Species delimitation in Pleurotus eryngii species-complex inferred from ITS and EF-1α gene sequences

Mycology

Volumn 1, Issue 4, 2010, Pages 269-280

  Mang, Stefania M ^a   Figliuolo, Giovanni ^a  

^a UNIVERSITY OF BASILICATA   (Italy)

Author keywords

Elongation factor 1 alpha; ITS; M13 marker; Pleurotus; Taxonomy

Indexed keywords

FOENICULUM VULGARE; PLEUROTUS; PLEUROTUS ERYNGII;

EID: 79958707701     PISSN: 21501203     EISSN: 21501211     Source Type: Journal    
DOI: 10.1080/21501203.2010.536171     Document Type: Article

References (83)

1. Albertó EO, Petersen HR, Hughes KW, Lechner B. 2002. Miscellaneous notes on Pleurotus. Persoonia 18: 55-69.
2. Alejandro R, Todd W. 2005. Evolution of a large ribosomal RNA multigene family in filamentous fungi: Birth and death of a concerted evolution paradigm. Proc Natl Acad Sci USA 102(14):5084-5089.
3. Appel DJ, Gordon TR. 1996. Relationships among pathogenic and nonpathogenic isolates of Fusarium oxysporum based on the partial sequence of the intergenic spacer region of the ribosomal DNA. Mol Plant-Microbe Interact. 9: 125-138.
4. Avise JC, Ball RM. 1990. Principles of genealogical concordance in species concepts and biological taxonomy. Oxford Surv. Evol. Biol. 7: 45-67.
5. Bentley AR, Cromey MG, Farrokhi-Nejad R, Leslie JF, Summerell BA, Burgess LW. 2006. Fusarium crown and root rot pathogens associated with wheat and grass stem bases on the South Island of New Zealand. Aust Plant Pathol. 35(5):495-502.
6. Bruns TD, Vilgalys R, Barns SM, Gonzalez D, Hibbett DS, Lane DJ, Simon L, Stickel S, Szaro TM, Weisburg WG, Sogin ML. 1992. Evolutionary relationships within the fungi: analyses of nuclear small subunit rRNA sequences.Mol Phylogenet Evol. 1: 231-241.
7. Candusso M, Basso MT. 1995. Comparative analysis of Pleurotus eryngii and P. nebrodensis. Documents Mycologique 100: 119-128.
8. Chen YC, Eisner JD, Kattar MM, Rassoulian-Barrett SL, Lafe K, Bui U, Limaye AP, Cookson BT. 2001. Polymorphic internal transcribed spacer region 1 DNA sequences identify medically important yeasts. J Clin Microbiol. 39: 4042-4051.
9. De Gioia T, Sisto D, Rana GL, Figliuolo G. 2005. Genetic structure of the Pleurotus eryngii species-complex. Mycol Res. 109(1):71-80.
10. Della Rosa V, Capuccio I, Fanelli C, Urbanelli S. 2004. Isolation and characterization of microsatellite markers in two basidiomycete species: Pleurotus eryngii and P. ferulae. Premier Note. Mol Ecol Notes 4: 271-273.
11. Dupont J, Jacquet C, Dennetière B, Lacoste S. 2007. Invasion of the French Paleolithic painted cave of Lascaux by members of the Fusarium solani species complex. Mycologia 99(4): 526-533.
12. Eck RV, Dayhoff MO. 1966. Atlas of Protein Sequence and Structure. Silver Springs (MD): National Biomedical Research Foundation.
13. Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
14. Figliuolo G, Di Stefano D. 2007. Is single bulb producing garlic Allium sativum or Alllium ampeloprasum? Sci Hortic. 114(4):243-249.
15. Forte L, Perrino EV, Terzi M. 2005. Le praterie a Stipa austroitalica Martinovsky' ssp. austroitalica dell'Alta Murgia (Puglia) e della Murgia Materana (Basilicata). [The prairies with Stipa austroitalica Martinovsky' ssp. austroitalica from "Alta Murgia" (Apulia) and "Murgia Materana" (Basilicata)] Fitosociologia 42: 83-103 (in Italian).
16. Gardes M, Bruns TD. 1993. ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Mol Ecol. 2: 113-118.
17. Geiser DM, Gueidan C, Miadlikowska J, Lutzoni F, Kauff F, Hofstetter V, Fraker E, Schoch CL, Tibell L, Untereiner WA, Aptroot A. 2007. Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae. Mycologia 98: 1054-1065.
18. Gonzalez P, Labarère J. 2000. Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mithocondrial small-subunit rRNA, V4, V5, V6 and V9 domains. Microbiology 146: 209-221.
19. Guarro J, Gene J, Stchigel A. 1999. Developments in fungal taxonomy. Clin Microbiol Rev. (12) 3: 454-500.
