Comparative Genome Analysis of Rathayibacter tritici NCPPB 1953 with Rathayibacter toxicus Strains Can Facilitate Studies on Mechanisms of Nematode Association and Host Infection

  • Park, Jungwook (Department of Microbiology, Pusan National University) ;
  • Lee, Pyeong An (Department of Applied Bioscience, Dong-A University) ;
  • Lee, Hyun-Hee (Department of Microbiology, Pusan National University) ;
  • Choi, Kihyuck (Department of Applied Bioscience, Dong-A University) ;
  • Lee, Seon-Woo (Department of Applied Bioscience, Dong-A University) ;
  • Seo, Young-Su (Department of Microbiology, Pusan National University)
  • Received : 2017.01.25
  • Accepted : 2017.04.23
  • Published : 2017.08.01


Rathayibacter tritici, which is a Gram positive, plant pathogenic, non-motile, and rod-shaped bacterium, causes spike blight in wheat and barley. For successful pathogenesis, R. tritici is associated with Anguina tritici, a nematode, which produces seed galls (ear cockles) in certain plant varieties and facilitates spread of infection. Despite significant efforts, little research is available on the mechanism of disease or bacteria-nematode association of this bacterium due to lack of genomic information. Here, we report the first complete genome sequence of R. tritici NCPPB 1953 with diverse features of this strain. The whole genome consists of one circular chromosome of 3,354,681 bp with a GC content of 69.48%. A total of 2,979 genes were predicted, comprising 2,866 protein coding genes and 49 RNA genes. The comparative genomic analyses between R. tritici NCPPB 1953 and R. toxicus strains identified 1,052 specific genes in R. tritici NCPPB 1953. Using the BlastKOALA database, we revealed that the flexible genome of R. tritici NCPPB 1953 is highly enriched in 'Environmental Information Processing' system and metabolic processes for diverse substrates. Furthermore, many specific genes of R. tritici NCPPB 1953 are distributed in substrate-binding proteins for extracellular signals including saccharides, lipids, phosphates, amino acids and metallic cations. These data provides clues on rapid and stable colonization of R. tritici for disease mechanism and nematode association.


Grant : Cooperative Research Program for Agriculture Science & Technology Development

