A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

However, a minor role for HGT cannot be ruled out. In fact, FSFs in a, b, or e Venn groups could be more influenced by HGT because they represent viruses infecting only a single superkingdom. For example, five FSFs that were detected only in archaeoviruses ( (table S5) ] appear more "cellular" than "viral" in nature. Here, the possibility that archaeoviruses picked these FSFs from archaeal hosts during infection cannot be ruled out with confidence. These FSFs were, however, more widespread in bacterial and eukaryal proteomes than in archaeal proteomes but were absent in their respective viruses (Fig. 3C ). This could be a result of the loss of viral lineages from Bacteria and Eukarya or from reductive evolution in Archaea itself (18, 36) , which would again negate HGT. In turn, b and e FSFs were more represented in bacterial and eukaryal proteomes, respectively (as expected), and did not have very high f values (Fig. 3C) . Specifically, 198 FSFs unique to bacterioviruses could be a result of HGT in either direction in Bacteria and viruses, especially because bacterioviruses are known to mediate gene exchange between bacterial species (for example, the 60% BV FSFs that could be potential VSFs; Table 1 ) and most of these FSFs originated very late in evolution ( fig. S2 , b group). Similar patterns were also observed for e FSFs ( fig. S2 , e group). Finally, only two FSFs ["DNA polymerase b, N-terminal domain-like" (a.60.6) and "Alkaline phosphatase-like" (c.76.1)] were shared by archaeoviruses and eukaryoviruses (ae). This is in line with previous understanding that eukaryoviruses are very distinct from archaeoviruses (46) and challenges the concept that eukaryoviruses originated from the merging of prokaryotic viruses [for example, (45); see Discussion]. In summary, the evolution of viruses follows a bidirectional route influenced by both the vertical inheritance of a structural core present in many distantly related viruses (that is, those infecting more than one superkingdom) and the HGT of FSFs from modern cells. The common core includes proteins mainly of cellular origin that likely originated in ancient cells.