Different evolutionary trends form the twilight zone of the bacterial pan-genome

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Horesh , G , Taylor-Brown , A , McGimpsey , S , Lassalle , F , Corander , J , Heinz , E & Thomson , N R 2021 , ' Different evolutionary trends form the twilight zone of the bacterial pan-genome ' , Microbial Genomics , vol. 7 , no. 9 , 000670 . https://doi.org/10.1099/mgen.0.000670

Title: Different evolutionary trends form the twilight zone of the bacterial pan-genome
Author: Horesh, Gal; Taylor-Brown, Alyce; McGimpsey, Stephanie; Lassalle, Florent; Corander, Jukka; Heinz, Eva; Thomson, Nicholas R.
Contributor organization: Department of Mathematics and Statistics
Helsinki Institute for Information Technology
Jukka Corander / Principal Investigator
Biostatistics Helsinki
Date: 2021-09
Language: eng
Number of pages: 10
Belongs to series: Microbial Genomics
ISSN: 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000670
URI: http://hdl.handle.net/10138/335629
Abstract: The pan-genome is defined as the combined set of all genes in the gene pool of a species. Pan-genome analyses have been very useful in helping to understand different evolutionary dynamics of bacterial species: an open pan-genome often indicates a free-living lifestyle with metabolic versatility, while closed pan-genomes are linked to host-restricted, ecologically specialized bacteria. A detailed understanding of the species pan-genome has also been instrumental in tracking the phylodynamics of emerging drug resistance mechanisms and drug-resistant pathogens. However, current approaches to analyse a species' pan-genome do not take the species population structure into account, nor do they account for the uneven sampling of different lineages, as is commonplace due to over -sampling of clinically relevant representatives. Here we present the application of a population structure- aware approach for classify-ing genes in a pan-genome based on within-species distribution. We demonstrate our approach on a collection of 7500 Escherichia coli genomes, one of the most-studied bacterial species and used as a model for an open pan-genome. We reveal clearly distinct groups of genes, clustered by different underlying evolutionary dynamics, and provide a more biologically informed and accurate description of the species' pan-genome.
Subject: evolutionary dynamics
1181 Ecology, evolutionary biology
1184 Genetics, developmental biology, physiology
11832 Microbiology and virology
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion

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