1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 2

Reclassification of Xanthomonas gardneri (ex Šutič 1957) Jones et al. 2006 as a later heterotypic synonym of Xanthomonas cynarae Trébaol et al. 2000 and description of X. cynarae pv. cynarae and X. cynarae pv. gardneri based on whole genome analyses Free

Corrigenda to this paper have been published here and here.

Abstract

Multilocus sequence analysis of Xanthomonas species revealed a very close relationship between   Xanthomonas cynarae  , an artichoke pathogen and Xanthomonas gardneri, a tomato and pepper pathogen. Results of whole genome sequence comparisons using average nucleotide identity between representative strains of   X. gardneri   and X. cynarae were well above the threshold of 95–96 %. Inoculations of   X. gardneri   strains in artichoke leaves caused mild disease symptoms, but only weak symptoms were observed in the bracts. Both   X. cynarae   and X. gardneri grew equally and caused typical bacterial spot symptoms in pepper after artificial inoculation. However,   X. cynarae   induced a hypersensitive reaction in tomato, while   X. gardneri   strains were virulent. Pathogenicity-associated gene clusters, including the protein secretion systems, type III effector profiles, and lipopolysaccharide cluster were nearly identical between the two species. Based on our results from whole genome sequence comparison,   X. gardneri   and   X. cynarae   belong to the same species. The name   X. cynarae   has priority and   X. gardneri   should be considered as a later heterotypic synonym. An emended description of   X. cynarae   (type strain=CFBP 4188, =DSM 16794) is given. However, due to the host specificity in artichoke and tomato, two pathovars, X. cynarae pv. cynarae and X. cynarae pv. gardneri, are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): artichoke, tomato and pepper pathogen , emended species and sequence based taxonomy
© 2019 IUMS

Erratum

An erratum has been published for this content:
Corrigendum: Reclassification of (ex Šutič 1957) Jones . 2006 as a later heterotypic synonym of Trébaol . 2000 and description of pv. and pv. based on whole genome analyses

Erratum

An erratum has been published for this content:
Corrigendum: Reclassification of (ex Šutic 1957) Jones . 2006 as a later heterotypic synonym of Trebaol . 2000 and description of pv. and pv. based on whole genome analyses
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003104
2018-11-20
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/2/343.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003104&mimeType=html&fmt=ahah

