New Genera and Species of Caulobacter and Brevundimonas Bacteriophages Provide Insights into Phage Genome Evolution

Abstract

Previous studies have identified diverse bacteriophages that infect Caulobacter vibrioides strain CB15 ranging from small RNA phages to four genera of jumbo phages. In this study, we focus on 20 bacteriophages whose genomes range from 40 to 60 kb in length. Genome comparisons indicated that these diverse phages represent six Caulobacter phage genera and one additional genus that includes both Caulobacter and Brevundimonas phages. Within species, comparisons revealed that both single base changes and inserted or deleted genetic material cause the genomes of closely related phages to diverge. Among genera, the basic gene order and the orientation of key genes were retained with most of the observed variation occurring at ends of the genomes. We hypothesize that the nucleotide sequences of the ends of these phage genomes are less important than the need to maintain the size of the genome and the stability of the corresponding mRNAs.

Keywords: Autographiviridae; Brevundimonas; Caulobacter; bacteriophages; genome comparisons; indels; new genera and species.

Figure 1

Viridic [16] heatmap of Caulobacter and Brevundimonas bacteriophages in the Autographiviridae family. The Lullwater (Lull), Cd1, and Percy phage genome clusters are indicated with brackets. Sphingomonas phage Scott and Xylella phage Coda were included as outgroups.

Figure 2

An alignment of a representative genome from each of the three Autographviridae clusters. The black lines indicate the position in the genome and the brown line is a sliding scale of the genome nucleotide consensus identity. The green lines indicate the position of genes, and the yellow lines indicate the positions of CDS. The red sections in the olive-colored consensus identity bar represent the positions of insertions or deletions (indels).

Figure 3

Lullwater cluster genome alignment. The black lines indicate the position in the genome and the brown line is a sliding scale of the genome nucleotide consensus identity. The green lines indicate the position of genes, and the yellow lines indicate the positions of CDS. The red sections in the olive-colored consensus identity bar represent the positions of insertions or deletions (indels).

Figure 4

Cd1 cluster genome alignment. The black lines indicate the position in the genome and the brown line is a sliding scale of the genome nucleotide consensus identity. The yellow lines indicate the positions of CDS. The red sections in the olive-colored consensus identity bar represent the positions of insertions or deletions (indels).

Figure 5

Percy cluster genome alignment. The black lines indicate the position in the genome and the brown line is a sliding scale of the genome nucleotide consensus identity. The green lines indicate the position of genes, and the yellow lines indicate the positions of CDS. The red sections in the olive-colored consensus identity bar represent the positions of insertions or deletions (indels).

Figure 6

Viridic [16] heatmap of Caulobacter bacteriophages belonging to the Jessavirus (defined by the lower black and blue boxes) and Riverwalk clusters (defined by the upper black boxes). Bordetella phage BPP-1 was included as an outgroup.

Figure 7

JessA cluster genome alignment. The black lines indicate the position in the genome and the brown line is a sliding scale of the genome nucleotide consensus identity. The green lines indicate the position of genes, and the yellow lines indicate the positions of CDS. The red sections in the olive-colored consensus identity bar represent the positions of insertions or deletions (indels).

Figure 8

RW cluster genome alignment. The black lines indicate the position in the genome and the green line is a sliding scale of the genome nucleotide consensus identity. The yellow lines indicate the positions of CDS.