Rapid Discrimination of Potato Scab-Causing Streptomyces Species Based on the RNase P RNA Gene Sequences

• Published in: The journal of microbiology 2011, 49(5), , pp.791-796
• Main Authors: Weon, H.Y., National Academy of Agricultural Science, RDA, Suwon, Republic of Korea, Song, J.K., National Academy of Agricultural Science, RDA, Suwon, Republic of Korea, Kim, B.Y., National Academy of Agricultural Science, RDA, Suwon, Republic of Korea, Hur, O.S., Agrobiodiversity Center, National Academy of Agricultural Science, RDA, Suwon, Republic of Korea, Park, I.C., National Academy of Agricultural Science, RDA, Suwon, Republic of Korea, Suh, J.W., Myong Ji University, Yongin, Republic of Korea
• Format: Article
• Language: English
• Subjects: 16S rRNA; Biomedical and Life Sciences; Cluster Analysis; Crops; Differentiation; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; DNA, Ribosomal - chemistry; DNA, Ribosomal - genetics; Genes; Life Sciences; Microbiology; Nucleotides; Pathogens; phylogenetic analysis; Phylogenetics; Phylogeny; Plant diseases; Plant Diseases - microbiology; Polymorphism, Genetic; potato scab; Potatoes; Republic of Korea; Ribonuclease P; Ribonuclease P - genetics; RNA, Ribosomal, 16S - genetics; rnpB; rnpB gene; Roots; rRNA 16S; Scab; Sequence Analysis, DNA; Solanum tuberosum; Solanum tuberosum - microbiology; STREPTOMYCES; Streptomyces - classification; Streptomyces - enzymology; Streptomyces - genetics; Streptomyces - isolation & purification; Topology; Variable region; 생물학
• ISSN: 1225-8873; 1976-3794
• DOI: 10.1007/s12275-011-1279-7

Scab disease significantly damages potatoes and other root crops. Some Streptomyces species have been reported as potato-scab pathogens. Identification of the phytopathogenic Streptomyces is mainly done on the basis of the 16S rRNA gene, but use of this gene has some limitations for discriminating these strains because they share high similarities of 16S rRNA gene sequences. We tested the RNase P RNA (rnpB) gene as a taxonomic marker to clarify the relationship among closely related scab-causing Streptomyces strains. The rnpB genes were analyzed for 41 strains including 9 isolates from Jeju, Korea. There were 4 highly variable regions including nucleotide gaps in the rnpB genes. Interspecies similarity of the rnpB gene in tested Streptomyces strains was lower than about 97%, while the intraspecies similarity was higher than about 98%. Phylogenetic analysis demonstrated that the rapB tree has similar topology to the 16S rRNA gene tree, but produces a more divergent phyletic lineage. These results revealed that the rnpB gene could he used as a powerful taxonomic tool for rapid differentiation of closely related Streptomyces species. In addition, it was also suggested that the variable regions marked as α, β, γ, and δ in the rnpB gene could be useful markers for the detection of specific Streptomyces species.