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 metazoan (animal) phyla. Indeed, while vertebrates had been thought an exception, it has recently been suggested that mammals may also possess a functional antiviral RNAi pathway, albeit involving few small RNAs that are challenging to detect. Here we use a metagenomic approach to test for the presence of antiviral RNAi in five divergent metazoan phyla (Porifera, Cnidaria, Echinodermata, Mollusca, and Annelida), and in a brown alga. We use metagenomic RNA sequencing to identify around 80 virus-like contigs in these lineages, and small RNA sequencing to identify small RNAs derived from those viruses. Contrary to our expectations, we were unable to identify canonical (i.e. Drosophila-like) viral small RNAs in any of these organisms, despite the presence of abundant micro-RNAs and putative piwi-interacting piRNAs. Instead, we identified an apparently novel class of virus-derived small RNAs in the mollusc, which have a piRNAlike length distribution but lack key signatures of piRNA biogenesis, and a novel class of 21U virusderived small RNAs in the brown alga. 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. This suggests either that the majority of metazoan phyla lack antiviral RNAi completely, such that antiviral RNAi has evolved independently in ecdysozoans, vertebrates, and molluscs, or that the antiviral RNAi response in most extant phyla-and the ancestral state of Metazoa-more closely resembles that of mammals than arthropods or nematodes.

Initial virome characterization of the common cnidarian lab modelNematostella vectensis

“…An overall comparison between the four available viromes of the sea anemones revealed a general similarity of N. vectensis to A. equina and Bolocera sp., while the viral community of E. pallida displayed considerable differences. For instance, in the A. equina dataset we found two novel viruses which display the highest homology to viral sequences found in N. vectensis (Caledonia beadlet anemone dicistro-like virus 3 isolate B and A, homology to Wenzhou picornalike virus 28 and Beihai picorna-like virus 71, respectively) [52]. The same number of viral sequences were common between our data dataset and Bolocera sp.…”

“…None of the identified sequences of Iridoviridae representatives was neither mapped in Artemia libraries, nor amplified from Artemia cDNA, which confirms that these dsDNA viruses are actively expressed and specific to Nematostella, or organisms comprising this holobiont, rather than food derived. Interestingly, members of Iridoviridae family were missing from all viromes available for other sea anemones species: E. pallida [16], Actinia equina [52] and Bolocera sp [4]. It seems plausible that such a major difference in the viral community composition between sea anemones might stem from the very distinct environmental conditions of these marine animals and therefore, a different ensemble of neighboring viral species.…”

Origins and Evolution of the Global RNA Virome

“…However, because of the apparent dominance of the viruses of the RdRp Branch 2 (“picornavirus supergroup” in general and “aquatic picorna-like viruses” clade in particular) in protists, this branch likely diversified first, whereas the diversification of Branches 3 and 4 occurred later, after ancestral protist viruses were transferred to marine invertebrates during the Cambrian explosion. The recent analysis of the viromes of ctenophores, sponges and cnidarians suggests that substantial diversification of RNA viruses occurred already in these deeply branching metazoa (120). Invertebrates brought their already highly diverse RNA virome to land at terrestrialization and subsequently inoculated land plants.…”

A new lineage of segmented RNA viruses infecting animals

“…Excel table giving the number of positive and negative sense forward-reads for each segment of Nete virus, with comparison ratios for high abundance viruses reported in Waldron et al (2018) and Medd et al (2018)…”