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Comparative genomics and functional analysis of the 936 group of lactococcal Siphoviridae phages

Comparative genomics and functional analysis of the 936 group of lactococcal Siphoviridae phages

Sci Rep. 2016 Feb 19;6:21345. doi: 10.1038/srep21345.

James Murphy, Francesca Bottacini, Jennifer Mahony, Philip Kelleher, Horst Neve, Aldert Zomer, Arjen Nauta, Douwe van Sinderen

Genome sequencing and comparative analysis of bacteriophage collections has greatly enhanced our understanding regarding their prevalence, phage-host interactions as well as the overall biodiversity of their genomes. This knowledge is very relevant to phages infecting Lactococcus lactis, since they constitute a significant risk factor for dairy fermentations. Of the eighty four lactococcal phage genomes currently available, fifty five belong to the so-called 936 group, the most prevalent of the ten currently recognized lactococcal phage groups. Here, we report the genetic characteristics of a new collection of 936 group phages. By combining these genomes to those sequenced previously we determined the core and variable elements of the 936 genome. Genomic variation occurs across the 936 phage genome, such as genetic elements that (i) lead to a +1 translational frameshift resulting in the formation of additional structures on the phage tail, (ii) specify a double neck passage structure, and (iii) encode packaging module-associated methylases. Hierarchical clustering of the gene complement of the 936 group phages and nucleotide alignments allowed grouping of the ninety 936 group phages into distinct clusters, which in general appear to correspond with their geographical origin.

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