Supported by : Rural Development Administration


  1. Agarkova, I. V., Vidaver, A. K., Postnikova, E. N., Riley, I. T. and Schaad, N. W. 2006. Genetic characterization and diversity of Rathayibacter toxicus. Phytopathology 96:1270-1277.
  2. Akhtar, M. A. 1987. Outbreaks and new records. Pakistan. Bacterial gumming disease of wheat. FAO Plant Prot. Bull. 35:102.
  3. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
  4. Alva, V., Nam, S. Z., Soding, J. and Lupas, A. N. 2016. The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Res. 44:W410-W415.
  5. Anderson, I. and Brass, A. 1998. Searching DNA databases for similarities to DNA sequences: when is a match significant? Bioinformatics 14:349-356.
  6. Arif, M., Busot, G. Y., Mann, R., Rodoni, B., Liu, S. and Stack, J. P. 2016. Emergence of a new population of Rathayibacter toxicus: an ecologically complex, geographically isolated bacterium. PLoS One 11:e0156182.
  7. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., Rapp, B. A. and Wheeler, D. L. 2000. GenBank. Nucleic Acids Res. 28:15-18.
  8. Bradbury, J. F. 1973. Corynebacterium tritici. In: C.M.I. descriptions of pathogenic fungi and bacteria, eds. by Commonwealth Mycological Institute and C.A.B. International Mycological Institute, pp. 371-380. Commonwealth Mycological Institute, Kew, UK.
  9. Bradbury, J. F. 1986. Guide to plant pathogenic bacteria. CAB International Mycological Institute, Slough, UK. 332 pp.
  10. Buiate, E. A., Xavier, K. V., Moore, N., Torres, M. F., Farman, M. L., Schardl, C. L. and Vaillancourt, L. J. 2017. A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola. BMC Genomics 18:67.
  11. Carlson, R. R. and Vidaver, A. K. 1982. Taxonomy of Corynebacterium plant pathogens, including a new pathogen of wheat, based on polyacrylamide gel electrophoresis of cellular proteins. Int. J. Syst. Bacteriol. 32:315-326.
  12. Chaisson, M. J. and Tesler, G. 2012. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 13:238.
  13. Chin, C. S., Alexander, D. H., Marks, P., Klammer, A. A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E. E., Turner, S. W. and Korlach, J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10:563-569.
  14. Darling, A. C., Mau, B., Blattner, F. R. and Perna, N. T. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14:1394-1403.
  15. Davis, M. J., Gillaspie, A. G., Vidaver, A. K. and Harris, R. W. 1984. Clavibacter: a new genus containing some phytopathogenic coryneform bacteria, including Clavibacter xyli subsp. xyli sp. nov., subsp. nov. and Clavibacter xyli subsp. cynodontis subsp. nov., pathogens that cause ratoon stunting disease of sugarcane and bermudagrass stunting disease. Int. J. Syst. Bacteriol. 34:107-117.
  16. De Bruyne, E., Swings, J. and Kersters, K. 1992. Enzymatic relatedness amongst phytopathogenic coryneform bacteria and its potential use for their identification. Syst. Appl. Microbiol. 15:393-401.
  17. Delcher, A. L., Harmon, D., Kasif, S., White, O. and Salzberg, S. L. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27:4636-4641.
  18. Divon, H. H., Ziv, C., Davydov, O., Yarden, O. and Fluhr, R. 2006. The global nitrogen regulator, FNR1, regulates fungal nutrition-genes and fitness during Fusarium oxysporum pathogenesis. Mol. Plant Pathol. 7:485-497.
  19. Dowson, W. J. 1942. On the generic name of the gram-positive bacterial plant pathogens. Trans. Br. Mycol. Soc. 25:311-314.
  20. Duveiller, E. and Fucikovsky, L. 1997. Other plant pathogenic bacteria reported on wheat. In: The bacterial diseases of wheat: concepts and methods of disease management, eds. by E. Duveiller, L. Fucikovsky and K. Rudolph, p. 66. CIMMYT, Distrito Federal, Brazil.
  21. Evtushenko, L. I. and Dorofeeva, L. V. 2012. Genus XXII. Rathayibacter. In: Bergey's manual of systematic bacteriology, eds. by W. Whitman, M. Goodfellow, P. Kampfer, H. J. Busse, M. Trujillo, W. Ludwig, K. Suzuki and A. Parte, pp. 953-964. Springer, New York, NY, USA.
  22. Fattah, F. A. 1988. Effects of inoculation methods on the incidence of ear-cockle and 'tundu' on wheat under field conditions. Plant Soil 109:195-198.
  23. Finn, R. D., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Mistry, J., Mitchell, A. L., Potter, S. C., Punta, M., Qureshi, M., Sangrador-Vegas, A., Salazar, G. A., Tate, J. and Bateman, A. 2016. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 44:D279-D285.
  24. Galperin, M. Y., Makarova, K. S., Wolf, Y. I. and Koonin, E. V. 2015. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43:D261-D269.
  25. Grissa, I., Vergnaud, G. and Pourcel, C. 2007. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 35:W52-W57.
  26. Gupta, A. and Chattoo, B. B. 2008. Functional analysis of a novel ABC transporter ABC4 from Magnaporthe grisea. FEMS Microbiol. Lett. 278:22-28.
  27. Hyatt, D., Chen, G. L., Locascio, P. F., Land, M. L., Larimer, F. W. and Hauser, L. J. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119.
  28. Jago, M. V. and Culvenor, C. C. 1987. Tunicamycin and corynetoxin poisoning in sheep. Aust. Vet. J. 64:232-235.
  29. Jones, A. M. and Wildermuth, M. C. 2011. The phytopathogen Pseudomonas syringae pv. tomato DC3000 has three highaffinity iron-scavenging systems functional under iron limitation conditions but dispensable for pathogenesis. J. Bacteriol. 193:2767-2775.
  30. Kanehisa, M. and Goto, S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28:27-30.
  31. Kanehisa, M., Sato, Y. and Morishima, K. 2016. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428:726-731.
  32. Kopf, M., Klahn, S., Voss, B., Stüber, K., Huettel, B., Reinhardt, R. and Hess, W. R. 2014. Finished genome sequence of the unicellular cyanobacterium Synechocystis sp. strain PCC 6714. Genome Announc. 2:e00757-14.
