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Open Access Research article

Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle

Joanna Załuga1*, Pieter Stragier1, Steve Baeyen2, Annelies Haegeman2, Johan Van Vaerenbergh2, Martine Maes2 and Paul De Vos13

Author Affiliations

1 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, Gent B-9000, Belgium

2 Plant Sciences Unit - Crop Protection, Institute for Agricultural and Fisheries Research - ILVO, Burg. Van Gansberghelaan 96, Merelbeke B-9820, Belgium

3 BCCM/LMG Bacteria collection - Laboratory of Microbiology Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, Gent B-9000, Belgium

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BMC Genomics 2014, 15:392  doi:10.1186/1471-2164-15-392

Published: 22 May 2014

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.

Keywords:
Non-pathogenic Clavibacter; Bacterial wilt and canker; Tomato seeds; Genome sequencing; Quarantine; Plant pathogen