Molecular Biology Reports

, Volume 39, Issue 7, pp 7355–7364 | Cite as

Molecular classification and phylogenetic relationships of selected edible Basidiomycetes species

  • Farhat Ahmadi Avin
  • Subha Bhassu
  • Tan Yee Shin
  • Vikineswary Sabaratnam


Morphological identification of edible mushrooms can sometimes prove troublesome, because phenotypic variation in fungi can be affected by substrate and environmental factors. One of the most important problems for mushroom breeders is the lack of a systematic consensus tool to distinguish different species, which are sometimes morphologically identical. Basidiomycetes as one of the largest groups of edible mushrooms have become more important in recent times for their medicinal and nutritional properties. Partial rDNA sequences, including the Internal Transcribed Spacer I-5.8SrDNA-Internal Transcribed Spacer II, were used in this study for molecular identification and assessment of phylogenetic relationships between selected edible species of the Basidiomycetes. Phylogenetic trees showed five distinct clades; each clade belonging to a separate family group. The first clade included all the species belonging to the Pleurotaceae (Pleurotus spp.) family; similarly, the second, third, fourth, and fifth clades consist of species from the Agaricaceae (Agaricus sp.), Lyophllaceae (Hypsigygus sp.), Marasmiaceae (Lentinula edodes sp.) and Physalacriaceae (Flammulina velutipes sp.) families, respectively. Moreover, different species of each family were clearly placed in a distinct sub-cluster and a total of 13 species were taken for analysis. Species differentiation was re-confirmed by AMOVA analysis (among the populations: 99.67%; within: 0.33%), nucleotide divergence, haplotyping and P value. Polymorphism occurred throughout the ITS regions due to insertion–deletion and point mutations, and can be clearly differentiated within the families as well as genera. Moreover, this study proves that the sequence of the ITS region is a superior molecular DNA barcode for taxonomic identification of Basidiomycetes.


Basidiomycetes ITS region rDNA AMOVA Haplotype group DNA barcode 



This study was supported by a research Grant (PS291-2009C) and 66-02-03-0074 from the Institute of Research Management and Monitoring (IPPP), University of Malaya. We are grateful to Dr. Anke from the Unit for the Enhancement of Academic Performance (ULPA), University of Malaya and Dr. Jesu Arockiaraj for editing. We would also like to thank the mushroom farmers for their cooperation and help.


