Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes.

ABSTRACT: Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. We apply our method to pairs of genes from the Staphylococcus aureus accessory genome of over 75,000 annotated gene families using a database of over 40,000 whole genomes. We find many pairs of genes that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of rapidly coevolving genes, primarily co

SUBMITTER: Mehta RS 

PROVIDER: S-EPMC10251594 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature