Mycobiology

The Korean Society of Mycology (한국균학회)
권호 표지
DOI QR코드

DOI QR Code

Phylogenetic Relationship in Different Commercial Strains of Pleurotus nebrodensis Based on ITS Sequence and RAPD

  • Alam, Nuhu (Department of Biology, University of Incheon) ;
  • Shim, Mi-Ja (Department of Life Science, University of Seoul) ;
  • Lee, Min-Woong (Department of Biology, Dongguk University) ;
  • Shin, Pyeong-Gyun (Mushroom Research Division, Dept. of Herbal Crop Research, National Inst. of Horticulture & Herbal Science, RDA) ;
  • Yoo, Young-Bok (Mushroom Research Division, Dept. of Herbal Crop Research, National Inst. of Horticulture & Herbal Science, RDA) ;
  • Lee, Tae-Soo (Department of Biology, University of Incheon)
  • Published : 2009.09.30
Download PDF
⟨ Previous Next ⟩

Abstract

The molecular phylogeny in nine different commercial cultivated strains of Pleurotus nebrodensis was studied based on their internal transcribed spacer (ITS) region and RAPD. In the sequence of ITS region of selected strains, it was revealed that the total length ranged from 592 to 614 bp. The size of ITS1 and ITS2 regions varied among the strains from 219 to 228 bp and 211 to 229 bp, respectively. The sequence of ITS2 was more variable than ITS1 and the region of 5.8S sequences were identical. Phylogenetic tree of the ITS region sequences indicated that selected strains were classified into five clusters. The reciprocal homologies of the ITS region sequences ranged from 99 to 100%. The strains were also analyzed by RAPD with 20 arbitrary primers. Twelve primers were efficient to applying amplification of the genomic DNA. The sizes of the polymorphic fragments obtained were in the range of 200 to 2000 bp. RAPD and ITS analysis techniques were able to detect genetic variation among the tested strains. Experimental results suggested that IUM-1381, IUM-3914, IUM-1495 and AY-581431 strains were genetically very similar. Therefore, all IUM and NCBI gene bank strains of P. nebrodensis were genetically same with some variations.