  1. 1.
    Vikineswary S, Abdullah N, Ibrahim N, How TY, Daud F, Jones EBG (2007) Edible and medical mushroom. In: Jones EBG, Hyde KD, Vikineswary S (eds) Malaysia fungal diversity. University of Malaya and Ministry of Natural Resources and Environment, Malaysia, pp 287–301Google Scholar
  2. 2.
    Gonzalez P, Labarère J (2000) Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6 and V9 domains. Microbiology 146(1):209–221PubMedGoogle Scholar
  3. 3.
    Ravash R, Shiran B, Alavi AA, Bayat F, Rajaee S, Zervakis GI (2010) Genetic variability and molecular phylogeny of Pleurotus eryngii species-complex isolates from Iran, and notes on the systematics of Asiatic populations. Mycol Prog 9(2):181–194CrossRefGoogle Scholar
  4. 4.
    Choi DB, Ding JL, Cha WS (2007) Homology search of genus Pleurotus using an internal transcribed spacer region. Kor J Chem Eng 24(3):408–412CrossRefGoogle Scholar
  5. 5.
    Ito Y, Fushimi T, Yanagi SO (1998) Discrimination of species and strains of basidiomycete genus Coprinus by random amplified polymorphic DNA (RAPD) analysis. Mycoscience 39(4):361–365CrossRefGoogle Scholar
  6. 6.
    White T, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR protocols a guide to methods and applications. Academic Press, San Diego, pp 315–322Google Scholar
  7. 7.
    Seifert KA (2009) Progress towards DNA barcoding of fungi. Mol Ecol Resour 9:83–89PubMedCrossRefGoogle Scholar
  8. 8.
    Stajic M, Sikorski J, Wasser SP, Nevo E (2005) Genetic similarity and taxonomic relationships within the genus Pleurotus (higher Basidiomycetes) determined by RAPD analysis. Mycotaxon 93:247–256Google Scholar
  9. 9.
    Ro HS, Kim SS, Ryu JS, Jeon CO, Lee TS, Lee HS (2007) Comparative studies on the diversity of the edible mushroom Pleurotus eryngii: ITS sequence analysis, RAPD fingerprinting, and physiological characteristics. Mycol Res 111(6):710–715PubMedCrossRefGoogle Scholar
  10. 10.
    Zervakis GI, Venturella G, Papadopoulou K (2001) Genetic polymorphism and taxonomic infrastructure of the Pleurotus eryngii species-complex as determined by RAPD analysis, isozyme profiles and ecomorphological characters. Microbiology 147(11):3183–3194PubMedGoogle Scholar
  11. 11.
    Seifert KA, Samson RA, DeWaard JR, Houbraken J, Lévesque CA, Moncalvo JM, Louis-Seize G, Hebert PDN (2007) Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proc Natl Acad Sci USA 104(10):3901–3906PubMedCrossRefGoogle Scholar
  12. 12.
    Nguyen H, Seifert K (2008) Description and DNA barcoding of three new species of Leohumicola from South Africa and the United States. Persoonia 21:57–69PubMedCrossRefGoogle Scholar
  13. 13.
    Chang YS, Lee SS (2004) Utilization of Macrofungi species in Malaysia. Fungal Divers 15:15–22Google Scholar
  14. 14.
    Weiland JJ (1997) Rapid procedure for the extraction of DNA from fungal spores and mycelia. Fungal Genet Newslett 44:60–63Google Scholar
  15. 15.
    Gardes M, Bruns T (1993) ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol Ecol 2(2):113–118PubMedCrossRefGoogle Scholar
  16. 16.
    Xu K, Kanno M, Yu H, Li Q, Kijima A (2011) Complete mitochondrial DNA sequence and phylogenetic analysis of Zhikong scallop Chlamys farreri (Bivalvia: Pectinidae). Mol Biol Rep 38(5):3067–3074PubMedCrossRefGoogle Scholar
  17. 17.
    Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24(8):1596–1599PubMedCrossRefGoogle Scholar
  18. 18.
    Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132(3):365–386PubMedGoogle Scholar
  19. 19.
    Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11):1451–1452PubMedCrossRefGoogle Scholar
  20. 20.
    Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol bioinform online 1:47–50Google Scholar
  21. 21.
    Siddiquee S, Tan SG, Yusuf UK, Fatihah NH, Hasan MM (2012) Characterization of Malaysian Trichoderma isolates using random amplified microsatellites (RAMS). Mol Biol Rep 39(1):715–722PubMedCrossRefGoogle Scholar
  22. 22.
    Shnyreva A, Shtaer O (2006) Differentiation of closely related oyster fungi Pleurotus pulmonarius and P. ostreatus by mating and molecular markers. Rus J Genet 42(5):539–545CrossRefGoogle Scholar
  23. 23.
    Lechner BE, Petersen R, Rajchenberg M, Albertó E (2002) Presence of Pleurotus ostreatus in Patagonia, Argentina. Revista iberoamericana de micología 19(2):111–114PubMedGoogle Scholar
  24. 24.
    Fries E (1989) 1836–1838. Epicrisis systematis mycologici, synopsis hymenomycetum. Uppsala, SwedenGoogle Scholar
  25. 25.
    Singer R (1951) The” Agaricales”(Mushrooms) in modern taxonomy. Lilloa 22: 1–830. 1959. New and interesting species of basidiomycetes. VI. Mycologia 51:375–400CrossRefGoogle Scholar
  26. 26.
    Pegler D, Yi-Jian YA (1995) The distinction between Lentinus sajor-caju and Pleurotus ostreatus and their taxonomy. Acta Botanica Yunnanica 17(3):305–311Google Scholar
  27. 27.
    Li X, Yao Y (2005) Revision of the taxonomic position of the Phoenix Mushroom. Mycotaxon 91:61–74Google Scholar
  28. 28.
    Iraçabal B, Zervakis G, Labarère J (1995) Molecular systematics of the genus Pleurotus: analysis of restriction polymorphisms in ribosomal DNA. Microbiology 141:1479–1490CrossRefGoogle Scholar
  29. 29.
    Guzmán G, Montoya L, Mata G, Salmones D (1994) Studies in the genus Pleurotus. III: The varieties of P. ostreatus-complex based in interbreeding strains and in the study of basidiomata obtained in culture. Mycotaxon 50:365–378Google Scholar
  30. 30.
    Zervakis G, Sourdis J, Balis C (1994) Genetic variability and systematics of eleven Pleurotus species based on isozyme analysis. Mycol Res 98(3):329–341CrossRefGoogle Scholar
  31. 31.
    Song H, Buhay JE, Whiting MF, Crandall KA (2008) Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proc Natl Acad Sci USA 105(36):13486–13491PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Farhat Ahmadi Avin
    • 1
    • 2
  • Subha Bhassu
    • 2
  • Tan Yee Shin
    • 1
  • Vikineswary Sabaratnam
    • 1
  1. 1.Mushroom Research Centre (MRC), Institute of Biological Sciences, Faculty of ScienceUniversity of MalayaKuala LumpurMalaysia
  2. 2.Division of Genetics and Molecular Biology, Faculty of ScienceCenter for Biotechnology in Agriculture Research (CEBAR), Institute of Biological Sciences, University of MalayaKuala LumpurMalaysia

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