Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948

Hongan Long, Way Sung, Samuel F. Miller, Matthew S. Ackerman, Thomas G. Doak, Michael Lynch

Research output: Contribution to journalArticle

22 Citations (Scopus)

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 themutation rate varies around the chromosome, with the lowest mutation rate foundnear the originof replication. Consistent with observations fromother studies, wefind that site-specificmutation rates are heavily influenced by the immediately flanking nucleotides, indicating thatmutations are context dependent.

Original languageEnglish (US)
Pages (from-to)262-271
Number of pages10
JournalGenome Biology and Evolution
Volume7
Issue number1
DOIs
StatePublished - Jan 1 2014
Externally publishedYes

Fingerprint

Pseudomonas fluorescens
DNA Mismatch Repair
Mutation Rate
topology
repair
mutation
DNA
INDEL Mutation
Genome
Prophages
Intergenic DNA
Virulence Factors
Microbial Drug Resistance
Pseudomonas
substitution
genome
genetic variation
Nucleotides
Chromosomes
intergenic DNA

Keywords

  • mutation hotspots
  • Neutral evolution
  • nonrandom mutations
  • phage evolution

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948. / Long, Hongan; Sung, Way; Miller, Samuel F.; Ackerman, Matthew S.; Doak, Thomas G.; Lynch, Michael.

In: Genome Biology and Evolution, Vol. 7, No. 1, 01.01.2014, p. 262-271.

Research output: Contribution to journalArticle

Long, Hongan ; Sung, Way ; Miller, Samuel F. ; Ackerman, Matthew S. ; Doak, Thomas G. ; Lynch, Michael. / Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948. In: Genome Biology and Evolution. 2014 ; Vol. 7, No. 1. pp. 262-271.
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