Genomic Analysis of Prophage Distribution in Xylella fastidiosa Reveals Extensive Diversity and Horizontal Gene Transfer

Xylella fastidiosa is a plant pathogenic bacterium responsible for significant agricultural and environmental impact. Prophages, genetic elements of viral origin integrated into bacterial genomes, play a key role in bacterial evolution by facilitating horizontal gene transfer and recombination, processes that drive host and environmental adaptation. In this study, we analyzed the diversity and distribution of prophages across 89 X. fastidiosa strains representing the three main subspecies: fastidiosa, multiplex and pauca, as well as the two proposed subspp. sandyi and morus, representative of 28 sequence types (ST). A total of 410 prophages were identified as PHASTEST-intact candidates, with a notable prevalence in strains of the subspp. sandyi and multiplex. Comparative analyses of the high-confidence prophage regions revealed 105 unique prophages, highlighting their role in enhancing genetic diversity through horizontal gene transfer and recombination. While some prophages were strain-specific, others were shared across multiple strains of the same subspecies or ST, suggesting clonal propagation. Genomic comparisons showed clear distinctions between prophages and lytic phages and highlighted similarities among prophages from different subspecies, reflecting shared evolutionary processes. These findings will support future studies on the functional roles of specific prophage genes, their contributions to X. fastidiosa virulence and host range, and their potential applications in phage-based biocontrol.