Comparative genomics of 9 novel bacteriophages.

American Foulbrood Disease, caused by the bacterium , is one of the most destructive diseases of the honeybee, . Our group recently published the sequences of 9 new phages with the ability to infect and lyse . Here, we characterize the genomes of these phages, compare them to each other and to other sequenced phages, and putatively identify protein function. The phage genomes are 38-45 kb in size and contain 68-86 genes, most of which appear to be unique to phages. We classify phages into 2 main clusters and one singleton based on nucleotide sequence identity. Three of the new phages show sequence similarity to other sequenced phages, while the remaining 6 do not. We identified functions for roughly half of the phage proteins, including structural, assembly, host lysis, DNA replication/metabolism, regulatory, and host-related functions. Structural and assembly proteins are highly conserved among our phages and are located at the start of the genome. DNA replication/metabolism, regulatory, and host-related proteins are located in the middle and end of the genome, and are not conserved, with many of these genes found in some of our phages but not others. All nine phages code for a conserved N-acetylmuramoyl-L-alanine amidase. Comparative analysis showed the phages use the "cohesive ends with 3' overhang" DNA packaging strategy. This work is the first in-depth study of phage genomics, and serves as a marker for future work in this area.