Evolutionary History of Bacteriophages in the Genus Paraburkholderia

Abstract

The genus <i>Paraburkholderia</i> encompasses mostly environmental isolates with diverse predicted lifestyles. Genome analyses have shown that bacteriophages form a considerable portion of some <i>Paraburkholderia</i> genomes. Here, we analyzed the evolutionary history of prophages across all <i>Paraburkholderia</i> spp. Specifically, we investigated to what extent the presence of prophages and their distribution affect the diversity/diversification of <i>Paraburkholderia</i> spp., as well as to what extent phages coevolved with their respective hosts. Particular attention was given to the presence of CRISPR-Cas arrays as a reflection of past interactions with phages. We thus analyzed 36 genomes of <i>Paraburkholderia</i> spp., including those of 11 new strains, next to those of three <i>Burkholderia</i> species. Most genomes were found to contain at least one full prophage sequence. The highest number was found in <i>Paraburkholderia</i> sp. strain MF2-27; the nine prophages found amount to up to 4% of its genome. Among all prophages, potential moron genes (e.g., DNA adenine methylase) were found that might be advantageous for host cell fitness. Co-phylogenetic analyses indicated the existence of complex evolutionary scenarios between the different <i>Paraburkholderia</i> hosts and their prophages, including short-term co-speciation, duplication, host-switching and phage loss events. Analysis of the CRISPR-Cas systems showed a record of diverse, potentially recent, phage infections. We conclude that, overall, different phages have interacted in diverse ways with their <i>Paraburkholderia</i> hosts over evolutionary time.