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.

Expansion of the Metazoan Virosphere: Progress, Pitfalls, and Prospects

“…First, the nature and quantity of the nucleic acid provides useful clues. Endogenous DNA copies can be identified by a comparison of PCR and RT-PCR (or DNA and RNA sequencing) (Webster et al 2015;Shi et al 2016a;Medd et al 2018;Waldron et al 2018). Functional DNA viruses must express their proteins, so the absence of viral mRNAs argues against active replication.…”

“…Third, the distribution of virus-like sequences across metagenomic pools and host individuals (e.g. surveyed by PCR) can help to confirm a genuine viral origin, and narrow down the true host (Webster et al 2015;Waldron et al 2018). Presence/absence patterns can help to weed out EVEs, as-unless it is very recent in origin-an EVE insertion is likely to be present in all host genomes, but virus prevalence is likely be below 100% and variable among populations and over time (Webster et al 2015;Waldron et al 2018).…”

“…surveyed by PCR) can help to confirm a genuine viral origin, and narrow down the true host (Webster et al 2015;Waldron et al 2018). Presence/absence patterns can help to weed out EVEs, as-unless it is very recent in origin-an EVE insertion is likely to be present in all host genomes, but virus prevalence is likely be below 100% and variable among populations and over time (Webster et al 2015;Waldron et al 2018). Across host individuals, the co-occurrence of virus-like and other sequences can be used to correctly infer hosts, as viruses that infect a contaminating microparasite will co-occur with it.…”

“…20nt in Lepidoptera, 21nt in Drosophila, 22nt in C. elegans) (Félix et al 2011;Lewis et al 2018) and a 3' 2-O-methyl group, making them distinguishable from degradation products. Their size distribution and base composition also distinguish them from TE-and EVE-derived piwi-associated RNAs (Palatini et al 2017;Lewis et al 2018;Waldron et al 2018). …”

“…Tokarz et al 2018). The focus has subsequently expanded to include neglected animal lineages, identifying hundreds of new RNA viruses in arthropods and other invertebrates (Webster et al 2015;Shi et al 2016a;Roberts et al 2018;Waldron et al 2018), and recently in divergent and under-sampled chordates (Geoghegan et al 2018;Shi et al 2018).…”