References

  1. Ridé M. Sur une maladie nouvelle de l’artichaut (Cynara scolymus). C R SeUances Acad Sci 1956; 243:174–177
     [Google Scholar]
  2. Trébaol G, Gardan L, Manceau C, Tanguy JL, Tirilly Y et al. Genomic and phenotypic characterization of Xanthomonas cynarae sp. nov., a new species that causes bacterial bract spot of artichoke (Cynara scolymus L.). Int J Syst Evol Microbiol 2000; 50:1471–1478 [View Article][PubMed]
     [Google Scholar]
  3. Potnis N, Timilsina S, Strayer A, Shantharaj D, Barak JD et al. Bacterial spot of tomato and pepper: diverse Xanthomonas species with a wide variety of virulence factors posing a worldwide challenge. Mol Plant Pathol 2015; 16:907–920 [View Article][PubMed]
     [Google Scholar]
  4. Šutič D. Bakterioze crvenog patlidzana (Tomato bacteriosis). In Posebna Izd Inst Zasht Bilja Beograd (Special Edition) vol. 6 Beograd: Institute of Plant Protein; 1957 pp. 1–65 (English summary: Rev App Mycl 36:734-735)
    [Google Scholar]
  5. Dye DW. Cultural and biochemical reaction of additional Xanthomonas species. New Zeal J Sci 1966; 9:913–919
     [Google Scholar]
  6. de Ley J. Modern molecular methods in bacterial taxonomy: evaluation, application, prospects. In Proceedings of the 4th International Conference of Plant Pathogenic Bacteria vol. 1 1978 pp. 347–357
     [Google Scholar]
  7. de Vos P, Goor M, Gillis M, de Ley J. Ribosomal ribonucleic acid cistron similarities of phytopathogenic Pseudomonas species. Int J Syst Bacteriol 1985; 35:169–184 [View Article]
     [Google Scholar]
  8. Jones JB, Lacy GH, Bouzar H, Stall RE, Schaad NW. Reclassification of the xanthomonads associated with bacterial spot disease of tomato and pepper. Syst Appl Microbiol 2004; 27:755–762 [View Article][PubMed]
     [Google Scholar]
  9. Constantin EC, Cleenwerck I, Maes M, Baeyen S, van Malderghem C et al. Genetic characterization of strains named as Xanthomonas axonopodis pv. dieffenbachiae leads to a taxonomic revision of the X. axonopodis species complex. Plant Pathol 2016; 65:792–806 [View Article]
     [Google Scholar]
  10. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
     [Google Scholar]
  11. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  12. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
     [Google Scholar]
  13. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article][PubMed]
     [Google Scholar]
  14. Young JM, Park DC, Shearman HM, Fargier E. A multilocus sequence analysis of the genus Xanthomonas. Syst Appl Microbiol 2008; 31:366–377 [View Article][PubMed]
     [Google Scholar]
  15. Merda D, Briand M, Bosis E, Rousseau C, Portier P et al. Ancestral acquisitions, gene flow and multiple evolutionary trajectories of the type three secretion system and effectors in Xanthomonas plant pathogens. Mol Ecol 2017; 26:5939–5952 [View Article][PubMed]
     [Google Scholar]
  16. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  17. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  18. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  19. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
     [Google Scholar]
  20. Almeida NF, Yan S, Cai R, Clarke CR, Morris CE et al. PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes. Phytopathology 2010; 100:208–215 [View Article][PubMed]
     [Google Scholar]
  21. Potnis N, Krasileva K, Chow V, Almeida NF, Patil PB et al. Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper. BMC Genomics 2011; 12:146 [View Article][PubMed]
     [Google Scholar]
  22. Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K et al. IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. PLoS One 2012; 7:e40151 [View Article][PubMed]
     [Google Scholar]
  23. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  24. Galán JE, Collmer A. Type III secretion machines: bacterial devices for protein delivery into host cells. Science 1999; 284:1322–1328[PubMed]
     [Google Scholar]
  25. Büttner D, He SY. Type III protein secretion in plant pathogenic bacteria. Plant Physiol 2009; 150:1656–1664 [View Article][PubMed]
     [Google Scholar]
  26. Noël L, Thieme F, Nennstiel D, Bonas U. Two novel type III-secreted proteins of Xanthomonas campestris pv. vesicatoria are encoded within the hrp pathogenicity island. J Bacteriol 2002; 184:1340–1348 [View Article][PubMed]
     [Google Scholar]
  27. Block A, Li G, Fu ZQ, Alfano JR. Phytopathogen type III effector weaponry and their plant targets. Curr Opin Plant Biol 2008; 11:396–403 [View Article][PubMed]
     [Google Scholar]
  28. Schwartz AR, Potnis N, Timilsina S, Wilson M, Patané J et al. Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity. Front Microbiol 2015; 6:535 [View Article][PubMed]
     [Google Scholar]
  29. Slater H, Alvarez-Morales A, Barber CE, Daniels MJ, Dow JM. A two-component system involving an HD-GYP domain protein links cell-cell signalling to pathogenicity gene expression in Xanthomonas campestris. Mol Microbiol 2000; 38:986–1003 [View Article][PubMed]
     [Google Scholar]
  30. Patil PB, Sonti RV. Variation suggestive of horizontal gene transfer at a lipopolysaccharide (lps) biosynthetic locus in Xanthomonas oryzae pv. oryzae, the bacterial leaf blight pathogen of rice. BMC Microbiol 2004; 4:40 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003104
Loading
Reclassification of Xanthomonas gardneri (ex Šutič 1957) Jones et al. 2006 as a later heterotypic synonym of Xanthomonas cynarae Trébaol et al. 2000 and description of X. cynarae pv. cynarae and X. cynarae pv. gardneri based on whole genome analyses
Int J Syst Evol Microbiol 69, 343 (2019); https://doi.org/10.1099/ijsem.0.003104
/content/journal/ijsem/10.1099/ijsem.0.003104
/content/journal/ijsem/10.1099/ijsem.0.003104
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error