Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome
Open accessAbstract
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.
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Testing whether an ancestral change in one trait consistently leads to the same change in the other trait would suggest the co-evolution is due to a causal link.
“To distinguish which scenario is more likely, we could test whether an ancestral change in one trait consistently leads to the same change in the other trait, which would suggest the co-evolution is due to a causal link42,43,51,85–87 (Fig. 3).”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [86]
The Methods section describes testing gene-pair presence and absence patterns, not whether ancestral changes in one trait are consistently followed by changes in another. The Discussion says this method misses asymmetrical dependencies and calls for further investigation of direct interactions, but does not propose the claimed ancestral-change test or say that its result would suggest a causal link (page unavailable). (LLM, conf=0.75)
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A phylogenetic approach to comparative genomics
Dewar, A. E., Belcher, L. J., & West, S. A. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-024-00803-0 · Cited by 41 · see citing works
- Authors
- Whelan, F. J., Hall, R. J., & McInerney, J. O.
- Affiliations
- University of Nottingham (GB)
- Corresponding author
- McInerney, James O
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2021-05-08
- Volume
- 38
- Issue
- 9
- Pages
- 3697-3708
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC8382901
- OpenAlex
- W3159742497
- Cited by
- 46
- References
- 0
- Citations by year
- 2026: 11 · 2025: 10 · 2024: 9 · 2023: 7 · 2022: 5 · 2021: 4
- FWCI
- 2.20
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Molecular Biology and Evolution (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion, cc-by)
- Repository@Nottingham (University of Nottingham) (acceptedVersion, other-oa)
- Repository@Nottingham (University of Nottingham) (submittedVersion, cc-by)
- Repository@Nottingham (University of Nottingham) (submittedVersion, cc-by-nc-nd)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion, other-oa)
- Funders
- Marie Skłodowska-Curie Individual Fellowship (793818)
- BBSRC (BB/N018044/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- pan-genome, accessory genome, Pseudomonas, gene co-occurrence, selection, genetic interactions
- MeSH terms
- Phylogeny, Prokaryotic Cells, Genome
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