Evolutionary genomics of piRNA mediated transposon silencing in Drosophila

Abstract

Thesis (Ph. D.)--University of Rochester. Department of Biology, 2016.Transposable elements (TEs) are abundant throughout the genomes of most living organisms. A recently identified piwi-interacting RNA (piRNA) pathway has been shown to defend against TEs in the Drosophila germline. This dissertation research is an evolutionary genomic analysis of the piRNA pathway in closely related Drosophila species. In Chapter 1, we characterize the rate of evolution for proteins affecting 26 RNAi knockdown phenotypes, which include three phenotypes related to regulation of transposon integration. When RNAi phenotypes are grouped into categories according to cellular function, we find that genes involved in the greatest number of phenotypic categories are also significantly more likely to have a history of rapid protein evolution. Defining pleiotropy using phenotypic categories yields different results than studies that define pleiotropy based on physical interactions. In Chapter 2, we characterize the expression diversity of several families of TEs using piRNAs. Comparative genomic analysis of piRNA expression finds dynamic changes in expression levels of several families of TEs in D. melanogaster and the D. simulans clade. Measuring ping-pong activity— a signature of piRNA amplification finds higher mean piRNA amplification in D. simulans and D. mauritiana, suggesting increased activity of several TEs in these species compared to D. melanogaster. Furthermore, McDonald-Kreitman tests identify three genes in the piRNA pathway as having experienced recent positive selection in D. simulans, and one gene each in D. melanogaster and D. mauritiana. All four genes are components of nuage, which is a macromolecular complex that mediate protein-protein and protein-RNA interactions. Our results are consistent with a model of antagonistic co-evolution between TEs and the piRNA pathway. In Chapter 3, we use single-molecule sequencing to perform a detailed comparative analysis of the flamenco piRNA cluster in both D. melanogaster and D. mauritiana. Our analysis reveals that there is very little sequence homology of flamenco between the two species, indicating rapid turnover of TE sequence. Furthermore, spatial heterogeneity in piRNA abundance in the flamenco region identifies two putative piRNA clusters adjacent to flamenco that may be functionally distinct. This study is the first practical demonstration of re-constructing the genome sequence of highly repetitive piRNA clusters in closely related Drosophila species