Diversity and comparative genomic analysis of Pseudomonas syringae pv. actinidiae prophages

Pseudomonas syringae pv. actinidiae is a pandemic agent of bacterial canker in kiwifruit. The virulence of bacteria can be mediated by horizontal gene transfer in a co-evolutionary process with other microorganisms, enriching their genetic repertoire and enhancing adaptation strategies and fitness. Temperate bacteriophages can integrate into bacterial genomes, increasing genetic diversity and potentially improving bacterial fitness and virulence. To better understand the role of prophages in bacterial fitness and virulence, a bioinformatics analysis was performed on 88 genomes. Prophages were identified, annotated, and analyzed for their genomic content and integration sites. In total, 432 prophage-like sequences were identified, with an average of 4.7 prophages per genome, of which 88 were intact. The GC content of prophages (58.8%) was similar to that of host genomes (58.5%), and genome sizes ranged from 19 to 68.2 kb. Genomic and proteomic analysis revealed substantial diversity, grouping into 10 clusters with clonal profiles and broad geographical distribution. These results suggest ancestral acquisition, probably before clonal distribution. Prophages encode putative virulence factors, including metabolic-related proteins (45.7%), lipoproteins (34.3%), transporters (8.6%), transcriptional regulators (37.1%), and other factors (36%) which contribute to bacterial stress tolerance, biofilm formation, motility, quorum sensing , metabolism and competition. Some intact prophages (36.4%) exhibit specific integration sites with homology to host tRNA genes, indicating alternative attachment sites. The study supports the hypothesis that temperate phages contribute to the genetic diversity and pathogenicity by providing accessory genetic material, contributing to bacterial colonization and survival within the host. • Pseudomonas syringae pv. actinidiae genomes reveal high diversity of prophage sequences. • Prophages played an active role in bacterial genome evolution, bacterial survival and pathogenicity. • This study offers foundation for future investigations to develop temperate-based interventions for plant pathogen control.