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Purifying selection, sequence composition, and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont.

Publication ,  Journal Article
Williams, LE; Wernegreen, JJ
Published in: Genome biology and evolution
January 2012

Comparative genomics of closely related bacterial strains can clarify mutational processes and selective forces that impact genetic variation. Among primary bacterial endosymbionts of insects, such analyses have revealed ongoing genome reduction, raising questions about the ultimate evolutionary fate of these partnerships. Here, we explored genomic variation within Blochmannia vafer, an obligate mutualist of the ant Camponotus vafer. Polymorphism analysis of the Illumina data set used previously for de novo assembly revealed a second Bl. vafer genotype. To determine why a single ant colony contained two symbiont genotypes, we examined polymorphisms in 12 C. vafer mitochondrial sequences assembled from the Illumina data; the spectrum of variants suggests that the colony contained two maternal lineages, each harboring a distinct Bl. vafer genotype. Comparing the two Bl. vafer genotypes revealed that purifying selection purged most indels and nonsynonymous differences from protein-coding genes. We also discovered that indels occur frequently in multimeric simple sequence repeats, which are relatively abundant in Bl. vafer and may play a more substantial role in generating variation in this ant mutualist than in the aphid endosymbiont Buchnera. Finally, we explored how an apparent relocation of the origin of replication in Bl. vafer and the resulting shift in strand-associated mutational pressures may have caused accelerated gene loss and an elevated rate of indel polymorphisms in the region spanning the origin relocation. Combined, these results point to significant impacts of purifying selection on genomic polymorphisms as well as distinct patterns of indels associated with unusual genomic features of Blochmannia.

Duke Scholars

Published In

Genome biology and evolution

DOI

EISSN

1759-6653

ISSN

1759-6653

Publication Date

January 2012

Volume

4

Issue

1

Start / End Page

44 / 51

Related Subject Headings

  • Symbiosis
  • Replication Origin
  • Recombination, Genetic
  • Polymorphism, Genetic
  • Mutation
  • Mitochondria
  • Microsatellite Repeats
  • Genotype
  • Genome, Bacterial
  • Evolution, Molecular
 

Citation

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ICMJE
MLA
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Williams, L. E., & Wernegreen, J. J. (2012). Purifying selection, sequence composition, and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont. Genome Biology and Evolution, 4(1), 44–51. https://doi.org/10.1093/gbe/evr128
Williams, Laura E., and Jennifer J. Wernegreen. “Purifying selection, sequence composition, and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont.Genome Biology and Evolution 4, no. 1 (January 2012): 44–51. https://doi.org/10.1093/gbe/evr128.
Williams, Laura E., and Jennifer J. Wernegreen. “Purifying selection, sequence composition, and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont.Genome Biology and Evolution, vol. 4, no. 1, Jan. 2012, pp. 44–51. Epmc, doi:10.1093/gbe/evr128.
Journal cover image

Published In

Genome biology and evolution

DOI

EISSN

1759-6653

ISSN

1759-6653

Publication Date

January 2012

Volume

4

Issue

1

Start / End Page

44 / 51

Related Subject Headings

  • Symbiosis
  • Replication Origin
  • Recombination, Genetic
  • Polymorphism, Genetic
  • Mutation
  • Mitochondria
  • Microsatellite Repeats
  • Genotype
  • Genome, Bacterial
  • Evolution, Molecular