Data Sheet 1_Diversity and evolution of quorum-sensing systems in Rhizobium.pdf

Quorum-sensing (QS) systems based on acyl-homoserine lactones (AHLs) regulate gene expression in response to cell density in many bacteria, including Rhizobium. These systems, typically composed of LuxI-like synthases and LuxR-like regulators, control processes such as plasmid conjugation, biofilm formation, and plant interactions. However, their evolutionary dynamics and genomic distribution in Rhizobium remain poorly understood. We analyzed 142 complete Rhizobium genomes using comparative genomics, phylogenetic reconstruction, and genomic context analysis. LuxI/LuxR homologs were identified based on sequence similarity and Pfam domain architecture, and their genomic contexts were examined. Phylogenetic relationships and coevolution between LuxI/LuxR pairs were assessed using cophylogenetic approaches. QS systems showed a highly heterogeneous distribution across Rhizobium genomes: some strains lacked canonical systems, whereas others encoded one or multiple systems in chromosomes and/or plasmids. Chromosomal QS systems were associated with multiple distinct genomic contexts, supporting at least seven independent acquisition events. In contrast, plasmid-encoded systems exhibited substantially greater diversity in both sequence and genomic organization. Phylogenetic and comparative analyses revealed dynamic gains and losses of QS systems, variable coevolution among LuxI/LuxR pairs, and evidence of partner recruitment. Notably, plasmids appear to act as major reservoirs of QS systems and likely sources of their transfer to chromosomes. These findings indicate that QS systems in Rhizobium evolve through a combination of horizontal gene transfer, genomic rearrangement, and differential retention across replicons. The higher diversity and mobility of plasmid-encoded systems highlight their central role in shaping QS evolution and functional innovation. Overall, this study provides a comprehensive framework for understanding the diversification and evolutionary trajectories of QS systems in complex multipartite bacterial genomes.