Two plasmid-borne virulence genomic islands of Clavibacter michiganensis are genetically diverse and determine the development of wilt symptoms in host plants.

Plasmids contribute to the efficient adaptation of bacteria to specific niches in nature. The gram-positive bacterium Clavibacter michiganensis carries two plasmid-borne important virulence genes, celA and pat-1, necessary for wilting in tomato. The 88 C. michiganensis field isolates collected between 2011 and 2020 were examined for phenotypic variation, including virulence in host plants. Four isolates lacking plasmids with celA, pat-1, or both failed to cause wilting, and nine isolates, including these four, failed to cause wilting in Nicotiana benthamiana. Whole genome analyses revealed 11 distinct plasmid types, including 9 newly identified, and 10 bacterial groups with different plasmid compositions, despite having almost identical chromosomes. Comparative genomic analyses revealed significant genetic diversity among the plasmids, while three plasmids containing the genomic island (GI) α with celA or GIβ with pat-1 and three newly identified plasmids carrying both islands shared large blocks of synteny. In addition, GIα is closely associated with mobile genetic elements, suggesting the genetic rearrangement or transfer at this locus. These results suggest that C. michiganensis harbors a wide variety of virulence and nonvirulence plasmids, and that there is genetic rearrangement among plasmids in GI regions, determining bacterial virulence in plants.