ArticlePLoS computational biology2020
Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 21 citations in OpenAlex.
- From hijackers to architects: the role of prophages in bacterial genome evolution.Journal of bacteriology · 2026Review
- Article
- Pseudomonas aeruginosa maintains an inducible array of novel and diverse prophages over lengthy persistence in cystic fibrosis lungs.FEMS microbiology letters · 2025Article
- Escherichia coli phage-inducible chromosomal island aids helper phage replication and represses the locus of enterocyte effacement pathogenicity island.The ISME journal · 2025Article
- Exploring the diversity and evolutionary strategies of prophages in Hyphomicrobiales, comparing animal-associated with non-animal-associated bacteria.BMC microbiology · 2024Article
- Endogenous virophages are active and mitigate giant virus infection in the marine protistProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Analysis of CRISPR/Cas Genetic Structure, Spacer Content and Molecular Epidemiology in BrazilianPathogens (Basel, Switzerland) · 2023Article
- The Prophage and Us-Shiga Toxin Phages Revisited.Pathogens (Basel, Switzerland) · 2023Article
- Comparative Genome Analysis of 19Antibiotics (Basel, Switzerland) · 2022Article
- Host life-history traits influence the distribution of prophages and the genes they carry.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Novel lineages of single-stranded DNA phages that coevolved with the symbiotic bacteriaFrontiers in microbiology · 2022Article
- Analysis of intact prophages in genomes ofFrontiers in microbiology · 2022Article
- Prophage Genomics and Ecology in the FamilyMicroorganisms · 2021Article
- Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Integrated into their bacterial hosts' genomes, prophage sequences exhibit a wide diversity of length and gene content, from highly degraded cryptic sequences to intact, functional prophages that retain a full complement of lytic-function genes. We apply three approaches-bioinformatics, analytical modelling and computational simulation-to understand the diverse gene content of prophages. In the bioinformatics work, we examine the distributions of over 50,000 annotated prophage genes identified in 1384 prophage sequences, comparing the gene repertoires of intact and incomplete prophages. These data indicate that genes involved in the replication, packaging, and release of phage particles have been preferentially lost in incomplete prophages, while tail fiber, transposase and integrase genes are significantly enriched. Consistent with these results, our mathematical and computational approaches predict that genes involved in phage lytic function are preferentially lost, resulting in shorter prophages that often retain genes that benefit the host. Informed by these models, we offer novel hypotheses for the enrichment of integrase and transposase genes in cryptic prophages. Overall, we demonstrate that functional and cryptic prophages represent a diversity of genetic sequences that evolve along a parasitism-mutualism continuum.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.