Pangenomics to understand the prophage dynamics in the radiating lineages of P. brasiliense
Bacterial pathogens of the genus Pectobacterium are responsible for soft rot and blackleg disease ina wide range of crops and have a global impact on food production. Pangenome studies of this genushave shown that genetic diversity is particularly high in pathogenic species. The emergence of newstrains and their competitive succession is frequently observed in Pectobacterium species, in particularP. brasiliense. With a focus on one such recently emerged P. brasiliense lineage in the Netherlands thatcause blackleg in potatoes, we studied genome evolution in this genus using the pangenome approach.We identified 30,156 homology groups in the pangenome build with the 454 Pectobacterium speciesgenomes. The expansion of this pangenome was mainly contributed by the accessory genome andprophages contributed 16% of the pangenome. Blackleg causing P. brasiliense isolates had increasedgenome size with high levels of prophage integration compared to the non-causing isolates. To studythe diversity and dynamics of these prophages across pangenome, we developed an approach to traceprophages across genomes using pangenome homology group signatures. Our approach identified lineage-specific as well as generalist bacteriophages infecting Pectobacterium species. Our results capture ongoingdynamics of mobile genetic elements even in the clonal lineage as per the core genome phylogeny andprovide mechanistic insights into diverse strain emergence in P. brasiliense.