Comparative Genome Analyses of Clavibacter michiganensis Type Strain LMG7333T Reveal Distinct Gene Contents in Plasmids From Other Clavibacter Species

Abstract

Clavibacter michiganensis, a Gram-positive, plant-pathogenic bacterium belonging to Actinobacteria, is a causal agent of bacterial canker in tomatoes. Although LMG7333T is the type strain of C. michiganensis, it has not been used in many studies, probably because of a lack of the complete genome sequence being available. Therefore, in this study, the complete genome sequence of this type strain was obtained, and comparative genome analysis was conducted with the genome sequences of two other C. michiganensis strains and type strains of Clavibacter species, of which their complete genome sequences are available. C. michiganensis LMG7333T carries one chromosome and two plasmids, pCM1 and pCM2, like two other C. michiganensis strains. All three chromosomal DNA sequences were almost identical. However, the DNA sequences of two plasmids of LMG7333T are similar to those of UF1, but different from those of NCPPB382, indicating that both plasmids carry distinct gene content among C. michiganensis strains. Moreover, 216 protein-coding sequences (CDSs) were only present in the LMG7333T genome compared with type strains of other Clavibacter species. Among these 216 CDSs, approximately 83% were in the chromosome, whereas others were in both plasmids (more than 6% in pCM1 and 11% in pCM2). However, the ratio of unique CDSs of the total CDSs in both plasmids were approximately 38% in pCM1 and 30% in pCM2, indicating that the high gene content percentage in both plasmids of C. michiganensis are different from those of other Clavibacter species, and plasmid DNAs might be derived from different origins. A virulence assay with C. michiganensis LMG7333T using three different inoculation methods, root-dipping, leaf-clipping, and stem injection, resulted in typical disease symptoms, including wilting and canker in tomato. Altogether, our results indicate that two plasmids of C. michiganensis carry distinct gene content, and the genome information of the type strain LMG7333T will help to understand the genetic diversity of the two plasmids of Clavibacter species, including C. michiganensis.

Variations of the Bacterial Community in Wheat (<em>Triticum aestivum</em>), Oats (<em>Avena sativa</em> L.), Barley (<em>Hordeum vulgare</em> L.) and Triticale (<em>Triticosecale</em>) from Three Regions of the Republic of Crimea

“…Clavibacter michiganensis it is a gram-positive bacterium [56]. this bacterium affects mainly the xylem vessels on the plants [57].…”

A host shift as the origin of tomato bacterial canker caused byClavibacter michiganensis

“…For instance, Thapa and co-workers (Thapa et al, 2017) showed that certain CAZymes (Carbohydrate-Active Enzymes) families involved in cellulose and hemicellulose degradation are abundant in the C. michiganensis genome. Although these previously identified pathogenicity factors have been unambiguously shown to be related to the development of the disease, there is also evidence that some of these factors are absent from strains capable of causing symptoms of the disease (Oh et al, 2022;Tancos et al, 2015) and that virulent strains can infect tomato plants without leading to symptoms (Gitaitis, 1991). Together, these observations suggest that other factors are required for triggering the disease and symptom development (Sharabani et al, 2013(Sharabani et al, , 2014.…”

Comparative genomic analysis of Ralstonia solanacearum reveals candidate avirulence effectors in HA4-1 triggering wild potato immunity

“…translucens strains have been obtained, and the T3Es were identified, giving an insight into the pathovar-specific population structure (Shah et al, 2021). The comparative genome analysis of Clavibacter michiganensis, the causal agent of bacterial canker in tomatoes, shows the distinct gene contents in the plasmids (Oh et al, 2022). The first R. solanacearum genome GMI1000 was sequenced in 2002 and has been widely utilized in R. solanacearum studies (Salanoubat et al, 2002).…”