Keywords

References

  1. Bruns, T. D., White, T. J. and Taylor, J. W. 1991. Fungal molecular systematics. Ann. Rev. Ecol. S. 22:525-564 https://doi.org/10.1146/annurev.es.22.110191.002521
  2. Chang, S. T. and Miles, P. G. 1988. Pleurotus - a mushroom of broad adaptability. In: edible mushroom and their cultivation. pp. 265-275. CRC press, Inc. Boca Raton, USA
  3. Choi, D., Kang, S. H., Song, Y. H., Kwun, K. H., Jeong, K. J. and Cha, W. S. 2005. Exopolysaccharide production in liquid culture of Pleurotus ferulae. J. MicrobioI. Biotech. 146:209-221
  4. Cubero, O. F., Crespo, A. N. A., Fatehi, F. and Bridge, P. D. 1999. DNA extraction and PCR amplification method suitable for fresh, herbarium stored, lichenized and other fungi. Pl. Syst. Evol. 216:243-249 https://doi.org/10.1007/BF01084401
  5. Felsenstein, J. 1985. Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39:783-791 https://doi.org/10.2307/2408678
  6. Kawai, G, Babasaki, K. and Neda, H. 2008. Taxonomic position of Chinese Pleurotus "Bai-ling-Gu": it belongs to Pleurotus eryngii (DC.: Fr) Quel. And evolved independently in China. Mycoscience 49:75-87 https://doi.org/10.1007/s10267-007-0392-2
  7. Lee, S. B. and Taylor, J. W. 1990. Isolation of DNA from fungal mycelia and single spores. In: PCR protocol: A guide to methods and applications. pp. 282-287. Eds. Innis, M. A., Gelfand,D. H., Sninsky, J. J. and White, T. J. Academic Press, SanDiego, USA
  8. Lee, T. S., Bak, W. C., Kang, H. D., Kim, S. K., Byun, B. H., Yi, C. K., Lee, W. K. and Min, D. S. 1997. Classification of Korean Lentinula edodes strains by random amplified poIymorphic DNA (RAPD) Markers. Korean J. Mycol. 25:219-225
  9. Lopandic, K., Monlar, O. and Prillinger, H. 2005. Application of ITS sequence analysis, RAPD and AFLP fingerprinting in characterizing the yeast genus Fellomyces. Microbiol. Res.160:13-26 https://doi.org/10.1016/j.micres.2004.09.005
  10. Nei, M. and Li, W. H. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc.Natl. Acad. Sci. USA 76:5269-5273 https://doi.org/10.1073/pnas.76.10.5269
  11. Park, H. G, Ko, H. G, Kim, S. H. and Park, W. O. 2004. Molecular identification of Asian isolates of medicinal mushroom Hericium erinaceum by phylogenetic analysis of nuclear ITS rDNA. J. Microbiot. Biotech. 14:816-821
  12. Paul, B. 2002. ITS region of the rDNA of Pythium loneandrum, a new species: ITS taxonomy and compared with related Species. FEMS Microbiol. Lett. 202:239-242 https://doi.org/10.1111/j.1574-6968.2001.tb10810.x
  13. Ro, H. S., Kim, S. S., Ryu, J. S., Jeon, C. O., Lee, T. S. and Lee H. S. 2007. Comparative studies on the diversity of the edible mushroom Pleurotus eryngii: ITS sequence analysis, RAPD fingerprinting and physiological characteristics. Mycol. Res. 3:710-715
  14. Saitou, N. and Nei, M. 1987. The neighbor-joining method: a method for reconstructing phylogenetic tree. Mot. Biol. Evol.4:406-425
  15. Shen, J., Guo, H., Cheng, Y., Wei, X., Guo, G, Liu, G. and Jia, S. 2005. The exploitation and cultivation of Pleurotus nebrodensis in China. In: Tan et al. (eds.) Proceedings 5th International Conference on Mushroom Biology and Mushroom Products.Acta Edulis Fungi 12:354-359
  16. Tan, Q., Wang, Z., Cheng, J., Guo, Q. and Guo, L. 2005. Cultiva-tion of Pleurotus spp. in China. In: Tan et al. (eds.). Proceed-ings of the 5th International Conference on Mushroom Biology and Mushroom Products. Acta Edulis Fungi 12:338-349
  17. Thompson, J. D., Higgins, D. G. and Gibson, T. J. 1994. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighing position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680 https://doi.org/10.1093/nar/22.22.4673
  18. Tuchwell, D. S., Nicholson, M. J., Mc-Sweeney, C. S., The-odorou, M. K. and Brookman, J. L. 2005. The rapid assessment of ruminal fungi to presumptive genera using ITS1 and ITS2 RNA secondary structures to produce group specific fingerprints. Microbiotogy 151:1557-1567
  19. Venturella, G. 2000. Typification of Pleurotus nebrodensis. Mycotaxon 75:229-231
  20. Wang, H. and Ng, T. B. 2004. Eryngin, a novel antifungal Peptide from fruiting bodies of the edible mushroom Pteurotus eryngii. Peptides 25:1-5. https://doi.org/10.1016/j.peptides.2003.11.014
  21. White, T. J., Bruns, T., Lee, S. and Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for Phylogenetics. In: PCR protocol: a guide to methods and applications, pp. 315-322. Eds. Innis, M. A., Gelfand, D. H., Sninsky,J. J. and White, T. J. Academic Press, San Diego, CA
  22. Williams, J. G. K., Kubelik, A. R., Livak, K. J., Rafalski, J. A. and Tingey, S. V. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18:6531-6535 https://doi.org/10.1093/nar/18.22.6531

Cited by

  1. based on ITS sequence and RAPD vol.37, pp.4, 2009, https://doi.org/10.4489/MYCO.2009.37.4.258
  2. based on ITS Sequences and RAPD vol.38, pp.2, 2010, https://doi.org/10.4489/MYCO.2010.38.2.089
  3. A Phylogenetic Relationship between Foreign and Korean Strains of Flammulina velutipes Identified by rDNA-ITS Sequence Analysis vol.22, pp.1, 2012, https://doi.org/10.5352/JLS.2012.22.1.62
  4. Genetic Variation Based on Random Amplified Polymorphic DNA (RAPD) and Internal Transcribed Spacer (ITS) Region Sequences in Lepista nuda vol.22, pp.11, 2012, https://doi.org/10.5352/JLS.2012.22.11.1470
  5. on Mouse Sarcoma 180 vol.40, pp.4, 2012, https://doi.org/10.5941/MYCO.2012.40.4.236
  6. Secondary Structure of the Ribosomal Internal Transcribed Spacer (ITS) Region of Hypsizygus marmoreus vol.23, pp.10, 2013, https://doi.org/10.5352/JLS.2013.23.10.1260
  7. Characteristic Odorants from Bailingu Oyster Mushroom (Pleurotus eryngii var. tuoliensis) and Summer Oyster Mushroom (Pleurotus cystidiosus) vol.63, pp.7, 2014, https://doi.org/10.5650/jos.ess14043
  8. Genome Instability In Fruit Body Derived Lines Generated From Fruiting Pfle Somatic Hybrid Lines And Development Of Hybrid Strain Specific Scar Marker In Edible Mushroom vol.23, pp.2, 2015, https://doi.org/10.2478/johr-2015-0022