Complete genome sequence of a marine roseophage provides evidence into the evolution of gene transfer agents in alphaproteobacteria

Roseophage RDJL Phi 1 is a siphovirus isolated from South China Sea on Roseobacter denitrificans OCh114. Its virion encapsulates 62.7 kb genome that encodes 87 gene products. RDJL Phi 1 shares similar genome organization and gene content with the marine bacteriophage Phi JL001 and Pseudomonas phages YuA and M6, which are different from those of typical lambda- or Mu-like phages. Four hallmark genes (ORFs 81 to 84) of RDJL Phi 1 were highly homologous to RcGTA-like genes 12 to 15. The largest gene (ORF 84) was predicted to encode a tail fibre protein that could be involved in host recognition. Extended phylogenetic and comparative genomic analyses based on 77 RcGTA-like element-containing bacterial genomes revealed that RcGTA-like genes 12 to 15 together appear to be a conserved modular element that could also be found in some phage or prophage genomes. Our study suggests that RcGTA-like genes-containing phages and prophages and complete RcGTAs possibly descended from a same prophage ancestor that had diverged and then evolved vertically. The complete genome of RDJL Phi 1 provides evidence into the hypothesis that extant RcGTA may be a prophage remnant.