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CC BY 4.0 · AIMS Genet 2017; 04(03): 192-201
DOI: 10.3934/genet.2017.3.192
Research Article

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

Chih-Sheng Chen
Institute of Microbiology and Biochemistry, College of Life Science, National Taiwan University, Taipei, Taiwan (R.O.C)
,
Ching-Tsan Huang
Institute of Microbiology and Biochemistry, College of Life Science, National Taiwan University, Taipei, Taiwan (R.O.C)
,
Ruey-Shyang Hseu
Institute of Microbiology and Biochemistry, College of Life Science, National Taiwan University, Taipei, Taiwan (R.O.C)
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Abstract

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.

Keywords

Ophiocordyceps sinensis - nrDNA - species complex - cryptic species


Publication History

Received: 28 December 2016

Accepted: 25 July 2017

Article published online:
10 May 2021

© 2017. The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution License, permitting unrestricted use, distribution, and reproduction so long as the original work is properly cited. (https://creativecommons.org/licenses/by/4.0/)

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Rüdigerstraße 14, 70469 Stuttgart, Germany

 

  • References

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