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 – 2018-2022
Supervisors: Alexandra Calteau and David Vallenet
- Bazin A, Médigue C, Vallenet D, Calteau A. panModule: detecting conserved modules in the variable regions of a pangenome graph. BioRxiv
- Muir, A., Gurung, I., Cehovin, A., Bazin, A., Vallenet, D., & Pelicic, V.. (2020). Construction of a complete set of neisseria meningitidis mutants and its use for the phenotypic profiling of this human pathogen. Nature communications, 11(1), 1–13.
- Bazin A, Gautreau G, Médigue C, Vallenet D, Calteau A. panRGP: a pangenome-based method to predict genomic islands and explore their diversity. Bioinformatics. 2020 Dec 30;36(Suppl_2):i651-i658.
- Gautreau G, Bazin A, Gachet M, Planel R, Burlot L, Dubois M, Perrin A, Médigue C, Calteau A, Cruveiller S, Matias C, Ambroise C, Rocha EPC, Vallenet D. PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph. PLoS Comput Biol. 2020 Mar 19;16(3):e1007732.
- Vallenet D, Calteau A, Dubois M, Amours P, Bazin A, Beuvin M, Burlot L, Bussell X, Fouteau S, Gautreau G, Lajus A, Langlois J, Planel R, Roche D, Rollin J, Rouy Z, Sabatet V, Médigue C. MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. Nucleic Acids Res. 2020 Jan 8;48(D1):D579-D589.