Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes (original) (raw)
Fig 1
Distribution of small RNA pathways across the Metazoa.
Phylogeny of selected metazoan (animal) phyla (topology follows [180]) with a table recording the reported range of modal lengths for miRNAs, piRNAs, and viRNAs detectable by bulk sequencing from wild-type organisms (miRNA modes taken from miRbase). Entries marked ‘No’ have been reported to be absent, and those marked ‘?’ are untested. Focal taxa in this study are marked in colour, and the target table entries are outlined. Vertebrate viRNAs are marked ‘(×)’ as mammalian virus-derived small RNAs are only detectable in tissues and experimental systems lacking viral suppressors of RNAi and/or an interferon response [31–35]. Note that piRNAs are absent from some, but not all, nematodes [57]. The column ‘dsRNA KD’ records whether dsRNA knockdown of gene expression using long dsRNA (i.e. a Dicer substrate) has been reported, as this may suggest the presence of an RNAi pathway capable of producing viRNAs from replicating viruses. The ‘Dcrs’ and ‘Agos’ columns record the inferred number of Dicers and (non-Piwi) Argonautes ancestrally present in each phylum, although the number of Dicers in Platyhelminthes is contentious as the putative second Dicer lacks the majority of expected Dicer domains. Broadly speaking, there are two competing hypotheses for the histories of Dicers and (non-Piwi) Argonautes in animals [47,50,181]. The first (labelled H1), posits that an early duplication in Dicer and/or Argonaute (marked D+ and A+ in dark green on the phylogeny) gave rise to at least two very divergent homologues of each gene in the lineage leading to the Metazoa, followed by subsequent losses (D- and A- in dark red). The second (H2), suggests that divergent homologues are the result of more recent duplications (D+ and A+ in pale green), and where homologs have high divergence it is as a result of rapid evolution. Note that these hypotheses are independent for Argonautes and Dicers, and one may be ancient but the other recent. For Dicers, at least, the ‘ancient’ duplication is arguably better supported [47], although it remains extremely difficult to determine orthology between the duplicates. In addition, Dicers and Argonautes have unambiguously diversified within some phyla (important examples marked A+ and D+ in grey)—as seen for the large nematode-specific WAGO clade of Argonautes (reviewed in [141]), and the multiple Argonautes in vertebrates.