  33. Krogh, A., Larsson, B., von Heijne, G. and Sonnhammer, E. L. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:567-580.
  34. Kumar, S., Stecher, G. and Tamura, K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33:1870-1874.
  35. Lagesen, K., Hallin, P., Rodland, E. A., Staerfeldt, H. H., Rognes, T. and Ussery, D. W. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100-3108.
  36. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., Mc-Gettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J. and Higgins, D. G. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
  37. Lee, I. M., Bartoszyk, I. M., Gundersen-Rindal, D. E. and Davis, R. E. 1997. Phylogeny and classification of bacteria in the genera Clavibacter and Rathayibacter on the basis of 16s rRNA gene sequence analyses. Appl. Environ. Microbiol. 63:2631-2636.
  38. Lowe, T. M. and Eddy, S. R. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
  39. Lukashin, A. V. and Borodovsky, M. 1998. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26:1107-1115.
  40. Maqbool, A., Horler, R. S., Muller, A., Wilkinson, A. J., Wilson, K. S. and Thomas, G. H. 2015. The substrate-binding protein in bacterial ABC transporters: dissecting roles in the evolution of substrate specificity. Biochem. Soc. Trans. 43:1011-1017.
  41. Medini, D., Donati, C., Tettelin, H., Masignani, V. and Rappuoli, R. 2005. The microbial pan-genome. Curr. Opin. Genet. Dev. 15:589-594.
  42. Mehta, Y. R. 2014. Spike diseases caused by bacteria. In: Wheat diseases and their management, ed. by Y. R. Mehta, pp. 105-121. Springer, New York, NY, USA.
  43. Moreira, L. M., Facincani, A. P., Ferreira, C. B., Ferreira, R. M., Ferro, M. I., Gozzo, F. C., de Oliveira, J. C., Ferro, J. A. and Soares, M. R. 2015. Chemotactic signal transduction and phosphate metabolism as adaptive strategies during citrus canker induction by Xanthomonas citri. Funct. Integr. Genomics 15:197-210.
  44. Paruthi, I. J. and Bhatti, D. S. 1985. Estimation of loss in yield and incidence of Anguina tritici on wheat in Haryana (India). Int. Nematol. Netw. Newsl. 2:13-16.
  45. Paruthi, I. J. and Gupta, D. C. 1987. Incidence of 'Tundu' in barley and kanki in wheat field infested with Anguina tritici. Haryana Agric. Univ. J. Res. 17:78-79.
  46. Petersen, T. N., Brunak, S., von Heijne, G. and Nielsen, H. 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8:785-786.
  47. Price, P. C., Fisher, J. M. and Kerr, A. 1979. On Anguina funesta n. sp. and its association with Corynebacterium sp., in infecting Lolium rigidum. Nematologica 25:76-85.
  48. Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J. and Glockner, F. O. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41:D590-D596.
  49. Rainey, F., Weiss, H., Prauser, H. and Stackebrandt, E. 1994. Further evidence for the phylogenetic coherence of actinomycetes with Group B-peptidoglycan and evidence for the phylogenetic intermixing of the genera Microbacterium and Aureobacterium as determined by 16S rDNA analysis. FEMS Microbiol. Lett. 118:135-139.
  50. Riley, I. T. 1992. Anguina tritici is a potential vector of Clavibacter toxicus. Australas. Plant Pathol. 21:147-149.
  51. Riley, I. T. and Ophel, K. M. 1992. Clavibacter toxicus sp. nov., the bacterium responsible for annual ryegrass toxicity in Australia. Int. J. Syst. Bacteriol. 42:64-68.
  52. Riley, I. T. and Reardon, T. B. 1995. Isolation and characterization of Clavibacter tritici associated with Anguina tritici in wheat from Western Australia. Plant Pathol. 44:805-810.
  53. Riley, I. T., Reardon, T. B. and McKay, A. C. 1988. Genetic analysis of plant pathogenic bacteria in the genus Clavibacter using allozyme electrophoresis. J. Gen. Microbiol. 134:3025-3030.
  54. Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M. A. and Barrell, B. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944-945.
  55. Sasaki, J., Chijimatsu, M. and Suzuki, K. 1998. Taxonomic significance of 2,4-diaminobutyric acid isomers in the cell wall peptidoglycan of actinomycetes and reclassification of Clavibacter toxicus as Rathayibacter toxicus comb. nov. Int. J. Syst. Bacteriol. 48:403-410.
  56. Shimizu, K. 2013. Regulation systems of bacteria such as Escherichia coli in response to nutrient limitation and environmental stresses. Metabolites 4:1-35.
  57. Sternes, P. R. and Borneman, A. R. 2016. Consensus pan-genome assembly of the specialised wine bacterium Oenococcus oeni. BMC Genomics 17:308.
  58. Takeuchi, M. and Yokota, A. 1994. Phylogenetic analysis of the genus Microbacterium based on 16S rRNA gene sequences. FEMS Microbiol. Lett. 124:11-16.
  59. UniProt Consortium. 2013. Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res. 41:D43-D47.
  60. Urban, M., Pant, R., Raghunath, A., Irvine, A. G., Pedro, H. and Hammond-Kosack, K. E. 2015. The Pathogen-Host Interactions database (PHI-base): additions and future developments. Nucleic Acids Res. 43:D645-D655.
  61. Wilson, R. A. and Talbot, N. J. 2009. Under pressure: investigating the biology of plant infection by Magnaporthe ory-zae. Nat. Rev. Microbiol. 7:185-195.
  62. Wooldridge, K. G. and Williams, P. H. 1993. Iron uptake mechanisms of pathogenic bacteria. FEMS Microbiol. Rev. 12:325-348.
  63. Yadeta, K. A. and Thomma, B. P. H. J. 2013. The xylem as battleground for plant hosts and vascular wilt pathogens. Front. Plant Sci. 4:97.
  64. Zgurskaya, H. I., Evtushenko, L. I., Akimov, V. N. and Kalakoutskii, L. V. 1993. Rathayibacter gen. nov., including the species Rathayibacter rathayi comb. nov., Rathayibacter tritici comb. nov., Rathayibacter iranicus comb. nov., and six strains from annual grasses. Int. J. Syst. Bacteriol. 43:143-149.

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