Recombination and microdiversity in coastal marine cyanophages

Summary Genetic exchange is an important process in bacteriophage evolution. Here, we examine the role of homologous recombination in the divergence of closely related cyanophage isolates from natural marine populations. Four core‐viral genes (coliphage T4 homologues g20 , g23 , g43 and a putative tail fibre gene) and four viral‐encoded bacterial‐derived genes ( psbA , psbD , cobS and phoH ) were analysed for 60 cyanophage isolates belonging to five Rhode Island Myovirus (RIM) strains. Phylogenetic analysis of the 60 concatenated sequences revealed well‐resolved sequence clusters corresponding to the RIM strain designations. Viral isolates within a strain shared an average nucleotide identity of 99.3–99.8%. Nevertheless, extensive microdiversity was observed within each cyanophage strain; only three of the 60 isolates shared the same nucleotide haplotype. Microdiversit