Characterization of Genomic Diversity In Bacteriophages Infecting Rhodococcus

Bacteriophages are globally ubiquitous viruses that infect bacteria. With nearly 4,000 sequenced genomes of phages infecting the phylum Actinobacteria available, genomic analyses of these actinobacteriophage genomes has been instrumental in uncovering a diverse genomic landscape often characterized by genome mosaicism. Here, we describe the genomic characterization of 57 sequenced phages capable of infecting the genus Rhodococcus. These phages were previously isolated at multiple institutions by students in the SEA-PHAGES program using four different species of Rhodococcus. Most Rhodococcus phages have been grouped into 4 clusters based on their genomic similarities; 13 phages are singletons too genetically distinct for clustering. These clusters and singletons contain Siphoviridae and Myoviridae phages, and most contain integrase and repressor genes indicative of a potential lysogenic life cycle. The genome size of these phages varies from 14,270 bp to 142,586 bp and their G+C% content ranges from 41.2-68.4%, while that of their Rhodococcus hosts typically exceeds 60%. Through comparative genomic analyses, it was revealed that these Rhodococcus phages display high intracluster similarity but low intercluster similarity, despite their shared ability to infect the same host genus. Additionally, these Rhodococcus phages share similarities with phages that infect other Actinobacterial hosts such as Gordonia, Streptomyces and Arthrobacter.