Drosophila melanogaster piRNA sequencing. Drosophila melanogaster

Transposable elements are a ubiquitous component of virtually all genomes across the tree of life. Since transposable elements are generally deleterious, host genomes encode multiple molecular mechanisms for repressing them. Recently, a class of small RNAs called Piwi-interacting RNAs (piRNAs) that are found in all animal germlines has been discovered to repress transposable elements. Here we analyzed the regulation of transposable elements by piRNAs in a natural population of Drosophila melanogaster using a combination of a Genome Wide Association Study and high throughput sequencing of ovarian piRNAs from 14 of the D. melanogaster lines. The results of our unbiased mapping approach show that piRNA clusters are the primary determinant of transposable element abundance in this population. Furthermore, our piRNA expression data indicates that differential expression of piRNA clusters is the major molecular mechanism underlying variation in transposable element abundance. Our study elucidates the mechanisms of transposable element control and the co-evolution of piRNAs and transposable elements in a natural population.