Genetic Stability and Evolution of thesigBAllele, Used for Listeria Sensu Stricto Subtyping and Phylogenetic Inference
Year: 2017
Type: article
Abstract: ABSTRACT Sequencing of single genes remains an important tool that allows the rapid classification of bacteria. Sequencing of a portion ofsigB, 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 ofsigBallelic typing for Listeria . For a data set of 4,280 isolates,sigBallelic typing showed a Simpson's index of diversity of 0.96. Analyses of 164sigBallelic 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 ofsigB, confirming its genetic stability. The molecular clock test provided evidence for unequal evolution rates across clades; Listeria welshimeri displayed the lowestsigBdiversity and was the only species in whichsigBevolved in a clocklike manner, implying a unique natural history. Among the four L. monocytogenes lineages,sigBevolution followed a molecular clock only in lineage IV. Moreover,sigBdisplayed a significant negative TajimaDvalue 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 sigBevolution. While comparison with a whole-genome sequence-based phylogeny revealed that thesigBphylogeny did not correctly reflect the ancestry of L. monocytogenes lineage IV, the availability of a largesigBAT database allowed accurate species classification. IMPORTANCEsigBallelic typing has been widely used for species delineation and subtyping of Listeria . However, an informative evaluation of this method from an evolutionary perspective was missing. Our data indicate that the genetic stability ofsigBis affected by neither frequent homologous recombination nor positive selection, which supports thatsigBallelic typing provides reliable subtyping and classification of Listeria sensu stricto strains. However, multigene data are required for accurate phylogeny reconstruction of Listeria . This study thus contributes to a better understanding of the evolution ofsigBand confirms the robustness of thesigBsubtyping system for Listeria .
DOI: 10.1128/aem.00306-17
Authors: Jingqiu Liao, Martin Wiedmann, Jasna Kovac
Institution: Cornell University
Language: English
Subfield: Biotechnology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W2605192249