Pink-Pigmented Variant of <i>Clavibacter michiganensis</i> Expands Phenotypic Range of Tomato Bacterial Canker Pathogen

Bacterial canker of tomato caused by the gram-positive corynebacterial species <i>Clavibacter michiganensis</i> is one of the most destructive seedborne 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. <i>C. michiganensis</i> 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 (cultivar 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 yielded positive results with <i>C. michiganensis</i>-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 <i>C. michiganensis</i>. Further, orthologous gene clusters in the pink-pigmented strains were more similar to the pathogenic members of <i>C. michiganensis</i> than to those of nonpathogenic tomato-associated <i>Clavibacter</i> species. The results obtained in this study demonstrate the emergence of a new pink-pigmented variant of <i>C. michiganensis</i> 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.