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Journal of Wood Science

Official Journal of the Japan Wood Research Society

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Qualitative and quantitative PCR methods using species-specific primer for detection and identification of wood rot fungi

Journal of Wood Science volume 55, pages 133–138 (2009)Cite this article

Abstract

Species-specific oligonucleotide primers for detecting wood rot fungi, Gloeophyllum trabeum, Trametes versicolor, Coniophora puteana, and Serpula lacrymans, and the primer detecting a group of related fungi to G. sepiarium were developed. These primer sequences were picked up from the internal transcribed spacer region between small-subunit rDNA and large-subunit rDNA. The species selectivities of the developed primers were checked. Real-time polymerase chain reaction (PCR) was carried out using these highly specific primers to quantitatively detect at least of 0.01 ng genome DNA of the target species. This quantitative PCR was also used to differentiate the target species DNA from mixed species DNA. A PCR-based technique using the species-specific primers would be applicable to multiple-sample assay in diagnosis of wood decay and to investigation of environmental fungal populations.

References

  1. Palfreyman JW, Vigrow A, Button D, Herarty B, King B (1991) The use of molecular methods to identify wood decay organisms. Wood Protect 1:5–22

    Google Scholar 

  2. Palfreyman J, Vigrow A (1994) Molecular analysis of certain isolates of Serpula lacrymans. FEMS Microbiol Lett 117:281–286

    Article  CAS  Google Scholar 

  3. Clausen C (1994) Dyed particle capture immunoassay for detection of incipient brown-rot decay. J Immunoassay 15:305–316

    Article  CAS  PubMed  Google Scholar 

  4. Palfreyman JW, Bruce A, Button D, Glanct H, Vigrow A, King B (2001) Immunological method for the detection and characterization of wood decay basidiomycetes. Int Biodeterior Biodegrad 48:74–78

    Article  Google Scholar 

  5. Clausen CA, Green F, Highley TL (1991) Early detection of brown-rot decay in southern yellow pine using immunodiagnostic procedures. Wood Sci Technol 26:1–8

    Article  Google Scholar 

  6. Jellison J, Goodell B (1988) Immunological detection of decay in wood. Wood Sci Technol 22:293–297

    Article  CAS  Google Scholar 

  7. Naumann A, Navarro-Gonzales M, Sudhakar P, Kues U, Polle A (2005) Fourier transformation infrared microscopy and imaging: detection of fungi in wood. Fungal Genet Biol 42:829–835

    Article  PubMed  Google Scholar 

  8. Erukhimovitch V, Pavlov V, Talyshinsky M, Souprun Y, Huleihel M (2005) FTIR microscopy as a method for identification of bacterial and fungal infections. J Pharm Biomed Anal 37:1105–1108

    Article  CAS  PubMed  Google Scholar 

  9. Horisawa S, Sakuma Y, Takata K, Doi S (2004) Identification of intra- and inter-species of the dry rot fungus Serpula lacrymans by PCR-RFLP and RAPD analysis. J Wood Sci 50:427–432

    Article  CAS  Google Scholar 

  10. Terashima K, Matsumoto T, Hasebe K, Fukumasa-Nakai Y (2002) Genetic diversity and strain-typing in cultivated strains of Lentinula edodes (the shii-take mushroom) in Japan by AFLP analysis. Mycol Res 106:34–39

    Article  CAS  Google Scholar 

  11. Maejer D, Mithen R, Lewis BG, Vos P, Oliver RP (1996) The use of AFLP fingerprinting for the detection of genetic variation in fungi. Mycol Res 100:1107–1111

    Article  Google Scholar 

  12. Barry T, Colleran G, Glennon M, Dunican LK, Gannon F (1991) The 16s/23s ribosomal spacer region as a target for DNA probes to identify eubacteria. PCR Methods Appl 1:51–56

    Article  CAS  PubMed  Google Scholar 

  13. Tooley PW, Goley ED, Carras MM, Frederick RD, Kuldau GA (2001) Characterization of Claviceps species pathogenic on sorghum by sequence analysis of the β-tubulin gene intron 3 region and EF-1 α gene intron 4. Mycologoia 93:541–551

