title: [Amplicon density-weighted algorithms for analyzing dissimilarity and dynamic alterations of RAPD polymorphisms of Cordyceps sinensis].
abstract: OBJECTIVE
  To examine the dynamic maturational alterations of random amplified polymorphic DNA (RAPD) molecular marker polymorphism resulted from differential expressions of multiple fungi in the caterpillar body, stroma and ascocarp portion of Cordyceps sinensis (Cs).
  
  
  METHODS
  Used the fuzzy, integral RAPD molecular marker polymorphism method with 20 random primers; used density-weighted cluster algorithms and ZUNIX similarity equations; compared RAPD polymorphisms of the caterpillar body, stroma and ascocarp of Cs during maturation; and compared RAPD polymorphisms of Cs and Hirsutella sinensis (Hs).
  
  
  RESULTS
  Density-unweighted algorithms neglected the differences in density of the DNA amplicons. Use of the density-weighted ZUNIX similarity equations and the clustering method integrated components of the amplicon density differences in similarity computations and clustering construction and prevented from the loss of the information of fungal genomes. An overall similarity 0.42 (< the overall dissimilarity 0.58) was observed for all compartments of Cs at different maturation stages. The similarities for the stromata or caterpillar bodies of Cs at 3 maturational stages were 0.57 or 0.50, respectively. During Cs maturation, there were dynamic Low→High→Low alterations of the RAPD polymorphisms between stromata and caterpillar bodies dissected from the same pieces of Cs. The polymorphic similarity was the highest (0.87) between the ascocarp and mature stroma, forming a clustering clade, while the premature stroma and caterpillar body formed another clade. These 2 clades merged into one cluster. Another clade containing the maturing stroma and caterpillar body merged with mature caterpillar body, forming another cluster. The RAPD polymorphic similarities between Hs and Cs samples were 0.55-0.69. Hs were separated from Cs clusters by the out-group control Paecilomyces militaris.
  
  
  CONCLUSIONS
  The wealthy RAPD polymorphisms change dynamically in the Cs compartments with maturation. The different RAPD polymorphism for Hs from those for Cs supports the hypothesis of integrated micro-ecosystem Cs with multiple fungi, but does not support the "single fungal species" hypothesis for Cs and the anamorph-teleomorph connection between Hs and Cs.
authors.affiliation: Pharmanex Beijing Clinical Pharmacology Center, Beijing 100088, China.
authors.forename: Yi-sang
authors.initials: YS
authors.lastname: Yao
authors.affiliation: Pharmanex Beijing Clinical Pharmacology Center, Beijing 100088, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Gao
authors.affiliation: Institute of Grassland Research, Qinghai Academy of Animal Husbandry and Veterinary Science, Xining 100088, China.
authors.forename: Yu-ling
authors.initials: YL
authors.lastname: Li
authors.affiliation: Institute of Grassland Research, Qinghai Academy of Animal Husbandry and Veterinary Science, Xining 100088, China.
authors.forename: Shao-li
authors.initials: SL
authors.lastname: Ma
authors.affiliation: Pharmanex Beijing Clinical Pharmacology Center, Beijing 100088, China.
authors.forename: Zi-mei
authors.initials: ZM
authors.lastname: Wu
authors.affiliation: Pharmanex Beijing Clinical Pharmacology Center, Beijing 100088, China.
authors.forename: Ning-zhi
authors.initials: NZ
authors.lastname: Tan
authors.affiliation: Department of Applied Biology and Chemistry Technology, Hong Kong Polytechnic University, Hong Kong.
authors.forename: Jian-yong
authors.initials: JY
authors.lastname: Wu
authors.affiliation: Department of Mechanical and Aerospace Engineering,University of California San Diego, La Jolla, CA 92093, USA.
authors.forename: Lu-qun
authors.initials: LQ
authors.lastname: Ni
authors.affiliation: Department of Applied Biology and Chemistry Technology, Hong Kong Polytechnic University, Hong Kong; NS Center for Anti-Aging Research, Provo, UT 84601, USA.
authors.forename: Jia-shi
authors.initials: JS
authors.lastname: Zhu
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D032661:Cordyceps / Q000235:genetics*; D017931:DNA Primers; D019105:Random Amplified Polymorphic DNA Technique
chemical_list: D017931:DNA Primers