Diverse conjugative and mobilisable elements underpin key adaptive traits in Xanthomonas

Horizontal gene transfer mediated by mobile genetic elements (MGEs) is a major driver of bacterial evolution and ecological adaptation. In the plant-associated genus Xanthomonas, multiple MGEs have been implicated in virulence, host specialisation, and environmental persistence, yet MGE diversity and evolutionary dynamics across the genus remain poorly understood. Here, we performed a comparative analysis of conjugative and mobilisable plasmids, integrative and conjugative elements (ICEs), integrative and mobilisable elements (IMEs), and their cargo genes across 516 complete genomes of three major Xanthomonas species: X. campestris, X. cissicola, and X. oryzae. We identified pronounced interspecific differences, with X. cissicola and X. campestris harbouring large and diverse MGE repertoires, comprising 28.3% and 26.7% of their respective pangenomes, whereas X. oryzae contained far fewer MGEs, making up only 3.6% of the identified pangenome. These differences were associated with host defence systems, including CRISPR-Cas and restriction-modification systems, and with variation in CRISPR spacer diversity. IMEs were the most abundant MGEs across all species, encoding diverse defence systems and accessory genes. ICEs exhibited signatures of horizontal transfer within and between species, and across genera. Notably, nearly identical ICEs carrying heavy-metal resistance genes were identified in Xanthomonas and Pseudomonas aeruginosa, indicating recent transfer between genera. MGEs collectively carried genes involved in virulence, interbacterial interactions, defence against phages, and plant cell wall degradation, with several elements associated with specific pathovars. Together, our findings establish MGEs as key drivers of genome plasticity and adaptive evolution in Xanthomonas, shaped by a dynamic interplay with host defence systems.