A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

In turn, there are three possible routes to explain the origin of class II proteins: (i) they originated in cells and transferred to viruses; (ii) they originated in viruses and transferred to cells; and (iii) they spread vertically from the common ancestor of cells and viruses or by means of shared innovation. Each of the three possibilities has known examples. However, the gene flow from virus to cell numerically exceeds the gene flow in the opposite direction [for example, transfer of the RNA polymerase gene of dsRNA viruses to eukaryotes (103), provirus genes integrated in mitochondria (104), endogenization of viruses (105) , and syncytin protein involved in mammalian placenta development (106) ; see also (22) ]. Similarly, Cortez et al. (100) showed that a significant fraction of archaeal and bacterial genes (~15 to 20%) are of foreign origin, most likely inherited from viruses or plasmids. This is not surprising given the abundance of integrated viral-like elements in eukaryotic genomes (for example,~50% in humans). Our discovery of 66 bona fide VSFs and 43 additional VSFs that were hidden in cellular proteomes (Table 1) is additional support for this argument. Together, we argue that the gene-creation and gene-transfer abilities of viruses have been significantly underestimated by some authors [for example, (76) ]. We falsify the idea that viral genomes only evolve by acquiring genes from host species.