A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

Viruses infecting the three superkingdoms share a conserved core of ancient FSFs We calculated the "virus count" for each replicon type in major host groups to determine the virus-host relationships of viruses in our data set (Fig. 3A) . The exercise revealed that most RNA viral subgroups were exclusive to eukaryotes (for example, minus-ssRNA and retrotranscribing viruses) (Fig. 3A) . In turn, a large number of DNA viruses (mostly Caudovirales) infected prokaryotic hosts. The bias in the distribution of replicon types in superkingdoms (that is, DNA viruses in prokaryotes and RNA viruses in eukaryotes) leads to an interesting possibility about the early origin of RNA viruses and their loss in prokaryotes [see Discussion (43) ]. Virus-host relationships have been described in detail previously (43) (44) (45) . Here, the more relevant question was asked: Do viruses infecting distantly related hosts share common protein folds? To answer, we generated a Venn diagram describing viral FSF repertoires. FSFs that were shared by archaeoviruses (a), bacterioviruses (b), and eukaryoviruses (e) were pooled into the abe Venn group; those shared by viruses infecting two different superkingdoms were pooled into the ab, ae, or be group; and those unique to viruses infecting a single superkingdom were pooled into the a, b, and e groups (Venn group nomenclature avoids ambiguity with that of Fig. 1A ) (Fig. 3B ). We stress that FSFs in the abe group do not mean that these were present in a virus capable of infecting Archaea, Bacteria, and Eukarya. To date, no virus is known to infect organisms in more than one superkingdom. Instead, it simply refers to the count of FSFs that were shared between archaeoviruses, bacterioviruses, and eukaryoviruses.