Understanding the dependencies of genes on one another in pangenomes.

20年来，我们已经知道，原核生物（和真核生物）基因组是由一个分布的泛基因组组成的，这个泛基因组由一个特定分组（种、属或更高一级的分类单元）的所有成员共有的“核心”基因组和一个在该分组的一些（但不是所有）基因组中发现的“辅助”基因组组成。理解这种情况发生的原因和方式一直是一场斗争，但这几乎是原核生物的普遍规律——物种的泛基因组比任何单个基因组中发现的基因都多。这是不寻常的情况下，有大量的数据指出存在一个特定的进化特征，但是，没有伴随的综合理论，是由经验数据很好地支持。该计划将产生对原核泛基因组的全面了解。具体来说，我们将把泛基因组视为生态系统，并应用生态系统理论和模型来理解泛基因组的起源和进化。我们将收集和分析经验（基因组）数据，以估计泛基因组模型参数，并了解基因如何在泛基因组设置中相互作用。研究结果将改变我们对泛基因组的看法，改变我们对它们在进化中的作用的理解，更重要的是，我们将了解影响泛基因组进化的一系列复杂的相互作用。

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.