Abstract:
Background: The genus Clavibacter harbors economically important plant pathogens infecting agricultural crops
such as potato and tomato. Although the vast majority of Clavibacter strains are pathogenic, there is an increasing
number of non-pathogenic isolates reported. Non-pathogenic Clavibacter strains isolated from tomato seeds are
particularly problematic because they affect the current detection and identification tests for Clavibacter michiganensis
subsp. michiganensis (Cmm), which is regulated with a zero tolerance in tomato seed. Their misidentification as
pathogenic Cmm hampers a clear judgment on the seed quality and health.
Results: To get more insight in the genetic features linked to the lifestyle of these bacteria, a whole-genome sequence of
the tomato seed-borne non-pathogenic Clavibacter LMG 26808 was determined. To gain a better understanding of the
molecular determinants of pathogenicity, the genome sequence of LMG 26808 was compared with that of the pathogenic
Cmm strain (NCPPB 382). The comparative analysis revealed that LMG 26808 does not contain plasmids pCM1 and pCM2
and also lacks the majority of important virulence factors described so far for pathogenic Cmm. This explains its apparent
non-pathogenic nature in tomato plants. Moreover, the genome analysis of LMG 26808 detected sequences from a plasmid
originating from a member of Enterobacteriaceae/Klebsiella relative. Genes received that way and coding for antibiotic
resistance may provide a competitive advantage for survival of LMG 26808 in its ecological niche. Genetically, LMG
26808 was the most similar to the pathogenic Cmm NCPPB 382 but contained more mobile genetic elements. The
genome of this non-pathogenic Clavibacter strain contained also a high number of transporters and regulatory genes.
Conclusions: The genome sequence of the non-pathogenic Clavibacter strain LMG 26808 and the comparative analyses
with other pathogenic Clavibacter strains provided a better understanding of the genetic bases of virulence and
adaptation mechanisms present in the genus Clavibacter.