    Article  CAS  Google Scholar 

  14. Roux J, Steenkamp ET, Marasas WFO, Wingfield MJ, Wingfield BD (2001) Characterization of Fusarium graminearum from Acacia and Eucalyptus using β-tubulin and histonegene sequences. Mycologia 93:704–711

    Article  CAS  Google Scholar 

  15. Erwin, Takemoto S, Hwang W-J, Takeuchi M, Itoh T, Imamura Y (2008) Anatomical characterization of decayed wood in standing light red meranti and identifi cation of the fungi isolated from the decayed area. J Wood Sci 54:233–241

    Article  CAS  Google Scholar 

  16. Suhara H, Maekawa N, Kubahashi T, Kondo R (2005) Specific detection of a basidiomycete, Phelebia brebispora accociated with butt rot of Chamaecyparis obtusa, by PCR-based analysis. J Wood Sci 51:83–88

    Article  CAS  Google Scholar 

  17. Schmidt O, Moreth U (1998) Genetic studies on house rot fungi and a rapid diagnosis. Holz Roh Werkst 56:421–425

    Article  CAS  Google Scholar 

  18. Schmidt O, Moreth U (2000) Species-specific PCR primers in the rDNA-ITS region as a diagnostic tool for Serpula lacrymans. Mycol Res 104:69–72

    Article  CAS  Google Scholar 

  19. Woo TH, Patel BK, Cinco M, Smythe LD, Symonds ML, Norris MA, Dohnt MF (1998) Real-time homogeneous assay of rapid cycle polymerase chain reaction product for identification of Leptonema illini. Anal Biochem 259:112–117

    Article  CAS  PubMed  Google Scholar 

  20. Kageyama A, Sakamoto M, Benno Y (2000) Rapid identification and quantification of Collinsella aerofaciens using PCR. FEMS Microbiol Lett 183:43–47

    Article  CAS  PubMed  Google Scholar 

  21. Lyons SR, Griffen AL, Leys EJ (2000) Quantitative real-time PCR for Porphyromonas gingivalis and total bacteria. J Clin Microbiol 38:2362–2365

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Schweigkofler W, O’Donnell K, Garbelotto M (2004) Detection and quantification of airborne conidia of Fusarium circinatum, the causal agent of pine pitch canker, from two California sites by using a real-time PCR approach combined with a simple spore trapping method. Appl Environ Microbiol 70:3512–3520

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. White TJ, Burns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic, San Diego, pp 315–332

    Google Scholar 

  24. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 11:4673–4680

    Article  Google Scholar 

  25. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365–386

    CAS  PubMed  Google Scholar 

  26. Schmidt O, Moreth U (1999) Identification of the dry rot fungus, Serpula lacrymans, and the wild merulius, S. himantioides, by amplified ribosomal DNA restriction analysis (ARDEA). Holzforschung 53:123–128

    Article  CAS  Google Scholar 

  27. White NA, Dehal PK, Duncan JM, Williams NA, Gartland JS, Palfreyman JW, Cooke DEL (2006) Molecular analysis of intraspecific variation between building and “wild” isolates of Serpula lacrymans and their relatedness to S. himantioides. Mycol Res 105:447–452

    Article  Google Scholar 

  28. Ranjard L, Poly F, Lata JC, Mougel C, Thioulouse J, Nazaret S (2001) Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Appl Environ Microbiol 67:4479–4487

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Department of Environmental Systems Engineering, Faculty of Engineering, Kochi University of Technology, 185 Miyanokuchi, Kami, Kochi, 782-8502, Japan

    Sakae Horisawa

  2. Graduate School of Science and Engineering, Ehime University, Matsuyama, 790-8577, Japan

    Yoh Sakuma

  3. Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Ibaraki, Japan

    Shuichi Doi

Authors
  1. Sakae Horisawa
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  2. Yoh Sakuma
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  3. Shuichi Doi
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Corresponding author

Correspondence to Sakae Horisawa.

Additional information

Part of this article was presented at the International Symposium on Wood Science and Technology (IAWPC 2005), Yokohama, November 2005

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Horisawa, S., Sakuma, Y. & Doi, S. Qualitative and quantitative PCR methods using species-specific primer for detection and identification of wood rot fungi. J Wood Sci 55, 133–138 (2009). https://doi.org/10.1007/s10086-008-1011-3

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  • DOI: https://doi.org/10.1007/s10086-008-1011-3

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