P-591 - Evolutionary genomics unveils recombination events involved in speciation, adaptation and lifestyle of the genus Clavibacter and C. michiganensis

The genus Clavibacter comprises 10 species of bacterial pathogens affecting major crops. The role of homologous recombination in evolution and host adaptation of Clavibacter and C. michiganensis was investigated. Complete genomes of 25 Clavibacter species were sequenced using Oxford Nanopore MinION and Illumina NovaSeq. Pan-core genome analysis was performed using Roary, incorporating 25 new genomes and 109 from the NCBI GenBank. Homologous recombination events were identified using ClonalFrameML and fastGear, while donor-recipient patterns were analyzed with HERO. ClonalFrameML detected 5,252 recombination events, showing extensive recombination. FastGear inferred 2,494 ancestral and 2,758 recent recombination events. C. tessellarius and C. zhangzhiyongii exhibited the highest ancestral recombination rates, suggesting frequent genetic exchange. Likewise, C. michiganensis showed high ancestral recombination, possibly linked to introduction and spread of bacteria via the tomato seed trade. Clusters of new species displayed elevated mosaicism in recent recombination, indicating ongoing speciation. Recombination network analysis revealed 7 recombining highways; 6 were found in uncharacterized Clavibacter clusters, marking them as evolving lineages. Overall, 3,079 genes underwent recombination, with hotspots linked to niche adaptation and lifestyle. In conclusion, homologous recombination played a role in the evolutionary dynamics of Clavibacter and C. michiganensis, influencing genetic diversity and host adaptation mechanisms.