A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

Genome reduction: A better way to think about the viral mode of evolution Analyses of FSF use (that is, total number of unique FSFs in a proteome) and reuse (total number of FSFs) (Fig. 1 , C and D) revealed that giant viruses, such as Megavirus lba and Pandoravirus salinus, overlapped many parasitic and symbiotic microbial species (mostly Mycoplasma and Proteobacteria) (see table S4 for use and reuse values in all proteomes). To confirm and as a control, we plotted FSF use and reuse for viruses and only "free-living" organisms that eliminated the overlap between large dsDNA viruses and microbial parasites ( fig. S1 ). Giant viruses were not too far away from archaeal species that also have experienced genome reduction in the past (18, 36) . The analysis suggests that proteomes of viruses, especially giant dsDNA viruses, are similar in size to many well-known cellular parasites and also share with them a similar lifestyle (that is, benefitting from host resources). This shows that one unifying property for cells and viruses could be common parasitic lifestyle. Because the small proteomes of cellular parasites are likely a result of reductive evolution (37) (38) (39) , it would seem logical to extend this argument to the evolution of the viral supergroup [as previously argued (40) (41) (42) ], albeit cautiously for RNA viruses with small proteome complements (read below).