Ancient and novel small RNA pathways compensate for the loss of piRNAs in multiple independent nematode lineages.

Small RNA pathways act at the front line of defence against transposable elements across the Eukaryota. In animals, Piwi interacting small RNAs (piRNAs) are a crucial arm of this defence. However, the evolutionary relationships among piRNAs and other small RNA pathways targeting transposable elements are poorly resolved. To address this question we sequenced small RNAs from multiple, diverse nematode species, producing the first phylum-wide analysis of how small RNA pathways evolve. Surprisingly, despite their prominence in Caenorhabditis elegans and closely related nematodes, piRNAs are absent in all other nematode lineages. We found that there are at least two evolutionarily distinct mechanisms that compensate for the absence of piRNAs, both involving RNA-dependent RNA polymerases (RdRPs). Whilst one pathway is unique to nematodes, the second involves Dicer-dependent RNA-directed DNA methylation, hitherto unknown in animals, and bears striking similarity to transposon-control mechanisms in fungi and plants. Our results highlight the rapid, context-dependent evolution of small RNA pathways and suggest piRNAs in animals may have replaced an ancient eukaryotic RNA-dependent RNA polymerase pathway to control transposable elements.We thank Sylviane Moss for high-throughput sequencing support. We thank Charles Bradshaw for help with computation and IT. We thank Marie-Anne Felix and Frank Jiggins for critical comments on the manuscript. We thank Matt Berriman (Wellcome Trust Sanger Centre, Hinxton, Cambridge, UK) for allowing us to use unpublished genomic sequencing data for N. brasiliensis. We thank Einhardt Schierenberg (University of Cologne, Germany) and Werner Armonies (Alfred Wegener Institute, Sylt, Germany) for help with collection of E. brevis.This is the final version of the article, originally published in PLoS Biology, 2015, 13(2): e1002061. doi:10.1371/journal.pbio.100206