20. Helgason T, Watson IJ, Young PW. 2003. Phylogeny of the Glomerales and Diversisporales (Fungi Glomeromycota) from actin and elongation factor 1 alpha sequences. FEMS Microbiol Lett. 229: 127-132.
21. Hibbett DS. 1992. Ribosomal DNA and Fungal Systematics. Trans Mycol Soc Jpn. 33: 533-566.
22. Hilber O. 1982. Die Gattung Plerurotus (Fr.) Kummer. Bibliotheca Mycologica 87. Vaduz, Germany: J. Kramer; p 464 S.
23. Hopple JS, Vilgalys R. 1999. Phylogenetic Relationships in the mushroom genus Coprinus and dark-spored allies based on sequence data from the nuclear gene coding for the large ribosomal subunit RNA: Divergent domains, outgroups, and monophyly. Mol Phylogenet Evol. 13(1):1-19.
24. Inzenga G. 1863. Nuova specie di agarico del Prof. Giuseppe Inzenga. Giornale Reale Istituto Incoraggiamento Agricoltura Siciliana Palermo 1: 161-164.
25. James TY, Moncalvo JM, Li S, Vilgalys R. 2001. Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune. Genetics 157(1):149-61.
26. Kawai G, Babasaki K, Neda H. 2008. Taxonomic position of a Chinese Pleurotus "Bai-Ling-Gu" it belongs to Pleurotus eryngii (DC.:Fr.) Quèl. and evolved independently in China. Mycoscience 49: 75-87.
27. Kristensen R, Torp M, Kosiak-Jensen A. 2005. Phylogeny and toxigenic potential is correlated with Fusarium species as revealed by partial translation elongation factor 1 alpha gene sequences. Mycol Res. 109(2):173-186.
28. Lanzi M. 1894. I funghi della provincia di Roma. Memorie dell'accademia pontificia dei nuovi lincei, Roma, vol. IX, Pt. II.
29. Latouche GN, Daniel HM, Lee OC, Mitchell TG, Sorrel TC, Meyer W. 1997. Comparison of use of phenotypic and genotypic characteristics for identification of species of the anamorph genus Candida and related teleomorph yeast species. J Clin Microbiol. 35(12):3171-3180.
30. Lewinsohn D, Wasser SP, Reshetnikov SV, Hadar Y, Nevo E. 2002. The Pleurotus eryngii species-complex in Israel: distribution and morphological description of a new taxon. Mycotaxon 81: 51-67.
31. Linnaeus C. 1758. Systema naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, 10th edition (in Latin), Holmiae (Laurentii Salvii), vol. 1-2, 1384 p.
32. Mang S. 2008. Genome analysis of Pleurotus speciescomplex using gene sequences with taxonomic value [PhD dissertation]. [Basilicata (IT)]: University of Basilicata. 129 p. Available from: University of Basilicata Library.
33. Mang S, Figliuolo G. 2008. Phylogenetic relationships among Pleurotus eryngii specimens from different eco-geographic sites of the Mediterranean Region. Proceedings of the 6th International Conference on Mushroom Biology and Mushroom Products 29th September- 3rd October, Bonn, Germany.
34. Mansfield MA, Kuldau GA. 2007. Microbiological and molecular determination of mycobiota in fresh and ensiled maize silage. Mycologia 99(2):269-278.
35. Maphosa L, Wingfield BD, Coetzee MPA, Mwenje E, Wingfield M. 2006. Phylogenetic relationships among Armillaria species inferred from partial elongation factor 1-alpha DNA sequence data. Aust J Plant Pathol. 35: 513-520.
36. Marongiu P, Maddau L, Frisulo S, Marras F. 2005. A multigene approach for the taxonomic determination of Pleurotus eryngii isolates. In: Tan Q, Zhang J, Chen M, Cao H, Buswell JA, editors. Mushroom Biology and Mushroom Products. Shanghai, China: Shanghai Xinhua Printing Co.; pp 89-91.
37. Maruyama T, Kawahara N, Yokoyama K, Makino Y, Fukiharu T, Goda Y. 2005. Phylogenetic relationship of psychoactive fungi based on rRNA gene for a large subunit and their identification using the TaqMan assay (II). Forens Sci Int. 163: 51-58.
38. Mayr E. 1942. Systematics and the Origin of the Species from the Viewpoint of a Zoologist. Columbia University Press: New York. 334 p.
