Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages

Comparative phage genomics can retrace part of the evolutionary history of phage modules encoding phage‐specific functions such as capsid building or establishment of the lysogenic state. The diagnosis of relatedness is not based exclusively on sequence similarity, but includes topological considerations of genome organization. The gene maps from the λ‐, ψM2‐, L5‐, Sfi21‐, Sfi11‐, φC31‐, sk1‐ and TM4‐like phages showed a remarkable synteny of their structural genes defining a λ supergroup within Siphoviridae (Caudovirales with long non‐contractile tails). A hierarchy of relatedness within the λ supergroup suggested elements of vertical evolution in the capsid module of Siphoviridae. Links to P22‐like Podoviridae and P2‐like Myoviridae were also detected. Numerous cases of horizontal gene transfer were observed, but recent transfers were limited to interbreeding phage populations. We suggest that tailed phages are the result of both vertical and horizontal evolution and are thus a good model system for web‐like phylogenies.