RESEARCH ARTICLE Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals

The Piwi pathway is deeply conserved amongst animals because one of its essential func-tions is to repress transposons. However, many Piwi-interacting RNAs (piRNAs) do not base-pair to transposons and remain mysterious in their targeting function. The sheer num-ber of piRNA cluster (piC) loci in animal genomes and infrequent piRNA sequence conser-vation also present challenges in determining which piC loci are most important for development. To address this question, we determined the piRNA expression patterns of piC loci across a wide phylogenetic spectrum of animals, and reveal that most genic and intergenic piC loci evolve rapidly in their capacity to generate piRNAs, regardless of known transposon silencing function. Surprisingly, we also uncovered a distinct set of piC loci with piRNA expression conserved deeply in Eutherian mammals. We name these loci Euthe-rian-Conserved piRNA cluster (ECpiC) loci. Supporting the hypothesis that conservation o