39. Matheny PB, Wang Z, Manfred B, Curtis JM, Lim YW, Nilsson RH, Hughes KW, Hofstetter V, Ammirati JF, Schoch CL, Langer E, Langer G, McLaughlin DJ, Wilson AW, Froslev T, Ge Z-W, Kerrigan RW, Slot JC, Yang Z-L, Baroni T, Fischer M, Hosaka K, Matsuura K, Seidl MT, Vauras J, Hibbett DS. 2007. Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Mol Phylogenet Evol. 43: 430-541.
40. Moncalvo JM, Lutzoni FM, Rehner SA, Johnson J, Vilgalys R. 2000. Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. Syst Biol. 49: 278-305.
41. Mou C, Cao Y, Ma J. 1987. A new variety of Pleurotus eryngii and its cultural characters (in Chinese) Acta Mycol Sin. 6: 153-156.
42. Nei M, Li WH. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76: 5269-5273.
43. Nei M, Kumar S. 2000. Molecular Evolution and Phylogenetics. New York: Oxford University Press.
44. O'Donnell K. 1992. Ribosomal DNA internal transcribed spacers are highly divergent in the phytopathogenic ascomycete Fusarium sambuccinum (Giberella palicuris). Curr Genet. 22: 213-220.
45. Padamsee M, Matheny B, Dentinger BTM, McLaughlin DJ. 2008. The mushroom family Psathyrellaceae: Evidence for large scale polyphyly of the genus Psathyrella. Mol Phylogenet Evol. 46: 415-429.
46. Park HG, Ko HG, Kim SH, Park WO. 2004. Molecular identification of Asian isolates of medicinal mushroom Hericium erinaceum by phylogenetic analysis of nuclear ITS rDNA. J Microbiol Biotechnol. 14: 816-821.
47. Quélet L. 1872. Les Champignons du Jura e des Vosges Montbéliard (France): H. Barbier. 320 pp.
48. Rehner S. 2001. Primers for Elongation Factor 1-α (EF1-α). Insect Biocontrol Laboratory: USDA, ARS, PSI. Available from: rehner@ba.ars.usda.gov.
49. Reverberi M, Fanelli C, Della Rosa V, Marras F, Maddau L, Fabbri AA, Urbanelli S. 2000. Molecular and physiological characterisation of the Pleurotus eryngii complex. Proceedings of the 5th Congress of the European Foundation for Plant Pathology; p 37-40.
50. Ro H-S, Kim SS, Ryu JS, Jeon C-O, Lee TS, 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.
51. Rodrigues-Estrada AE, 2008. Molecular phylogeny and increases of yield and the antioxidants selenium and ergothioneine in basidiomata of Pleurotus eryngii. [Ph.D. dissertation]. The Pennsylvania State University. Available from:http://etda.libraries.edu./theses/approved/WorldWideFiles/ETD-2822/RodriquezEstradaDissertation2008.pdf
52. Rodriguez Estrada AE, Royse DJ, Jimenez-Gasco MM. 2008. Nucleotide sequence polymorphisms of the partial β-tubulin gene in two varieties of Pleurotus eryngii. Mushroom Sci. 17: 83-96,
53. Rodriguez Estrada AE, Jimenez Gasco MM, Royse DJ. 2010. Pleurotus eryngii species complex: Sequence analysis and phylogeny based on partial EF1α and RPB2 genes. Fung Biol. 114: 421-428.
54. Saitou N, Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol. 4: 406-425.
55. Sambrook J, Russell DW. 2001. Molecular Cloning: A Laboratory Manual, 3rd Edition, vol. 2. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press.
56. Sreenivasaprasad S, Brown AE, Mills PR. 1992. DNA sequence variation and interrelationships among Colletotrichum isolates causing strawberry anthracnose. Physiol Mol Plant Pathol. 41: 265-281.
57. Steward JE, Kim MS, James RL, Dumroese RK, Klopfenstein NB. 2006. Molecular characterization of Fusarium oxysporum and Fusarium commune isolates from a conifer nursery. Phytopathology 96: 1124-1133.
58. Swann EC, Taylor JW. 1995. Phylogenetic perspectives on basidiomycete systematics: evidence from the 18S rRNA gene. Can J Bot. 73:S862-S868.
59. Tamura K, Nei M. 1983. Estimation of the number of nucleotide substitutions in the control region of mithocondrial DNA in humans and chimpanzees. Mol Biol Evol. 10: 512-526.
60. Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 101: 11030-11035.
61. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 24: 1596-1599.
62. Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fisher MC. 2000. Phylogenetic species recognition and species concepts in fungi. Fung Genet Biol. 31: 21-32.
