RT Journal Article
SR Electronic
T1 Evidence for selection in a prokaryote pangenome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.10.28.359307
DO 10.1101/2020.10.28.359307
A1 Fiona J Whelan
A1 Rebecca J Hall
A1 James O McInerney
YR 2020
UL http://biorxiv.org/content/early/2020/10/28/2020.10.28.359307.abstract
AB 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 StatementThe authors have declared no competing interest.