ArticleGenome biology and evolution2014
Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948.
Article in Genome biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 71 citations in OpenAlex.
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- Elevated rates and biased spectra of mutations in anaerobically cultured lactic acid bacteria.mBio · 2025Article
- Mutational features of chromids and chromosomes inMicrobiology spectrum · 2025Article
- Mutation bias and adaptation in bacteria.Microbiology (Reading, England) · 2023Review
- The divergence of mutation rates and spectra across the Tree of Life.EMBO reports · 2023Review
- Generalised interrelations among mutation rates drive the genomic compliance of Chargaff's second parity rule.Nucleic acids research · 2023Article
- De Novo Structural Variations of Escherichia coli Detected by Nanopore Long-Read Sequencing.Genome biology and evolution · 2023Article
- Mutation bias and the predictability of evolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Review
- CDMAP/CDVIS: context-dependent mutation analysis package and visualization software.G3 (Bethesda, Md.) · 2023Article
- Silver nanoparticles elevate mutagenesis of eukaryotic genomes.G3 (Bethesda, Md.) · 2023Article
- Hypermutator strains of Pseudomonas aeruginosa reveal novel pathways of resistance to combinations of cephalosporin antibiotics and beta-lactamase inhibitors.PLoS biology · 2022Article
- The Impact of RNA-DNA Hybrids on Genome Integrity in Bacteria.Annual review of microbiology · 2022Review
- A near-deterministic mutational hotspot in Pseudomonas fluorescens is constructed by multiple interacting genomic features.Molecular biology and evolution · 2022Article
- Context-Dependent Substitution Dynamics in Plastid DNA Across a Wide Range of Taxonomic Groups.Journal of molecular evolution · 2022Article
- A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes.Nature communications · 2021Article
- Unexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control Strains.Genome biology and evolution · 2021Article
- The insect-killing bacteriumMarine life science & technology · 2021Article
- Article
- Pseudouridines of tRNA Anticodon Stem-Loop Have Unexpected Role in Mutagenesis inMicroorganisms · 2020Article
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6 authors at 1 institution in 1 country.
Funding
Abstract
High levels of genetic diversity exist among natural isolates of the bacterium Pseudomonas fluorescens, and are especially elevated around the replication terminus of the genome, where strain-specific genes are found. In an effort to understand the role of genetic variation in the evolution of Pseudomonas, we analyzed 31,106 base substitutions from 45 mutation accumulation lines of P. fluorescens ATCC948, naturally deficient for mismatch repair, yielding a base-substitution mutation rate of 2.34 × 10(-8) per site per generation (SE: 0.01 × 10(-8)) and a small-insertion-deletion mutation rate of 1.65 × 10(-9) per site per generation (SE: 0.03 × 10(-9)). We find that the spectrum of mutations in prophage regions, which often contain virulence factors and antibiotic resistance, is highly similar to that in the intergenic regions of the host genome. Our results show that the mutation rate varies around the chromosome, with the lowest mutation rate found near the origin of replication. Consistent with observations from other studies, we find that site-specific mutation rates are heavily influenced by the immediately flanking nucleotides, indicating that mutations are context dependent.
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