The aim of this PhD thesis is to carry out methodological developments for the comparative study of pangenomes. Those developments will allow to explore the variable pangenome’s dynamic within and between bacterial clades.
Firstly, a tool for detecting variable regions in a pangenome graph using a partitioned pangenome will be produced. Regions of Genomic Plasticity (RGPs) are regions that are exchanged between strains by horizontal gene transfer (e.g. genomic islands) and regions lost differentially among lineages. They are of paramount importance to understand the adaptive potential of bacteria.
Most of those RGPs are poorly characterized. Methods will be developped to associate genes that are conserved together within those RGPs. This co-conservation is a strong evidence for functional linkage. This will help to functionally annotate unknown proteins or group.
Secondly, methodological developments will allow inter-pangenome comparisons and, thus, the exploration of the RGP dynamic between different species. The algorithms and tools developed during this thesis will be applied to study different bacterial groups for which a large amount of data is available.
PhD candidate: Adelme Bazin
Supervisors: Alexandra Calteau and David Vallenet