63. Tuchwell DS, Nicholson MJ, McSweeney CS, Theodorou MK, Brookman JL. 2005. The rapid assignment of ruminal fungi to presumptive genera using ITS1 and ITS2 RNA secondary structures to produce group-specific fingerprints. Microbiology 151: 1557-1567.
64. Urbanelli S, Fanelli C, Fabbri AA, Della Rosa V, Maddau L, Marras F, Reverberi M. 2002. Molecular genetic analysis of two taxa of the Pleurotus eryngii complex: P. eryngii (DC. Fr.) Quèl. var. eryngii and P. eryngii (DC. Fr.) Quèl. var. ferulae. Biol J Linn Soc. 75: 125-136.
65. Urbanelli S, Della Rosa V, Fanelli C, Fabbri AA, Reverberi M. 2003. Genetic diversity and population structure of the Italian fungi belonging to the taxa Pleurotus eryngii (DC.:Fr.) Quèl. and P. ferulae (DC.: Fr.) Quèl. Heredity 90: 253-259.
66. Urbanelli S, Della Rosa V, Punelli F, Porretta D, Reverberi M, Fabbri AA, Fanelli C. 2007. DNA-fingerprinting (AFLP and RFLP) for genotypic identification in species of the Pleurotus eryngii complex. Appl Microbiol Biotechnol. 74: 592-600.
67. Van Valen L. 1976. Ecological species, multispecies, and oaks. Taxon 25: 233-239.
68. van der Merwe M, Ericson L, Walker J, Thrall PH, Burdon JJ. 2007. Evolutionary relationships among species of Puccinia and Uromyces (Pucciniaceae, Uredinales) inferred from partial protein coding gene phylogenies. Mycol Res. 111: 163-175.
69. Venturella G. 2000. Typication of Plerurotus nebrodensis. Mycotaxon 75: 229-231.
70. Venturella G, Zervakis G, La Rocca S. 2000. Pleurotus eryngii var. elaeoselini var. nov. from Sicily. Mycotaxon 76: 419-427.
71. Venturella G, Zervakis G, Saitta A. 2002. Pleurotus eryngii var. thapsiae var. nov. from Sicily. Mycotaxon 81: 69-74.
72. Vilgalys R, Sun BL. 1994. Ancient and recent patterns of geographic speciation in the oyster mushroom Pleurotus revealed by phylogenetic analysis of ribosomal DNA sequences. Proc Natl Acad Sci USA 91: 4599-4603.
73. Vilgalys R, Smith A, Sun B, Miller OK. 1993. Intersterility groups in the Pleurotus ostreatus complex from the continental United States adjacent to Canada. Can J Bot. 71: 113-128.
74. Vinnere O. 2004. Approaches to Species Delineation in Anamorphic (mitosporic) Fungi: A Study on Two Extreme Cases. [PhD dissertation]. Acta Universitatis Upsaliensis, [Uppsala University]. 72 p. Available from: http//www.uu.se/,acta@ub.uu.se; ISSN 1104-232X ISBN 91-554-5832-7.
75. White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, MA, Gelfand DH, Sninsky JJ and White TJ, editors.) PCR protocols. A Guide to Methods and Applications. New York: Academic Press. pp 315-322.
76. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl Acid Res 18: 6531-6535.
77. Zervakis G and Balis C. 1996. A pluralistic approach in the study of Pleurotus species with emphasis on compatibility and physiology of the European morphotaxa. Mycol. Res. 100(6):717-731.
78. Zervakis G, Sourdis J, Balis C. 1994. Genetic variability and systematics of eleven Pleurotus species based on isozyme analysis. Mycol Res. 98(3):329-341.
79. Zervakis G, Katsaris P, Ioannidou E, Lahouvaris E, Philippoussis. 2001a. Facultative biotrophic basidiomycetes produce high quality edible mushrooms. Phytopathologia Mediterranea 40: 190.
80. Zervakis G, Venturella G, Papadopoulou K. 2001b. Genetic polymorphism and taxonomic infrastructure of the Pleurotus eryngii species-complex as determined by RAPD analysis, isozyme profiles and ecomorphological characters. Microbiology 147: 3183-3194.
81. Zervakis G, Moncalvo JM, Vilgalys R. 2004. Molecular phylogeny, biogeography and speciation of the mushroom species Pleurotus cystidiosus and allied taxa. Microbiology 150: 715-726.
82. Zhang J, Huang C, Li C. 2000. The cultivation of Pleurotus nebrodensis in China. In: Proceedings of the 5th International conference on Mushroom Biology and Mushroom Products, vol. 12(Suppl.):350-353.
83. Zhang J, Huang C, Ng, TB, Wang HX. 2006. Genetic polymorphism of ferula mushroom growing on Ferula sinkiangensis. Appl Microbiol Biotechnol. 71: 304-309.