Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome

Whelan, Fiona J.; Hall, Rebecca J.; McInerney, James O.

Abstract

A pangenome is the complete set of genes (core and accessory) present in a phylogenetic clade. We hypothesize that a pangenome's accessory gene content is structured and maintained by selection. To test this hypothesis, we interrogated the genomes of 40 Pseudomonas species for statistically significant coincident (i.e., co-occurring/avoiding) gene patterns. We found that 86.7% of common accessory genes are involved in ≥1 coincident relationship. Further, genes that co-occur and/or avoid each other - but are not vertically inherited - are more likely to share functional categories, are more likely to be simultaneously transcribed, and are more likely to produce interacting proteins, than would be expected by chance. These results are not due to coincident genes being adjacent to one another on the chromosome. Together, these findings suggest that the accessory genome is structured into sets of genes that function together within a given strain. Given the similarity of the Pseudomonas pangenome with open pangenomes of other prokaryotic species, we speculate that these results are generalizable.

Citation

Whelan, F. J., Hall, R. J., & McInerney, J. O. (2021). Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome. Molecular Biology and Evolution, 38(9), 3697-3708. https://doi.org/10.1093/molbev/msab139

• Journal Article Type: Article
• Acceptance Date: Apr 23, 2021
• Online Publication Date: May 8, 2021
• Publication Date: Sep 1, 2021
• Deposit Date: Jun 4, 2021
• Publicly Available Date: Jun 8, 2021
• Journal: Molecular Biology and Evolution
• Print ISSN: 0737-4038
• Electronic ISSN: 1537-1719
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 38
• Issue: 9
• Pages: 3697-3708
• DOI: https://doi.org/10.1093/molbev/msab139
• Keywords: Genetics; Ecology, Evolution, Behavior and Systematics; Molecular Biology
• Public URL: https://nottingham-repository.worktribe.com/output/5522101
• Publisher URL: https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab139/6272232