Comparative genomic analysis of Ralstonia solanacearum species complex

Ralstonia solanacearum species complex (RSSC) consist of a group of phytopathogenic bacteria that can infect many economically important crops, including tomatoes, potatoes, and bananas. RSSC are very diverse, capable of surviving up to 200 plant host species and various environmental reservoirs such as soils, river water and secondary wild plant hosts. The diversity of the RSSC is often credited to its large bipartite genome (5-6Mbp), that encodes multiple genes linked to virulence and survival across different niches. In this thesis, I investigated the genetic diversity of RSSC at worldwide (55 countries), country (the UK) and crop field (four tomato fields in China) levels. Worldwide, we found that the open pangenome of RSSC contained 18,080 genes. I estimate that the recombination across the phylogeny occurred five times frequently than mutation. Moreover, I show that insertion sequences linked to virulence and metal resistance genes played an important role in the accessory genome diversification of RSSC. Within the UK, I show that the diversification of the clonal phylotype IIB-1 strain is due to initial loss of accessory genes and movement of IS elements with estimated origin of the population dated between 1958 and 1988. At the field level, we show that two to three clonal lineages co-occur within all sampled fields. Interestingly, co-occurring lineages differ in their virulence traits and gene content, which could be due to due to adaptation to different niches within each field. The work presented here lays the groundwork for a systematic understanding of the ecological and evolutionary genomics of the RSSC species complex, at the local and global scale. It also demonstrates that instead of mutations, recombination and highly mobile transposases are important drivers of RSSC genetic diversity.