Understanding the dependencies of genes on one another in pangenomes.

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For 20 years, we have known that prokaryotic (and eukaryotic) genomes are structured into a distributed pangenome consisting of a 'core' genome common to all members of a particular grouping (species, genus or higher-level taxon), and an 'accessory' genome found in some, but not all genomes of that group. It has been a struggle to understand why and how this situation arises, but it is an almost universal rule of prokaryotic biology - species have pangenomes that consist of more genes than are found in any individual genome. It is unusual to be in a situation where there is an abundance of data that point to the existence of a particular evolutionary feature, but yet, there is no accompanying comprehensive theory that is well-supported by empirical data. This programme will generate a comprehensive understanding of prokaryotic pangenomes. Specifically, we will treat pangenomes as ecosystems and apply ecosystem theory and modelling in order to understand the origin and evolution of pangenomes. We will collect and analyse empirical (genomic) data in order to estimate pangenome model parameters, and to understand how genes interact with one another in a pangenome setting. The outcome will be a transformation in how we view pangenomes, what we understand about their roles in evolution and crucially, we will have an understanding of the complex set of interactions that shape the evolution of pangenomes.