Pink-pigmented variant of Clavibacter michiganensis expands phenotypic range of tomato bacterial canker pathogen.

Bacterial canker of tomato caused by the Gram-positive corynebacterial species Clavibacter michiganensis is one of the most destructive seed-borne diseases in both open air and greenhouse tomatoes. The pathogen is a regulated agent in all tomato-producing countries as translocation of infected tomato materials transports the bacterium into new areas. Clavibacter michiganensis is generally known to have yellow-pigmented colonies on culture media, which is a key differentiative phenotypic feature in standard diagnostic guidelines. During 2020 and 2021, pink-pigmented corynebacterial strains were isolated from tomato seeds (cv. Sun 6189F1) and plants showing severe canker symptoms in Southern Iran. The six pink-pigmented strains were pathogenic on tomato and pepper seedlings under greenhouse conditions, and gave positive results with C. michiganensis-specific primers pairs described in the literature. Phylogenomics and DNA similarity calculations showed that the pink-pigmented strains were highly similar to the authentic yellow-pigmented members of the pathogen. Thus, they were identified as a new phenotypic variant of tomato bacterial canker pathogen. Whole genome screenings accomplished with PCR-based assays showed that the pink strains contain all pathogenicity determinant genes described in C. michiganensis. Further, orthologous gene clusters in the pink-pigmented strains were more similar to the pathogenic members of C. michiganensis than to those of non-pathogenic tomato-associated Clavibacter species. Results obtained in this study demonstrate the emergence of a new pink-pigmented variant of C. michiganensis and highlight the importance of colony pigmentation/morphology in culture-based detection of the bacterium. The need for updating diagnostic guidelines on the colony variants of the pathogen is further discussed.