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A unique DNA repair and recombination gene (recN) sequence for identification and intraspecific molecular typing of bacterial wilt pathogen Ralstonia solanacearum and its comparative analysis with ribosomal DNA sequences

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Abstract

Ribosomal gene sequences are a popular choice for identification of bacterial species and, often, for making phylogenetic interpretations. Although very popular, the sequences of 16S rDNA and 16-23S intergenic sequences often fail to differentiate closely related species of bacteria. The availability of complete genome sequences of bacteria, in the recent years, has accelerated the search for new genome targets for phylogenetic interpretations. The recently published full genome data of nine strains of R. solanacearum, which causes bacterial wilt of crop plants, has provided enormous genomic choices for phylogenetic analysis in this globally important plant pathogen. We have compared a gene candidate recN, which codes for DNA repair and recombination function, with 16S rDNA/16-23S intergenic ribosomal gene sequences for identification and intraspecific phylogenetic interpretations in R. solanacearum. recN gene sequence analysis of R. solanacearum revealed subgroups within phylotypes (or newly proposed species within plant pathogenic genus, Ralstonia), indicating its usefulness for intraspecific genotyping. The taxonomic discriminatory power of recN gene sequence was found to be superior to ribosomal DNA sequences. In all, the recN-sequence-based phylogenetic tree generated with the Bayesian model depicted 21 haplotypes against 15 and 13 haplotypes obtained with 16S rDNA and 16-23S rDNA intergenic sequences, respectively. Besides this, we have observed high percentage of polymorphic sites (S 23.04%), high rate of mutations (Eta 276) and high codon bias index (CBI 0.60), which makes the recN an ideal gene candidate for intraspecific molecular typing of this important plant pathogen.

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Acknowledgements

The project was supported by National network project on Phytophthora, Fusarium and Ralstonia diseases of horticultural and field crops (PhytoFuRa). Various facilities provided by the directors, IISR, Calicut, and IARI, New Delhi, and the heads, Division of Plant Pathology, IARI, New Delhi, are gratefully acknowledged

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Authors and Affiliations

  1. Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110 012, India

    Aundy Kumar

  2. Division of Crop Protection, Indian Institute of Spices Research, Kozhikode, 673 012, India

    Thekkan Puthiyaveedu Prameela & Rajamma Suseelabhai

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  1. Aundy Kumar
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  2. Thekkan Puthiyaveedu Prameela
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  3. Rajamma Suseelabhai
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Correspondence to Aundy Kumar.

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Corresponding editor: ANAND KUMAR BACHHAWAT

MS received 14 November 2012; accepted 14 February 2013

Corresponding editor: Anand Kumar Bachhawat

[Kumar A, Prameela TP and Suseelabhai R 2013 A unique DNA repair and recombination gene (recN) sequence for identification and intraspecific molecular typing of bacterial wilt pathogen Ralstonia solanacearum and its comparative analysis with ribosomal DNA sequences. J. Biosci. 38 1–12] DOI 10.1007/s12038-013-9312-0

Supplementary materials pertaining to this article are available on the Journal of Biosciences Website at http://www.ias.ac.in/jbiosci/jun2013/supp/kumar.pdf

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Kumar, A., Prameela, T.P. & Suseelabhai, R. A unique DNA repair and recombination gene (recN) sequence for identification and intraspecific molecular typing of bacterial wilt pathogen Ralstonia solanacearum and its comparative analysis with ribosomal DNA sequences. J Biosci 38, 267–278 (2013). https://doi.org/10.1007/s12038-013-9312-0

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