Genes clvA, clvF and clvG are unique to Clavibacter michiganensis subsp michiganensis and highly conserved

Bacterial canker of tomato, caused by Clavibacter michiganensis subsp. michiganensis (Cmm), occurs worldwide. This study focuses on three genes, clvA (clavicidin) and two associated genes (clvF and clvG, encoding a putative ABC-type multidrug transport system ATPase and permease component, respectively). Loop-mediated amplification of clvA and PCR of clvA, clvF and clvG showed that these genes were present only in Cmm and not in other Clavibacter species/subspecies, as well as other genera of plant-associated bacteria. Sequences of clvA, clvF and clvG from 48 geographically diverse strains of Cmm were analyzed phylogenetically to determine sequence variation. Maximum parsimony (MP), neighbour-joining (NJ) and maximum likelihood (ML) analyses placed strains into subgroups irrespective of their geographical origins. Multi-locus sequence analysis (MLSA) of these three genes produced the same results. In sum, all three clv genes are unique and conserved in Cmm, further supporting the use of the clvA gene for identification of Cmm, using either a previously designed LAMP assay or PCR with additional primers developed in this study. The genes investigated here are novel targets for specific detection of Cmm and have numerous molecular diagnostic applications.