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

Joanna Załuga, Pieter Stragier, Steven Baeyens, Annelies Haegeman UGent, Johan Van Vaerenbergh, Martine Maes and Paul De Vos UGent (2014) BMC GENOMICS. 15.
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
Bacterial wilt and canker, Non-pathogenic Clavibacter, Tomato seeds, Plant pathogen, Quarantine, Genome sequencing, MICHIGANENSIS SUBSP MICHIGANENSIS, GRAM-POSITIVE BACTERIA, PLASMID TRANSFER, TOMATO PLANTS, PHYTOPATHOGENIC BACTERIUM, PROKARYOTIC GENOMES, VIRULENCE FACTORS, CONJUGAL TRANSFER, ESCHERICHIA-COLI, GENE-TRANSFER
journal title
BMC GENOMICS
BMC Genomics
volume
15
article number
392
pages
14 pages
Web of Science type
Article
Web of Science id
000338678300001
JCR category
BIOTECHNOLOGY & APPLIED MICROBIOLOGY
JCR impact factor
3.986 (2014)
JCR rank
26/163 (2014)
JCR quartile
1 (2014)
ISSN
1471-2164
DOI
10.1186/1471-2164-15-392
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
5638470
handle
http://hdl.handle.net/1854/LU-5638470
date created
2014-07-07 10:10:31
date last changed
2016-12-21 15:42:52
@article{5638470,
  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.},
  articleno    = {392},
  author       = {Za\unmatched{0142}uga, Joanna and Stragier, Pieter and Baeyens, Steven and Haegeman, Annelies and Van Vaerenbergh, Johan and Maes, Martine and De Vos, Paul},
  issn         = {1471-2164},
  journal      = {BMC GENOMICS},
  keyword      = {Bacterial wilt and canker,Non-pathogenic Clavibacter,Tomato seeds,Plant pathogen,Quarantine,Genome sequencing,MICHIGANENSIS SUBSP MICHIGANENSIS,GRAM-POSITIVE BACTERIA,PLASMID TRANSFER,TOMATO PLANTS,PHYTOPATHOGENIC BACTERIUM,PROKARYOTIC GENOMES,VIRULENCE FACTORS,CONJUGAL TRANSFER,ESCHERICHIA-COLI,GENE-TRANSFER},
  language     = {eng},
  pages        = {14},
  title        = {Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle},
  url          = {http://dx.doi.org/10.1186/1471-2164-15-392},
  volume       = {15},
  year         = {2014},
}

Chicago
Załuga, Joanna, Pieter Stragier, Steven Baeyens, Annelies Haegeman, Johan Van Vaerenbergh, Martine Maes, and Paul De Vos. 2014. “Comparative Genome Analysis of Pathogenic and Non-pathogenic Clavibacter Strains Reveals Adaptations to Their Lifestyle.” Bmc Genomics 15.
APA
Załuga, J., Stragier, P., Baeyens, S., Haegeman, A., Van Vaerenbergh, J., Maes, M., & De Vos, P. (2014). Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle. BMC GENOMICS, 15.
Vancouver
1.
Załuga J, Stragier P, Baeyens S, Haegeman A, Van Vaerenbergh J, Maes M, et al. Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle. BMC GENOMICS. 2014;15.
MLA
Załuga, Joanna, Pieter Stragier, Steven Baeyens, et al. “Comparative Genome Analysis of Pathogenic and Non-pathogenic Clavibacter Strains Reveals Adaptations to Their Lifestyle.” BMC GENOMICS 15 (2014): n. pag. Print.