Do Viruses Exchange Genes across Superkingdoms of Life?

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

Third, it can be argued that the f -value may not reflect phylogenetic diversity. For example, an f -value of 0.05 indicates rare presence but the FSF could be specific to a particular phylum or group of organisms (e.g., Firmicutes). However, and to emphasize, the f -value was coupled with known biochemical functions of the protein fold, i.e., viral-like (e.g., virion assembly) or cell-like (e.g., metabolism) functions, which was then used as composite variable to postulate the direction of candidate HGT event (see Nasir and Caetano-Anollés, 2013 for previous applications of the approach). When the molecular function of an FSF is well-known (i.e., cell-like or virus-like), it becomes easier to postulate a direction of gene transfer and to also exclude convergence as an alternative scenario. Moreover, FSFs that are specific to only one phylum (or a group of organisms) are likely not to be inherited vertically but after the divergence from the common ancestor of that group, a time period that follows virus-cell divergence.