Different evolutionary trends form the twilight zone of the bacterial pan-genome. Issue 9 (24th September 2021)

• Record Type: Journal Article
• Authors: Horesh, Gal; Taylor-Brown, Alyce; McGimpsey, Stephanie; Lassalle, Florent; Corander, Jukka; Heinz, Eva; Thomson, Nicholas R.
• Is Part Of: Microbial genomics. Volume 7:Issue 9(2021)
• Publication Date: 2021-09-24
• Subjects: evolutionary dynamics -- E. coli -- HGT -- pan-genome; Microbial genomics -- Periodicals; 572.8629
• DOI: 10.1099/mgen.0.000670
• Languages: English
• ISSNs: 2057-5858

Abstract

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 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.