Pangenomics to understand prophage dynamics in thePectobacteriumgenus and the radiating lineages ofP. Brasiliense

Abstract

AbstractBacterial pathogens of the genusPectobacteriumare responsible for soft rot and blackleg disease in a wide range of crops and have a global impact on food production. The emergence of new lineages and their competitive succession is frequently observed inPectobacteriumspecies, in particular inP. brasiliense. With a focus on one such recently emergedP. brasilienselineage in the Netherlands that causes blackleg in potatoes, we studied genome evolution in this genus using a reference-free graph-based pangenome approach. We clustered 1,977,865 proteins from 454Pectobacteriumspp. genomes into 30,156 homology groups. ThePectobacteriumgenus pangenome is open and its growth is mainly contributed by the accessory genome. Bacteriophage genes were enriched in the accessory genome and contributed 16% of the pangenome. Blackleg-causingP. brasilienseisolates had increased genome size with high levels of prophage integration. To study the diversity and dynamics of these prophages across the pangenome, we developed an approach to trace prophages across genomes using pangenome homology group signatures. We identified lineage-specific as well as generalist bacteriophages infectingPectobacteriumspecies. Our results capture the ongoing dynamics of mobile genetic elements, even in the clonal lineages. The observed lineage-specific prophage dynamics provide mechanistic insights intoPectobacteriumpangenome growth and contribution to the radiating lineages ofP. brasiliense.