Intragenomic conflict drives rapid evolution of piRNA pathway genes in Drosophila. Jeffrey P Vedanayagam, Daniel Garrigan. Department of Biology, University of Rochester, Rochester, NY.

   Piwi-interacting RNAs (piRNAs) defend against transposable elements (TEs) in the Drosophila germline. The piRNA pathway is a complex interplay of several genes whose function is essential for both piRNA biogenesis and TE silencing. Here, we analyze coding sequence polymorphism data from 25 genes involved in piRNA pathway in the two closely related species D. simulans and D. mauritiana. Species-specific McDonald-Kreitman test finds that eight of the genes show evidence of a significantly increased rate of amino acid substitution. D. simulans has an increased rate in armi, Hen1, spn-E, vas, aub, krimp and zuc genes, while D. mauritiana has an increased rate of amino acid substitution in csul gene. armi, spn-E and vasa are putative RNA helicases, and mael and zuc are putative nucleases. All these genes are known to be crucial for piRNA biogenesis. aub is essential for ping-pong amplification of piRNAs, while krimp is essential to recruit aub to nuage - a peri-nuclear organelle where piRNA biogenesis occur. csul ensures the methylation of symmetric arginine residues of piRNA effector proteins during piRNA biogenesis. Subsequently, we find that the piRNA pathway is enriched for genes experiencing positive selection relative to three randomly chosen molecular pathways: miRNA pathway, Notch-signaling pathway and NK cytotoxicity pathway. Compared to these random pathways, we also find that the piRNA pathway is enriched for species-specific amino acid substitutions that are fixed in one species and absent in the other species, contributing to species differences. Furthermore, a sliding window K_A/K_S analysis of piRNA pathway genes to D. melanogaster shows that highly divergent regions correspond to key protein domains in these genes. Comparative genomic analysis of these protein domains in the Drosophila phylogeny reveals that these domains evolve three times faster when present in a piRNA pathway gene as opposed to a non-piRNA pathway gene. Overall, these results provide candidate loci for transgenic studies of the effect of piRNA machinery on hybrid fitness in interspecific crosses.