Adaptative and ancient co-evolution of integrons withXanthomonasgenomes

Integrons are genetic elements that facilitate gene acquisition. They have been extensively studied in clinical bacteria, but their evolutionary role in phytopathogens remains underexplored. Here, we analysed complete genomes ofXanthomonasspecies to investigate the origin, distribution, and functional dynamics of integrons in this genus. We found that 93% of genomes harboured integrons. The integron-integrase geneintIwas predominantly located downstream ofilvD, indicating an ancestral acquisition of integrons, predating diversification within the genus. Phylogenetic analyses support vertical inheritance ofintI, with the exception of rare horizontal gene transfer events, notably inX. arboricola. Despite their widespread presence, full-lengthintIgenes and active integron platforms are only retained in some species, especiallyX. campestris, which shows high integron gene cassette variability and functional integron activity. In contrast, species such asX. cissicolaandX. phaseoliexhibit widespreadinIinactivation, likely occurring early in their divergence, leading to more stable cassette arrays and conserved integron-associated phenotypes. The number and diversity of genes within cassette arrays varied significantly by species and, to a lesser extent, by the ecological context of plant host cultivation. While most cassettes encoded proteins without a known function, those with annotated roles were associated with stress response mechanism, competitive exclusion, and plant-associated functions. Together, our findings demonstrate that integrons inXanthomonaslikely originated from a single ancient acquisition event, preceding genus-wide speciation, and have co-evolved withXanthomonaspathovars as they adapted to distinct plant hosts.