AIMS Genetics, 2017, 4(3): 192-201. doi: 10.3934/genet.2017.3.192.

Research article

Export file:

Format

  • RIS(for EndNote,Reference Manager,ProCite)
  • BibTex
  • Text

Content

  • Citation Only
  • Citation and Abstract

Evidence for two types of nrDNA existing in Chinese medicinal fungus Ophiocordyceps sinensis

Institute of Microbiology and Biochemistry, College of Life Science, National Taiwan University, Taipei, Taiwan (R.O.C)

Academic Editor:Mohamed.Hijri,Carsten Külheim

Nuclear ribosomal DNA (nrDNA) sequences are widely used in the molecular classification of fungi. Previous phylogenetic studies of highly-valued traditional Chinese medicinal fungus Ophiocordyceps sinensis were mostly based on 18S and internal transcribed spacer (ITS) regions (ITS1, 5.8S and ITS2) of nrDNA. However, the disparity manifest in the low sequences identities between different O. sinensis isolates has led to argumentative hypotheses for this phenomenon, such as the “species complex” or “cryptic species” hypotheses. In the present study, four types of nrDNA (GC, AT-1, AT-2, and T) were identified using four primer pairs to amplify the nrDNA of six O. sinensis isolates. We demonstrate that each O. sinensis isolate contained two types of nrDNA, the omnipresent GC-type and a coexistent type alternating between the remaining three. This crucial discovery challenges the established notion of one type of nrDNA per species. We therefore propose that the composition of nrDNA types should be taken into consideration in studies of fungal genetics and classification.
  Figure/Table
  Supplementary
  Article Metrics

Keywords Ophiocordyceps sinensis; nrDNA; species complex; cryptic species

Citation: Chih-Sheng Chen, Ching-Tsan Huang, Ruey-Shyang Hseu. Evidence for two types of nrDNA existing in Chinese medicinal fungus Ophiocordyceps sinensis. AIMS Genetics, 2017, 4(3): 192-201. doi: 10.3934/genet.2017.3.192

References

  • 1. Chen CS, Huang CT, Hseu RS (2009) Identification of Cordyceps sinensis by 18S nrDNA Sequencing and Characterization of Fermented Products in Taiwan. Food Biotechnol 23: 1-9.    
  • 2. Kinjo N, Zang M (2001) Morphological and phylogenetic studies on Cordyceps sinensis distributed in southwestern China. Mycoscience 42: 567-574.    
  • 3. Stensrud Ø, Schumacher T, Shalchian-Tabrizi K, et al. (2007) Accelerated nrDNA evolution and profound AT bias in the medicinal fungus Cordyceps sinensis. Mycol Res 111: 409-415.    
  • 4. Moncalvo JM, Wang HH, Hseu RS (1995) Gene phylogeny of the Ganoderma lucidum complex based on ribosomal DNA sequences. Comparison with traditional taxonomic characters. Mycol Res 99: 1489-1499.
  • 5. White TJ, Bruns T, Lee S, et al. (1990) Amplification and direct sequencing of fungal ribosomal DNA for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ et al., editors. PCR protocols: a guide to methods and applications, San Diego, California: Academic Press, Inc. pp. 315-322.
  • 6. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
  • 7. 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 22: 4673-4680.    
  • 8. Chen CS, Hseu RS (1999) Differentiation of Cordyceps sinensis (Berk.) Sacc. specimen using restriction fragment length polymorphism of 18S rRNA gene. J Chin Agri Chem Soc 37: 533-545.
  • 9. Chen CS, Hseu RS (2002) Differentiation of Cordyceps sinensis (Berk.) Sacc. with 18S rRNA Gene Sequences. Taiwan J Agri Chem Food Sci 40: 219-225.
  • 10. Chen CS, Ling CH, Hseu RS (2004) Differentiation of Cordyceps sinensis (Berk.) Sacc. with Internal Transcribed Spacer1, 5.8S and Internal Transcribed Spacer 2 rRNA Gene Sequences. Taiwan J Agri Chem Food Sci 42: 147-153.
  • 11. Chen YQ, Hu B, Xu F, et al. (2004) Genetic variation of Cordyceps sinensis, a fruit-body-producing entomopathogenic species from different geographical regions in China. FEMS Microbiol Lett 230: 153-158.    
  • 12. Chen YQ, Wang N, Qu L, et al. (2001) Determination of the anamorph of Cordyceps sinensis inferred from the analysis of the ribosomal DNA internal transcribed spacers and 5.8S rDNA. Biochem Syst Ecol 29: 597-607.    
  • 13. Ito Y, Hirano T (1996) First successful amplification of 18S ribosomal DNA of Cordyceps spp. by the PCR method. Mycoscience 37: 109-110.    
  • 14. Ito Y, Hirano T (1997) The determination of the partial 18 S ribosomal DNA sequences of Cordyceps species. Lett Appl Microbiol 25: 239-242.    
  • 15. Liu Z-Y, Yao Y-J, Liang ZQ, et al. (2001) Molecular evidence for the anamorph-teleomorph connection in Cordyceps sinensis. Mycol Res 105: 827-832.    
  • 16. O'Donnell K, Nirenberg HI, Aoki T, et al. (2000) A multigene phylogeny of the Gibberella fujikuroi species complex: detection of additional phylogenetically distinct species. Mycoscience 41: 61-78.    
  • 17. O'Donnell K, Kistler HC, Tacke BK, et al. (2000) Gene genealogies reveal global phylogeographic structure and reproductive isolation among lineages of Fusarium graminearum, the fungus causing wheat scab. Proc Natl Acad Sci USA 97: 7905-7910.    
  • 18. Dettman JR, Jacobson DJ, Taylor JW (2003) A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora. Evolution 57: 2703-2720.    
  • 19. Ko KS, Joung HS (2002) Three nonorthologous ITS1 types are present in a polypore fungus Trichaptum abietinum. Mol Phylogenet Evol 23: 112-122.    
  • 20. Baldwin BG, Sanderson MJ, Porter JM, et al. (1995) The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Ann Mo Bot Gard 82: 247-277.    
  • 21. Vogler AP, DeSalle R (1994) Evolution and phylogenetic information content of the ITS-1 region in the tiger beetle Cicindela dorsalis. Mol Biol Evol 11: 393-405.
  • 22. Zijlstra C, Lever AEM, Uenk BJ, et al. (1995) Differences between ITS regions of isolates of root-knot nematodes Meloidogyne hapla and M. chitwoodi. Phytopathology 85: 1231-1237.    
  • 23. Buckler ES, Ippolito A, Holtsford TP (1997) The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications. Genetics 145: 821-832.
  • 24. Birdsell JA (2002) Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution. Mol Biol Evol 19: 1181-1197.    
  • 25. Rocha EPC, Danchin A (2002) Base composition bias might result from competition for metabolic resources. Trends Genet 18: 291-294.    

 

Reader Comments

your name: *   your email: *  

Copyright Info: © 2017, Ruey-Shyang Hseu, et al., licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution Licese (http://creativecommons.org/licenses/by/4.0)

Download full text in PDF

Export Citation

Copyright © AIMS Press All Rights Reserved