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

  • Bacterial and Phytoplasma Diseases
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Abstract

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.

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Acknowledgments

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

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Authors and Affiliations

  1. Laboratory of Plant Pathology, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Shizuoka, 422-8529, Japan

    Radix Suharjo & Yuichi Takikawa

  2. Faculty of Agriculture, University of Lampung, Jl. Prof. Sumantri Brodjonegoro I, Gedong Meneng, Bandar Lampung, 35145, Indonesia

    Radix Suharjo

  3. National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

    Hiroyuki Sawada

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  1. Radix Suharjo
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  2. Hiroyuki Sawada
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Correspondence to Yuichi Takikawa.

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Suharjo, R., Sawada, H. & Takikawa, Y. Phylogenetic study of Japanese Dickeya spp. and development of new rapid identification methods using PCR–RFLP. J Gen Plant Pathol 80, 237–254 (2014). https://doi.org/10.1007/s10327-014-0511-9

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