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

Horesh, Gal, Taylor-Brown, Alyce, McGimpsey, Stephanie, Lassalle, Florent, Corander, Jukka, Heinz, Eva ORCID: https://orcid.org/0000-0003-4413-3756 and Thomson, Nicholas R. (2021) 'Different evolutionary trends form the twilight zone of the bacterial pan-genome'. Microbial Genomics, Vol 7, Issue 9, 000670.

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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.

Item Type:	Article
Subjects:	QU Biochemistry > Genetics > QU 460 Genomics. Proteomics QU Biochemistry > Genetics > QU 500 Genetic phenomena QU Biochemistry > Genetics > QU 550 Genetic techniques. PCR. Chromosome mapping QW Microbiology and Immunology > Bacteria > QW 138 Enterobacteriaceae
Faculty: Department:	Biological Sciences > Vector Biology Department
Digital Object Identifer (DOI):	https://doi.org/10.1099/mgen.0.000670
Depositing User:	Stacy Murtagh
Date Deposited:	28 Sep 2021 12:45
Last Modified:	28 Sep 2021 12:45
URI:	https://archive.lstmed.ac.uk/id/eprint/19039

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