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Evidence for selection in a prokaryote pangenome

View ORCID ProfileFiona J Whelan, View ORCID ProfileRebecca J Hall, View ORCID ProfileJames O McInerney
doi: https://doi.org/10.1101/2020.10.28.359307
Fiona J Whelan
1School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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Rebecca J Hall
1School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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James O McInerney
1School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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  • For correspondence: james.mcinerney@nottingham.ac.uk
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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 genomes 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 or horizontally co-inherited - are more likely to share Gene Ontology 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 interacting sets of genes co-selected to function together within a given strain. Given the simi larity of the Pseudomonas pangenome with open pangenomes of other prokaryotic species, we speculate that these results are generalizable.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 28, 2020.
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Evidence for selection in a prokaryote pangenome
Fiona J Whelan, Rebecca J Hall, James O McInerney
bioRxiv 2020.10.28.359307; doi: https://doi.org/10.1101/2020.10.28.359307
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Evidence for selection in a prokaryote pangenome
Fiona J Whelan, Rebecca J Hall, James O McInerney
bioRxiv 2020.10.28.359307; doi: https://doi.org/10.1101/2020.10.28.359307

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