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Mol Biol Evol. 2017 Jan;34(1):93-109. doi: 10.1093/molbev/msw224. Epub 2016 Oct 15.

Genome-Wide Biases in the Rate and Molecular Spectrum of Spontaneous Mutations in Vibrio cholerae and Vibrio fischeri.

Author information

1
Microbiology Graduate Program, University of New Hampshire, Durham, NH.
2
Department of Bioinformatics and Genomics, University of North Carolina Charlotte, Charlotte, NC.
3
Department of Biology, Indiana University, Bloomington, IN.
4
Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY.
5
Microbiology Graduate Program, University of New Hampshire, Durham, NH vaughn.cooper@pitt.edu.
6
Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA.

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 10-3/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.

KEYWORDS:

Vibrio cholerae; Vibrio fischeri; mutation accumulation; mutation rate; mutation spectra

PMID:
27744412
PMCID:
PMC5854121
DOI:
10.1093/molbev/msw224
[Indexed for MEDLINE]
Free PMC Article

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