simulans. Since this assembly is a mosaic from several populations, the population-level differences are likely affecting a species view of this genome.

Included are two alternate assemblies (dyak3r, dpse2r) to CAF1 assemblies. By these statistics, they are not significantly different. A close look shows that dpse2r picked up about 8 Dmel gene matches to dpse, while dyak3r is identical to dyak in gene matches. These statistics are based on found genes, those query proteins which matched in genomes with <= 1e-3 probability. See also charts showing counts of found genes, for nine MOD proteomes and for Dmel proteome. See also this PDF view of genome averages.

Figures show genome averages for matches to Drosophila melanogaster proteome measured with tBLASTn, with 95% confidence intervals. Species include three outgroups at left (cele,dpulex,agam), and twelve Drosophila species, Dmel .. Dgri, for CAF1 assemblies with two alternates (dpse2r, dyak3r).

Don Gilbert, April 2006

Developed at the Genome Informatics Lab of Indiana University Biology Department