ArticleMolecular biology and evolution2018
Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 84 citations in OpenAlex.
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- Complex temporal dynamics of phage-bacteria populations in an animal-associated marine system.Nature communications · 2026Article
- Towards accurate artificial intelligence models for strain-level phage-host prediction.Briefings in bioinformatics · 2026Article
- Temperate versus virulent phage lifestyle impacts microdiversity in soil environments.ISME communications · 2026Article
- Diversity and functional characterization of HNH endonucleases encoded by lactococcalMicrobial genomics · 2025Article
- Distinct shifts in bacteriophage diversity and abundance during various stages of Gouda-type cheese production.Applied and environmental microbiology · 2025Article
- Characterization of strictly lytic phages infectingMicrobiology spectrum · 2025Article
- Insight into crRNA Processing inInternational journal of molecular sciences · 2025Article
- Factors Affecting Phage-Bacteria Coevolution Dynamics.Viruses · 2025Review
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- Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces.Nature communications · 2024Article
- Infant gut DNA bacteriophage strain persistence during the first 3 years of life.Cell host & microbe · 2024Article
- Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles.The ISME journal · 2024Article
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- Genomic diversity and biogeographic distributions of a novel lineage of bacteriophages that infect marine OM43 bacteria.Microbiology spectrum · 2023Article
- Longitudinal Study ofApplied and environmental microbiology · 2023Article
- L-shaped distribution of the relative substitution rate (c/μ) observed for SARS-COV-2's genome, inconsistent with the selectionist theory, the neutral theory and the nearly neutral theory but a near-neutral balanced selection theory: Implication on "neutralist-selectionist" debate.Computers in biology and medicine · 2023Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
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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