Genomic Diversity of Type B3 Bacteriophages of Caulobacter crescentus

Abstract

The genomes of the type B3 bacteriophages that infect Caulobacter crescentus are among the largest phage genomes thus far deposited into GenBank with sizes over 200 kb. In this study, we introduce six new bacteriophage genomes which were obtained from phage collected from various water systems in the southeastern United States and from tropical locations across the globe. A comparative analysis of the 12 available genomes revealed a "core genome" which accounts for roughly 1/3 of these bacteriophage genomes and is predominately localized to the head, tail, and lysis gene regions. Despite being isolated from geographically distinct locations, the genomes of these bacteriophages are highly conserved in both genome sequence and gene order. We also identified the insertions, deletions, translocations, and horizontal gene transfer events which are responsible for the genomic diversity of this group of bacteriophages and demonstrated that these changes are not consistent with the idea that modular reassortment of genomes occurs in this group of bacteriophages.

Fig. 1

Mauve whole genome comparison of the CbK, Cr2, Cr5, CcrKarma, and CCrswift bacteriophage genomes. Red space corresponds to similar sequences. Regions that are entirely white correspond to inserted gene regions.

Fig. 2

The conserved locations of genes present in all 12 CbK-like genomes. The genomes are arranged in size from largest to smallest (Table 1), with Rogue on the outside track and Cr32 on the inner most track. The Colossus genome is omitted from this comparison.

Fig. 3

DNA plot image of the CbK genome gene categories. Gene positions correspond to the CbK genome. Starting at the outer perimeter of the circle, the green blocks represent the genes found in all 12 genomes, the light blue are conserved throughout the 11 CbK-like genomes. The pink blocks are conserved in the 10 CbK-like genomes excluding Rogue. Dark red blocks represent the indels in the CbK genome. Black blocks are the tRNA locations. The dark grey arrows represent the location of the Genomic modules, the structural module, lysis module, and DNA replication module respectively, clockwise from the top of the circle. The center plot is the GC content of the CbK genome with gold bars marking regions of above average %GC and purple bars marking the regions with below average %GC.

Fig. 4

Molecular Phylogenetic analysis by Maximum Likelihood method. The evolutionary relationships of the 11 CbK-like genomes were inferred by using the Maximum Likelihood method based on the Tamura-Nei model [25]. The tree with the highest log likelihood (−498908.1958) is shown. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths proportional to the number of substitutions per site. The analysis involved 11 genome nucleotide sequences. Codon positions included were 1st+2nd+3rd+Noncoding. All positions containing gaps and missing data were eliminated. There were a total of 179597 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [26].

Fig. 5

The DNA ligase regions of the CbK (top) and Colossus genomes. The green arrows represent the genes which are found in all 12 genomes. Homologous genes are connected by lines.