Annotation of piRNA Source Loci in the Genome of Non-model Insects

The PIWI-interacting RNA (piRNA) pathway plays a crucial role in the defense of metazoan genomes against parasitic transposable elements. The major source of piRNAs in the model organism Drosophila melanogaster is defective transposon copies located in piRNA clusters-genomic regions with a high piRNA density that are thought to serve as an immunological memory of past invasions by those elements. Different approaches have been used to annotate piRNA clusters in model organisms such as flies, mice, and rats, and software such as proTRAC or piClust are available for piRNA cluster annotation. However, these tools often make assumptions based on current knowledge of piRNA clusters from (mostly vertebrate) model organisms, which do not necessarily hold true for non-model insects in which the piRNA pathway is less understood. Here we describe a simple piRNA cluster annotation approach that utilizes very few assumptions on the biology of the piRNA pathway. The pipeline has been validated on mosquito genomes but can be easily used for other non-model insect species as well.