%0 Journal Article %A Horesh, Gal %A Taylor-Brown, Alyce %A McGimpsey, Stephanie %A Lassalle, Florent %A Corander, Jukka %A Heinz, Eva %A Thomson, Nicholas R. %T Different evolutionary trends form the twilight zone of the bacterial pan-genome %D 2021 %J Microbial Genomics, %V 7 %N 9 %@ 2057-5858 %C 000670 %R https://doi.org/10.1099/mgen.0.000670 %K pan-genome %K E. coli %K evolutionary dynamics %K HGT %I Microbiology Society, %X 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. %U https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000670