Do Viruses Exchange Genes across Superkingdoms of Life?

Malik, Shahana S.; Azem-e-Zahra, Syeda; Kim, Kyung Mo; Caetano-Anollés, Gustavo; Nasir, Arshan

Second, HGT can transfer protein domains and thus increase their representation in modern proteomes. We used the f -value as a proxy to evaluate the relative evolutionary spread of each FSF in cellular proteomes. When linked with the biochemical function of the protein fold (i.e., viral-like or cellular-like), the analysis indicated a likely direction of gene transfer (i.e., virus-to-cell or cell-to-virus) . For example, FSFs involved in a viral hallmark function such as virion synthesis and/or capsid assembly that had negligible presence in either host or nonhost superkingdoms (e.g., f < 1%) were treated as candidate virus-to-cell gene transfers. In turn, FSFs involved in cellular functions such as metabolism that were widespread among cellular proteomes (e.g., f > 60%) were treated as cell-to-virus candidate HGTs, except when these FSFs were also detected in the three virus groups (i.e., the abe group of 66 "universal" FSFs). This approach of inferring a qualitative likelihood of HGT is thus similar to the method of detecting anomalous phylogenetic distributions of genes where rare presence of a gene in closely related members is more likely a result of HGT rather than vertical evolution, especially because the latter would require invoking multiple events of gene loss that are less parsimonious than considering fewer HGT events (Philippe and Douady, 2003 ). The f -value approach is especially useful for viral genes that exhibit fast mutation rates and prohibit utilizing genome-scale alignment-dependent phylogenetic analysis (Abroi and Gough, 2011; Nasir and Caetano-Anollés, 2015) .