Conflict and Cooperation in Prokaryote Pangenomes

PhD students wanted

Applications accepted all year round. Self-Funded PhD Students Only

About the Project

Prokaryotes mediate most of the biogeochemical cycles on the planet, are responsible for large numbers of diseases and are used in pharmaceutical and biotechnology industries to make new and interesting compounds. One of the biggest surprises of the last 20 years has been the observation that while a typical prokaryote has a genome of a particular size, the species as a whole usually has many, many more genes. We say that prokaryote species have “pangenomes” – a collection of genes that are “core” to all members of the species and a set of genes that are present in only some of the members of the species. Why prokaryotes have pangenomes is a subject of debate (1). In this project we will develop analytical methods to help us understand how pangenomes are assembled and disassembled in prokaryotes. We will analyse large datasets of prokaryote genomes in order to examine (a) the order in which particular lineages of prokaryotes acquired new genes, (b) whether incoming genes displaced pre-existing genes and (c) what forces of conflict and cooperation exist between genes in pangenomes.


McInerney, J.O., McNally, A and O’Connell, M.J. (2017) Why Prokaryotes have Pangenomes. Nature Microbiology 2, 17040. [LINK]

Whelan, F.J, Hall, R.J. and McInerney, J.O. (2020) Evidence for selection in a prokaryote pangenome. bioRxiv 10.28.359307; doi:

Hall, R.J., Whelan, F.J., McInerney, J.O., Ou, Y., Domingo Sananes, M.R. (2020) Horizontal gene transfer as a source of conflict and cooperation in prokaryotes. Frontiers in Microbiology 11, 1569.

Whelan, F.J. Rusilowicz, M. and McInerney J.O. (2020) Coinfinder: detecting significant associations and dissociations
in pangenomes. Microbial Genomics. DOI 10.1099/mgen.0.000338

McInerney, J.O., Whelan, F.J., Domingo-Sananes, M.R., McNally, A., and O’Connell, M.J. (2020) Pangenomes and Selection: The Public Goods Hypothesis. In: The Pangenome (eds. Hervé Tettelin and Duccio Medini). Springer.