Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes

Abstract

RNA interference (RNAi)-related pathways target viruses and transposable element (TE) transcripts in plants, fungi, and ecdysozoans (nematodes and arthropods), giving protection against infection and transmission. In each case, this produces abundant TE and virus-derived 20-30nt small RNAs, which provide a characteristic signature of RNAi-mediated defence. The broad phylogenetic distribution of the Argonaute and Dicer-family genes that mediate these pathways suggests that defensive RNAi is ancient, and probably shared by most animal (metazoan) phyla. Indeed, while vertebrates had been thought an exception, it has recently been argued that mammals also possess an antiviral RNAi pathway, although its immunological relevance is currently uncertain and the viral small RNAs (viRNAs) are not easily detectable. Here we use a metagenomic approach to test for the presence of viRNAs in five species from divergent animal phyla (Porifera, Cnidaria, Echinodermata, Mollusca, and Annelida), and in a brown alga—which represents an independent origin of multicellularity from plants, fungi, and animals. We use metagenomic RNA sequencing to identify around 80 virus-like contigs in these lineages, and small RNA sequencing to identify viRNAs derived from those viruses. We identified 21U small RNAs derived from an RNA virus in the brown alga, reminiscent of plant and fungal viRNAs, despite the deep divergence between these lineages. However, contrary to our expectations, we were unable to identify canonical (i.e. Drosophila- or nematode-like) viRNAs in any of the animals, despite the widespread presence of abundant micro-RNAs, and somatic transposon-derived piwi-interacting RNAs. We did identify a distinctive group of small RNAs derived from RNA viruses in the mollusc. However, unlike ecdysozoan viRNAs, these had a piRNA-like length distribution but lacked key signatures of piRNA biogenesis. We also identified primary piRNAs derived from putatively endogenous copies of DNA viruses in the cnidarian and the echinoderm, and an endogenous RNA virus in the mollusc. The absence of canonical virus-derived small RNAs from our samples may suggest that the majority of animal phyla lack an antiviral RNAi response. Alternatively, these phyla could possess an antiviral RNAi response resembling that reported for vertebrates, with cryptic viRNAs not detectable through simple metagenomic sequencing of wild-type individuals. In either case, our findings show that the antiviral RNAi responses of arthropods and nematodes, which are highly divergent from each other and from that of plants and fungi, are also highly diverged from the most likely ancestral metazoan state.

Author summary

The presence of abundant virus-derived small RNAs in infected plants, fungi, nematodes, and arthropods suggests that Dicer-dependent antiviral RNAi is an ancient and conserved defence. Using metagenomic sequencing from wild-caught organisms we find that antiviral RNAi is variable across animals. We identify a distinctive group of virus-derived small RNAs in a mollusc, which have a piRNA-like length distribution but lack key signatures of piRNA biogenesis. We also report a group of 21U virus-derived small RNAs in a brown alga, which represents an origin of multicellularity separate from that of plants, fungi, and animals. The absence of virus-derived small RNAs from most of our animal samples may suggest either that the majority of animal phyla lack an antiviral RNAi response, or that these phyla possess an antiviral RNAi response resembling that reported for vertebrates, which is not detectable through simple metagenomic sequencing of wild-type individuals. In addition, we report abundant somatic piRNAs across anciently divergent animals suggesting that this is the ancestral state in Bilateria. Our study challenges a widely-held assumption that most invertebrates possess an antiviral RNAi pathway likely similar to that seen in Drosophila, other arthropods, and nematodes.