Open AccessDifferent evolutionary trends form the twilight zone of the bacterial pan-genome
Author(s) -
Gal Horesh,
Alyce Taylor–Brown,
Stephanie McGimpsey,
Florent Lassalle,
Jukka Corander,
Eva Heinz,
Nicholas R. Thomson
Publication year - 2021
Publication title -
microbial genomics
Language(s) - English
Resource type - Journals
ISSN - 2057-5858
DOI - 10.1099/mgen.0.000670
Subject(s) - genome , biology , evolutionary biology , bacterial genome size , population , genome evolution , gene , genetics , computational biology , demography , sociology
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 classifying 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.