title: Genetic Stability and Evolution of thesigBAllele, 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 ofsigB, which encodes a stress-responsive alternative sigma factor, has emerged as a commonly used molecular tool for the initial characterization of diverseListeriaisolates. In this study, evolutionary approaches were used to assess the validity ofsigBallelic typing forListeriaFor 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 6Listeriasensu strictospecies, 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 welshimeridisplayed the lowestsigBdiversity and was the only species in whichsigBevolved in a clocklike manner, implying a unique natural history. Among the fourL. monocytogeneslineages,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 ofListeriasensu strictosigBevolution. While comparison with a whole-genome sequence-based phylogeny revealed that thesigBphylogeny did not correctly reflect the ancestry ofL. monocytogeneslineage IV, the availability of a largesigBAT database allowed accurate species classification.IMPORTANCEsigBallelic typing has been widely used for species delineation and subtyping ofListeriaHowever, 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 ofListeria sensu strictostrains. However, multigene data are required for accurate phylogeny reconstruction ofListeriaThis study thus contributes to a better understanding of the evolution ofsigBand confirms the robustness of thesigBsubtyping system forListeria.
authors.affiliation: Department of Food Science, Cornell University, Ithaca, New York, USA.|Graduate Field of Microbiology, Cornell University, Ithaca, New York, USA.
authors.forename: Jingqiu
authors.initials: J
authors.lastname: Liao
authors.affiliation: Department of Food Science, Cornell University, Ithaca, New York, USA.
authors.forename: Martin
authors.initials: M
authors.lastname: Wiedmann
authors.affiliation: Department of Food Science, Cornell University, Ithaca, New York, USA jk2739@cornell.edu.
authors.forename: Jasna
authors.initials: J
authors.lastname: Kovac
mesh_terms: D000483:Alleles; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D015373:Bacterial Typing Techniques / Q000379:methods*; D019143:Evolution, Molecular; D014644:Genetic Variation; D008087:Listeria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification* / Q000378:metabolism; D008089:Listeria monocytogenes / Q000235:genetics / Q000378:metabolism; D008088:Listeriosis / Q000382:microbiology; D010802:Phylogeny; D011995:Recombination, Genetic; D012808:Sigma Factor / Q000235:genetics* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; C079011:SigB protein, Bacteria; D012808:Sigma Factor
keywords: allelic typing; homologous recombination; molecular clock; positive selection; sigB