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

• Published in: Journal of biosciences 2013-06, Vol.38 (2), p.267-278
• Main Authors: Kumar, Aundy, Prameela, Thekkan Puthiyaveedu, Suseelabhai, Rajamma
• Format: Article
• Language: English
• Subjects: Bacteria; Bacterial Proteins - genetics; bacterial wilt; Base Sequence; Bayes Theorem; Bayesian analysis; Biomedical and Life Sciences; Biomedicine; Cell Biology; Codon; Comparative analysis; correlation; crops; DNA Repair; DNA Restriction Enzymes - genetics; DNA, Ribosomal Spacer - genetics; Genes; genomics; genotyping; Haplotypes; intergenic DNA; Life Sciences; Microbiology; Molecular biology; Molecular Typing - methods; mutation; nucleotide sequences; Pathogens; Phylogeny; Plant Diseases - microbiology; plant pathogens; Plant Sciences; Polymorphism, Genetic; Ralstonia solanacearum; Ralstonia solanacearum - classification; Ralstonia solanacearum - genetics; Ralstonia solanacearum - isolation & purification; Recombination, Genetic; ribosomal DNA; RNA, Bacterial - genetics; RNA, Ribosomal, 16S - genetics; sequence analysis; Sequence Analysis, DNA; Zoology
• ISSN: 0250-5991; 0973-7138
• DOI: 10.1007/s12038-013-9312-0

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.