Genetic recombination in bacteriophage T4: single-burst analysis of cosegregants and evidence in favor of a splice/patch coupling model.

Shcherbakov, Victor P.; Plugina, Lidiya; Nesheva, M. A.

doi:10.1093/genetics/131.4.769

Cited by 11 publications

(1 citation statement)

References 57 publications

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“…During coinfection, temperate phages can recombine with prophages in the host genome ( De Paepe et al. 2014 ), whereas lytic phages can recombine with other lytic types ( Shcherbakov et al. 1992 ) or with prophages ( Bouchard and Moineau 2000 ).…”

Section: Introductionmentioning

confidence: 99%

Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades

Kupczok

Neve

Huang

et al. 2018

Molecular Biology and Evolution

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The evolution of asexual organisms is driven not only by the inheritance of genetic modification but also by the acquisition of foreign DNA. The contribution of vertical and horizontal processes to genome evolution depends on their rates per year and is quantified by the ratio of recombination to mutation. These rates have been estimated for bacteria; however, no estimates have been reported for phages. Here, we delineate the contribution of mutation and recombination to dsDNA phage genome evolution. We analyzed 34 isolates of the 936 group of Siphoviridae phages using a Lactococcus lactis strain from a single dairy over 29 years. We estimate a constant substitution rate of 1.9 × 10−4 substitutions per site per year due to mutation that is within the range of estimates for eukaryotic RNA and DNA viruses. The reconstruction of recombination events reveals a constant rate of five recombination events per year and 4.5 × 10−3 nucleotide alterations due to recombination per site per year. Thus, the recombination rate exceeds the substitution rate, resulting in a relative effect of recombination to mutation (r/m) of ∼24 that is homogenous over time. Especially in the early transcriptional region, we detect frequent gene loss and regain due to recombination with phages of the 936 group, demonstrating the role of the 936 group pangenome as a reservoir of genetic variation. The observed substitution rate homogeneity conforms to the neutral theory of evolution; hence, the neutral theory can be applied to phage genome evolution and also to genetic variation brought about by recombination.

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Section: Introductionmentioning

confidence: 99%