Phylogenetic diversity of Clavibacter michiganensis subsp. michiganensis isolates causing bacterial canker of tomato in Greece

Tomato bacterial canker, caused by Clavibacter michiganensis subsp. michiganensis (Cmm) (Li et al. 2018), is a common destructive disease worldwide. The bacterium colonizes plant’s vascular system causing characteristic symptoms such as wilting, cankers, brown and black discoloration of vessels, white spots on the fruit and leaves. In the present work, isolates were collected from infected tomato plants of 11 Greek Prefectures during the years 2003-2018, and the genetic variability was investigated. After initial identification, 93 selected Cmm strains were subjected to phylogenetic analyses based on the sequencing of multiple loci (Multi-Locus Sequencing Analysis, MLSA) utilizing four housekeeping genes (atpD, ppk, kdpA and sdhA). MLSA highlighted 4.1% variability in nucleotide sequences and classified the 93 Cmm strains into 38 haplotypes. Nevertheless, the phylogenetic grouping of the strains was not in accordance with the geographical distribution, a fact that probably advocates the introduction of the disease from infected propagating material. However, strains isolated from the same area in a different year were placed in the same group which means that the pathogen can remain active between growing seasons. The study provides important epidemiological information on the disease outbreaks and the spread of Cmm in Greece.