Genetic stability and evolution of the sigB allele, used for Listeria sensu stricto subtyping and phylogenetic inference

Jingqiu Liao, Martin Wiedmann, Jasna Kovac

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Sequencing of single genes remains an important tool that allows the rapid classification of bacteria. Sequencing of a portion of sigB, which encodes a stress-responsive alternative sigma factor, has emerged as a commonly used molecular tool for the initial characterization of diverse Listeria isolates. In this study, evolutionary approaches were used to assess the validity of sigB allelic typing for Listeria. For a data set of 4,280 isolates, sigB allelic typing showed a Simpson's index of diversity of 0.96. Analyses of 164 sigB allelic types (ATs) found among the 6 Listeria sensu stricto species, representing these 4,280 isolates, indicate that neither frequent homologous recombination nor positive selection significantly contributed to the evolution of sigB, confirming its genetic stability. The molecular clock test provided evidence for unequal evolution rates across clades; Listeria welshimeri displayed the lowest sigB diversity and was the only species in which sigB evolved in a clocklike manner, implying a unique natural history. Among the four L. monocytogenes lineages, sigB evolution followed a molecular clock only in lineage IV. Moreover, sigB displayed a significant negative Tajima D value in lineage II, suggesting a recent population bottleneck followed by lineage expansion. The absence of positive selection along with the violation of the molecular clock suggested a nearly neutral mechanism of Listeria sensu stricto sigB evolution. While comparison with a wholegenome sequence-based phylogeny revealed that the sigB phylogeny did not correctly reflect the ancestry of L. monocytogenes lineage IV, the availability of a large sigB AT database allowed accurate species classification.

Original languageEnglish (US)
Article numbere00306-17
JournalApplied and environmental microbiology
Volume83
Issue number12
DOIs
StatePublished - Jun 1 2017

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Listeria
genetic stability
Molecular Evolution
allele
Alleles
alleles
phylogenetics
phylogeny
Phylogeny
Listeria welshimeri
taxonomy
sigma factors
population bottleneck
homologous recombination
Sigma Factor
natural history
ancestry
recombination
Homologous Recombination
Natural History

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Food Science
  • Applied Microbiology and Biotechnology
  • Ecology

Cite this

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title = "Genetic stability and evolution of the sigB allele, used for Listeria sensu stricto subtyping and phylogenetic inference",
abstract = "Sequencing of single genes remains an important tool that allows the rapid classification of bacteria. Sequencing of a portion of sigB, which encodes a stress-responsive alternative sigma factor, has emerged as a commonly used molecular tool for the initial characterization of diverse Listeria isolates. In this study, evolutionary approaches were used to assess the validity of sigB allelic typing for Listeria. For a data set of 4,280 isolates, sigB allelic typing showed a Simpson's index of diversity of 0.96. Analyses of 164 sigB allelic types (ATs) found among the 6 Listeria sensu stricto species, representing these 4,280 isolates, indicate that neither frequent homologous recombination nor positive selection significantly contributed to the evolution of sigB, confirming its genetic stability. The molecular clock test provided evidence for unequal evolution rates across clades; Listeria welshimeri displayed the lowest sigB diversity and was the only species in which sigB evolved in a clocklike manner, implying a unique natural history. Among the four L. monocytogenes lineages, sigB evolution followed a molecular clock only in lineage IV. Moreover, sigB displayed a significant negative Tajima D value in lineage II, suggesting a recent population bottleneck followed by lineage expansion. The absence of positive selection along with the violation of the molecular clock suggested a nearly neutral mechanism of Listeria sensu stricto sigB evolution. While comparison with a wholegenome sequence-based phylogeny revealed that the sigB phylogeny did not correctly reflect the ancestry of L. monocytogenes lineage IV, the availability of a large sigB AT database allowed accurate species classification.",
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Genetic stability and evolution of the sigB allele, used for Listeria sensu stricto subtyping and phylogenetic inference. / Liao, Jingqiu; Wiedmann, Martin; Kovac, Jasna.

In: Applied and environmental microbiology, Vol. 83, No. 12, e00306-17, 01.06.2017.

Research output: Contribution to journalArticle

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