A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

To detect such transfers, we looked at the molecular functions of each ) and in 1 of 383 (0.3%) eukaryotic proteomes that were sampled, indicating a rare presence in eukaryotes. Because both FSFs are components of viral capsids and perform a "hallmark" viral function, their rare presence in eukaryotes is likely a result of horizontal gene transfer (HGT) from virus to host or a mistake in HMM assignment rather than shared innovation or vertical inheritance. Similarly, the "gp9" FSF (b.32.1) in the BV group helps in T4 bacteriophage attachment to its host, Escherichia coli (24) . It was only detected in 1 of 1115 (0.08%) bacterial proteomes that were sampled, again suggesting either virus-to-host HGT or erroneous assignment. Remarkably, 20 of 33 (60.06%) BV FSFs were part of our selection, suggesting that a large number of BV FSFs originated in viruses. Because bacterioviruses are known to mediate gene exchange between bacterial species (25), our finding is biologically significant and less likely attributable to mistakes in HMM assignments. These observations suggest that VSFs are spreading to other Venn groups and that their number is expected to grow once a pool of more diverse viruses is sequenced and HGT-associated relationships are determined. Some of the "cellonly" Venn groups (that is, A, B, E, AB, AE, BE, and ABE) may also be contaminated with viral FSFs because a large number of viral FSFs remain unknown as a result of sampling biases and technical limitations in virus discovery in different species.