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bioRxiv · 10.1101/2024.06.07.598014

The Pangenome of Escherichia coli

Chauhan, S. M.·Ardalani, O.·Hyun, J. C.·Phaneuf, P. V.·Monk, J. M.·Palsson, B. O.
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Abstract

Thousands of complete genome sequences for strains of a species that are now available enable the advancement of pangenome analytics to a new level of sophistication. We collected 2,377 publicly-available complete genomes of Escherichia coli for detailed pangenome analysis. The core genome and accessory genomes consisted of 2,398 and 5,182 genes, respectively. We developed a machine learning approach to define the accessory genes characterizing the major phylogroups of E. coli plus Shigella: A, B1, B2, C, D, E, F, G, and Shigella. The analysis resulted in a detailed structure of the genetic basis of the phylogroups differential traits. This pangenome structure was largely consistent with a housekeeping-gene-based MLST distribution, sequence-based Mash distance, and the Clermont quadruplex classification. The rare genome consisted of 163,619 genes, about 79% of which represented variations of 315 underlying transposon elements. This analysis generated a mathematical definition of the genetic basis for a species.

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Chauhan, S. M., Ardalani, O., Hyun, J. C., Phaneuf, P. V., Monk, J. M., Palsson, B. O.. 2024-06-08. The Pangenome of Escherichia coli. https://doi.org/10.1101/2024.06.07.598014

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