PgmNr D1530: flyDIVaS: A database for genus- and genome- wide divergence and selection in Drosophila.

Authors:
C. E. Stanley; R. J. Kulathinal


Institutes
Temple University, Philadelphia, PA.


Keyword: webtools and databases

Abstract:

Almost a decade ago, the 12 Drosophila Genomes project and the associated development of community-based resources including the AAA site (Assembly/Alignment/Annotation), transformed D. melanogaster into a premiere comparative model (Clark et al. 2007).  However, the analysis sets made available for evolutionary inference and biological discovery have become outdated. Here, we provide an updated and upgradable comparative genomics resource of Drosophila divergence and selection, flyDIVaS, based on the latest genomic assemblies, curated FlyBase annotations, and recent OrthoDB orthology calls. flyDIVaS is an online database containing D. melanogaster-centric orthologous gene sets, sequence alignments, divergence estimates (% gaps, dN, dS, dN/dS), and codon-based tests of positive selection. Out of 14K protein-coding D. melanogaster genes, ~80% have one aligned ortholog in the closely related species, D. simulans, and ~50% have 1-1 alignments in the original 12 sequenced species. Genes and their orthologs can be chosen from four taxonomic datasets differing in phylogenetic depth and coverage density, and visualized via interactive alignments and phylogenetic trees. Computationally-savvy users can also batch download entire comparative datasets. A preliminary functional survey finds conserved mitotic, cell cycle, and neural genes, highly diverged immune and reproduction-related genes, strong signals of divergence across tissue-specific genes, and an enrichment of positive selection among highly diverged genes. We encourage researchers to regularly use this resource as a tool for biological inference and discovery, as well as in their classrooms to help train the next generation of biologists to creatively use such genomic big data resources in an integrative manner. flyDIVaS will be annually updated and is freely available at www.flydivas.info.