Journal of General Plant Pathology

, Volume 80, Issue 3, pp 237–254 | Cite as

Phylogenetic study of Japanese Dickeya spp. and development of new rapid identification methods using PCR–RFLP

  • Radix Suharjo
  • Hiroyuki Sawada
  • Yuichi TakikawaEmail author
Bacterial and Phytoplasma Diseases


Forty-one representative Japanese Dickeya spp. (Erwinia chrysanthemi) strains isolated from 24 plants in Japan were investigated using multilocus sequence analysis of recA, dnaX, rpoD, gyrB and 16S rDNA; PCR–RFLP (restriction fragment length polymorphism) of recA, rpoD and gyrB genes; PCR genomic fingerprinting; and biochemical tests. Based on the recA, dnaX, rpoD, gyrB and 16S rDNA sequences and PCR genomic fingerprinting, the strains were essentially divided into six groups (I–VI). Group I corresponded to D. chrysanthemi, group II corresponded to D. dadantii, group III to D. dianthicola and group IV to D. zeae. Meanwhile, group V and group VI could not be assigned to any existing Dickeya species, and they were deduced to be two putative new species. The PCR–RFLP analysis of gyrB, rpoD and recA clearly differentiated the six groups of Dickeya strains. From the results of the biochemical tests, the strains were assigned to biovars 1, 3, 5, 8 and 9; only one strain (SUPP 2525) was not assignable to the existing biovars. We also showed that the PCR–RFLP analysis of rpoD, gyrB and recA can be used as a rapid technique to identify Japanese Dickeya strains.


Biochemical assays Dickeya strains Genomic fingerprinting MLSA (multilocus sequence analysis) PCR–RFLP 



This study was supported in part by grants provided by a research project of the NIAS Genebank.

Supplementary material

10327_2014_511_MOESM1_ESM.doc (379 kb)
Supplementary material 1 (DOC 379 kb)
10327_2014_511_MOESM2_ESM.doc (399 kb)
Supplementary material 2 (DOC 399 kb)


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Copyright information

© The Phytopathological Society of Japan and Springer Japan 2014

Authors and Affiliations

  • Radix Suharjo
    • 1
    • 2
  • Hiroyuki Sawada
    • 3
  • Yuichi Takikawa
    • 1
    Email author
  1. 1.Laboratory of Plant Pathology, Graduate School of Science and TechnologyShizuoka UniversityShizuokaJapan
  2. 2.Faculty of AgricultureUniversity of LampungBandar LampungIndonesia
  3. 3.National Institute of Agrobiological SciencesTsukubaJapan

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