Characterization of Genome Mosaicism in Cluster E Mycobacteriophages

Justin Allen, Maya Andari, Jack Miller, Michelle Zorawik, Andrew Kapinos, Canela Torres, Amanda C Freise, Jordan Moberg Parker

Despite their abundance, the evolutionary history of bacteriophages, which are viruses that infect bacteria, remains subject to speculation as these biological entities commonly exchange hereditary material. To overcome these challenges, genetically similar phages have been assigned into distinct groups, termed clusters. However, such allocations are incomplete since phage genomes are characterized by extensive mosaicism, meaning that their genes have originated from various viral and bacterial sources, often through horizontal gene transfer. Cluster E was previously determined to have conserved genomes, exchanging genes with only a limited number of clusters; however, continued isolation efforts and the subsequent increase of available sequences render such observations obsolete, leaving the current extent of genome mosaicism undetermined. Here we attempt to further characterize the inter-and intra-cluster relationships of Cluster E phages, and identify possible mechanisms that may have enabled the mosaicism. Qualitative pan-genome studies, which distinguished core and variable genes exclusive to Cluster E phages or shared with other clusters, revealed that Cluster E genomes remain highly conserved; yet, the number of shared phams has increased to over 50%, making the cluster less discrete than previously anticipated. While the factors that enable Cluster E’s genome mosaicism remain largely unknown, phylogenetic analyses revealed possible evidence of horizontal gene transfer for various HNH endonuclease phams and concurrent gene acquisition events for other genes, such as the minor tail proteins. These findings are of significance since they expand the current knowledge of Cluster E phages, as well as the nature and complexity of their interactions with other clusters.