Genome-wide biases in the rate and molecular spectrum of spontaneous mutations in vibrio cholerae and vibrio fischeri

Marcus M. Dillon, Way Sung, Robert Sebra, Michael Lynch, Vaughn S. Cooper

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

The vast diversity in nucleotide composition and architecture among bacterial genomes may be partly explained by inherent biases in the rates and spectra of spontaneous mutations. Bacterial genomes with multiple chromosomes are relatively unusual but some are relevant to human health, none more so than the causative agent of cholera, Vibrio cholerae. Here, we present the genome-wide mutation spectra in wild-type and mismatch repair (MMR) defective backgrounds of two Vibrio species, the low-%GC squid symbiont V. fischeri and the pathogen V. cholerae, collected under conditions that greatly minimize the efficiency of natural selection. In apparent contrast to their high diversity in nature, both wild-type V. fischeri and V. cholerae have among the lowest rates for base-substitution mutations (bpsms) and insertion-deletion mutations (indels) that have been measured, below 103/genome/generation. Vibrio fischeri and V. cholerae have distinct mutation spectra, but both are AT-biased and produce a surprising number of multi-nucleotide indels. Furthermore, the loss of a functional MMR system caused the mutation spectra of these species to converge, implying that the MMR system itself contributes to species-specific mutation patterns. Bpsm and indel rates varied among genome regions, but do not explain the more rapid evolutionary rates of genes on chromosome 2, which likely result from weaker purifying selection. More generally, the very low mutation rates of Vibrio species correlate inversely with their immense population sizes and suggest that selection may not only have maximized replication fidelity but also optimized other polygenic traits relative to the constraints of genetic drift.

Original languageEnglish (US)
Pages (from-to)93-109
Number of pages17
JournalMolecular Biology and Evolution
Volume34
Issue number1
DOIs
StatePublished - Jan 1 2017
Externally publishedYes

Fingerprint

Aliivibrio fischeri
Vibrio fischeri
Vibrio cholerae
cholera
mutation
genome
Genome
Mutation
DNA Mismatch Repair
INDEL Mutation
Bacterial Genomes
Vibrio
repair
Nucleotides
Multifactorial Inheritance
Genetic Drift
nucleotides
Decapodiformes
Chromosomes, Human, Pair 2
chromosomes

Keywords

  • Mutation accumulation
  • Mutation rate
  • Mutation spectra
  • Vibrio cholerae
  • Vibrio fischeri

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

Genome-wide biases in the rate and molecular spectrum of spontaneous mutations in vibrio cholerae and vibrio fischeri. / Dillon, Marcus M.; Sung, Way; Sebra, Robert; Lynch, Michael; Cooper, Vaughn S.

In: Molecular Biology and Evolution, Vol. 34, No. 1, 01.01.2017, p. 93-109.

Research output: Contribution to journalArticle

Dillon, Marcus M. ; Sung, Way ; Sebra, Robert ; Lynch, Michael ; Cooper, Vaughn S. / Genome-wide biases in the rate and molecular spectrum of spontaneous mutations in vibrio cholerae and vibrio fischeri. In: Molecular Biology and Evolution. 2017 ; Vol. 34, No. 1. pp. 93-109.
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