Decomposition of the pangenome matrix reveals a structure in gene distribution in the <i>Escherichia coli</i> species.

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,

SUBMITTER: Chauhan SM 

PROVIDER: S-EPMC11774025 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature