Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis

International Journal of Systematic and Evolutionary Microbiology

Volumn 50, Issue 3, 2000, Pages 1351-1371

  Fell, Jack W ^a   Boekhout, Teun ^b   Fonseca, Alvaro ^c   Scorzetti, Gloria ^a   Statzell Tallman, Adele ^a  

^a UNIVERSITY OF MIAMI   (United States)

^b CBS KNAW FUNGAL BIODIVERSITY CENTRE   (Netherlands)

^c UNIVERSIDADE NOVA DE LISBOA   (Portugal)

Author keywords

Hymenomycetes; Trichosporonales ord. nov.; Urediniomycetes; Ustilaginomycetes; Yeasts

Indexed keywords

RIBOSOME DNA;

ANALYTIC METHOD; ARTICLE; BASIDIOMYCETES; BIODIVERSITY; CONTROLLED STUDY; DNA DETERMINATION; HYMENOMYCETES; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; TAXONOMY; UNINDEXED SEQUENCE; UREDINIOMYCETES; USTILAGINOMYCETES;

AGARICOSTILBUM; BASIDIOMYCOTA; BENSINGTONIA; BULLERA; CRYPTOCOCCUS; CYSTOFILOBASIDIALES; CYSTOFILOBASIDIUM; ERYTHROBASIDIUM; FELLOMYCES; FILOBASIDIALES; FILOBASIDIELLA; FILOBASIDIUM; FUNGI; HYMENOMYCETES; KONDOA; KURTZMANOMYCES; LEUCOSPORIDIUM; MALASSEZIALES; MICROBOTRYUM; MICROSTROMATALES; RHODOSPORIDIUM; RHODOTORULA; SPORIDIOBOLUS; TREMELLALES; TRICHOSPORONALES; UDENIOMYCES; UREDINIOMYCETES; USTILAGINALES; USTILAGINOMYCETES;

EID: 0034115579     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/00207713-50-3-1351     Document Type: Article

References (72)

1. Bandoni, R. J. (1995). Dimorphic Heterobasidiomycetes: taxonomy and parasitism. Stud Mycol 39, 13-28.
2. Barnett, J. A., Paine, R. W. & Yarrow, D. (1990). Yeasts: Characteristics and Identification, 2nd edn. Cambridge: Cambridge University Press.
3. Bauer, R. & Oberwinkler, F. (1991). The colacosomes: new structures at the host parasite interface of a mycoparasitic basidiomycete. Bot Acta 104, 53-57.
4. Bauer, R., Oberwinkler, F. & Deml, G. (1989). Ultrastruktur der Basidiensepten phragmobasidialer Brandpilz. Z Mykol 55, 163-168.
5. Bauer, R., Oberwinkler, F. & Vanky, K. (1997). Ultrastructural markers and systematics in smut fungi and allied taxa. Can J Bot 75, 1273-1314.
6. Begerow, D., Bauer, R. & Oberwinkler, F. (1997). Phylogenetic studies on the nuclear large subunit ribosomal DNA of smut fungi and related taxa. Can J Bot 75, 2045-2056.
7. Begerow, D., Bauer, R. & Boekhout, T. (1999). Phylogenetic placements of Ustilaginomycetous anamorphs as deduced from nuclear LSU rDNA sequences. Mycol Res (in press).
8. Boekhout, T. & Nakase, T. (1998). Bullera Derx. In The Yeasts, a Taxonomic Study, 4th edn, pp. 731-741. Edited by C. P. Kurtzman & J. W. Fell. Amsterdam: Elsevier.
9. Boekhout, T., Fonseca, A. & Batenburg-van der Vegte, W. H. (1991). Bulleromyces genus novum (Tremellales) a teleomorph for Bullera alba, and the occurrence of mating in Bullera variabilis. Antonie Leeuwenhoek 59, 81-93.
10. Boekhout, T., Yamada, Y., Weijman, A. C. M., Roeijmans, H. J. & Batenburg-van der Vegte, W. H. (1992). The significance of coenzyme Q, carbohydrate composition and septal ultrastructure for the taxonomy of ballistoconidia-forming yeasts and fungi. Syst Appl Microbiol 15, 1-10.
11. Boekhout, T., Fell, J. W. & O'Donnell, K. (1995). Molecular systematics of some yeast-like anamorphs belonging to the Ustilaginales and Tilletiales. Stud Mycol 38, 175-183.
12. Boekhout, T., Belkum, A., van Leenders, A. C., Verbrugh, H. A., Mukamurangwa, P., Swinne, D. & Scheffers, W. A. (1997). Molecular typing of Cryptococcus neoformans: taxonomic and epidemiological aspects. Int J Syst Bacteriol 47, 432-442.
13. Boekhout, T., Bandoni, R. J., Fell, J. W. & Kwon-Chung, K. J. (1998). Discussion of teleomorphic and anamorphic genera of heterobasidiomycetous yeasts. In The Yeasts, a Taxonomic Study, 4th edn, pp. 609-626. Edited by C. P. Kurtzman & J. W. Fell. Amsterdam: Elsevier.
14. Chen, C. (1998). Morphological and molecular studies in the genus Tremella. Bibl Mycol 174, 1-225.
15. Diaz, M. R. & Fell, J. W. (2000). Systematics of psychrophilic yeasts in the genus Mrakia based on ITS and IGS rDNA sequence analysis. Autonie Leeuwenhoek 77, 7-12.
16. Dietrichson, E. (1954). Étude d'une collection norvégienne de levures. Ann Parasitol Hum Comp 29, 271-288, 460-498.
17. Fan, M., Currie, B. P., Gutell, R. R., Ragan, M. A. & Casadevall, A. (1994). The 16S-like, 5.8S and 23S-like rRNAs of the two varieties of Cryptococcus neoformans: sequence, secondary structure, phylogenetic analysis and restriction fragment polymorphisms. J Med Vet Mycol 32, 163-180.
18. Fell, J. W. (1995). rDNA targeted oligonucleotide primers for the identification of pathogenic yeasts in a polymerase chain reaction. J Ind Microbiol 14, 475-477.
19. Fell, J. W. & Blatt, G. (1999). Separation of strains of the yeasts Xanthophyllomyces dendrorhous and Phaffia rhodozyma based on rDNA IGS and ITS sequence analysis. J Ind Microbiol Biotechnol 21, 677-681.
20. Fell, J. W. & Kurtzman, C. P. (1990). Nucleotide sequence analysis of a variable region of the large subunit rRNA for identification of marine occurring yeasts. Curr Microbiol 21, 295-300.
21. Fell, J. W. & Statzell-Tallman, A. (1998). Cryptococcus Vuillemin. In The Yeasts, a Taxonomic Study, 4th edn, pp. 472-767. Edited by C. P. Kurtzman & J. W. Fell. Amsterdam: Elsevier.
22. Fell, J. W., Boekhout, T. & Freshwater, D. W. (1995). The role of nucleotide analysis in the systematics of the yeast genera Cryptococcus and Rhodotorula. Stud Mycol 38, 129-146.
23. Fell, J. W., Roeijmans, H. & Boekhout, T. (1999). Cystofilobasidiales, a new order of basidiomycetous yeasts. Int J Syst Bacteriol 49, 907-913.
24. Fonseca, A., Sampaio, J. P., Inacio, J. & Fell, J. W. (2000a). Emendation of the basidiomycetous yeast genus Kondoa and the description of Kondoa aeria sp. nov. Antonie Leeuwenhoek (in press).
25. Fonseca, A., Scorzetti, G. & Fell, J. W. (2000b). Diversity in the yeasts Cryptococcus albidus and related species as revealed by ribosomal DNA sequence analysis. Can J Microbiol 46, 7-27.
26. Golubev, W. I. (1999). Mastigobasidium, a new teleomorphic genus for the perfect state of ballistosporous yeast Bensingtonia intermedia. Int J Syst Bacteriol 49, 1301-1305.
27. Goto, S. (1963). On a new yeast genus Naganishia. J Ferment Technol 41, 459-462.
28. Guého, E., Kurtzman, C. P. & Peterson, S. W. (1989). Evolutionary affinities of heterobasidiomycetous yeasts estimated from 18S and 25S ribosomal RNA sequence divergence. Syst Appl Microbiol 12, 230-236.
29. Guého, E., Smith, M. Th., de Hoog, G. S., Billon-Grand, G., Christen, R. & Batenburg-van der Vegte, W. H. (1992). Contributions to a revision of the genus Trichosporon. Antonie Leeuwenhoek 61, 289-316.
30. Guého, E., Improvisi, L., Christen, R. & de Hoog, G. S. (1993). Phylogenetic relationships of Cryptococcus neoformans and some related basidiomycetous yeasts determined from partial large subunit rRNA sequences. Antonie Leeuwenhoek 63, 175-189.
31. Guého, E., Midgley, G. & Guillot, J. (1996). The Genus Malassezia with descriptions of four new species. Antonie Leeuwenhoek 69, 337-355.
32. Guillot, J. & Guého, E. (1995). The diversity of Malassezia yeasts confirmed by rRNA sequence and nuclear DNA comparisons. Antonie Leeuwenhoek 67, 297-314.
33. Hamamoto, M., Sugiyama, J. & Komagata, K. (1987). DNA-DNA reassociation studies of strains in the genera Rhodosporidium and Rhodotorula. J Gen Appl Microbiol 33, 57-63.
34. Haynes, K. A., Westerneng, T. J., Fell, J. W. & Moens, W. (1995). Detection and identification of pathogenic fungi by polymerase chain reaction amplification of large subunit ribosomal DNA. J Med Vet Mycol 33, 319-325.
35. Ikeda, R., Shinoda, T., Fukazawa, Y. & Kaufman, L. (1982). Antigenic characterization of Cryptococcus neoformans serotypes and its application to serotyping of clinical isolates. J Clin Microbiol 16, 22-29.
36. Johnson, E. A. & Phaff, H. J. (1978). Rhodotorula fujisanensis, a new taxonomic combination. Curr Microbiol 1, 223-225.
37. Kreger-van Rij, N. J. W. & Veenhuis, M. (1971). A comparative study of the cell wall structure of basidiomycetous and related yeasts. J Gen Microbiol 68, 87-95.
38. Kurtzman, C. P. & Fell, J. W. (1998). The Yeasts, a Taxonomic Study, 4th edn. Amsterdam: Elsevier.
39. Kwon-Chung, K. J. (1998). Filobasidiella Kwon-Chung. In The Yeasts, a Taxonomic Study, 4th edn, pp. 656-662. Edited by C. P. Kurtzman & J. W. Fell. Amsterdam: Elsevier.
40. McLaughlin, E., Frieders, M. & Lu, H. (1995). A microscopist's view of heterobasidiomycete phylogeny. Stud Mycol 38, 91-110.
41. Magee, B. B., D'Souza, T. M. & Magee, P. T. (1987). Strain and species identification by restriction fragment length polymorphisms in the ribosomal DNA repeat of Candida species. J Bacteriol 169, 1639-1643.
42. Mannarelli, B. M. & Kurtzman, C. P. (1998). Rapid identification of Candida albicans and other human pathogenic yeasts by using short oligonucleotides in a PCR. J Clin Microbiol 36, 1634-1641.
43. Mitchell, T. G., Freedman, E. Z., White, T. J. & Taylor, J. W. (1994). Unique oligonucleotide primers in PCR for identification of Cryptococcus neoformans. J Clin Microbiol 32, 253-255.
44. Moore, R. T. (1980). Taxonomic proposals for the classification of marine yeasts and other yeast-like fungi including the smuts. Bot Mar 23, 361-373.
45. Moore, R. T. (1998). Cytology and ultrastructure of yeasts and yeast-like fungi. In The Yeasts, a Taxonomic Study, 4th edn, pp. 33-44. Edited by C. P. Kurtzman & J. W. Fell. Amsterdam: Elsevier.
46. Nakase, T., Takematsu, A. & Yamada, Y. (1993). Molecular approaches to the taxonomy of ballistosporous yeasts based on the analysis of the partial nucleotide sequences of 18S ribosomal ribonucleic acids. J Gen Appl Microbiol 39, 107-134.
47. O'Donnell, K. L. & McLaughlin, D. J. (1984). Ultrastructure of meiosis in Ustilago maydis. Mycologia 76, 468-485.
48. Prillinger, H., Dörfler, C., Laaser, G. & Hauska, G. (1990). Ein Beitrag zur Systematik und Entwicklungsbiologie Höherer Pilze: Hefe-Typen der Basidiomyceten. Teil III: Ustilago-Typ. Z Mykol 56, 251-278.
49. Prillinger, H., Deml, G., Dörfler, C., Laaser, G. & Lockau, W. (1991). Ein Beitrag zur Systematik und Entwicklungsbiologie Höherer Pilze: Hefe-Typen der Basidiomyceten. Teil II: Microbotryum-Typ. Bot Acta 104, 5-17.
50. Prillinger, H., Oberwinkler, F., Umile, C., Tlachac, K., Bauer, R., Dörfler, C. & Taufratzhofer, E. (1993). Analysis of cell wall carbohydrates (neutral sugars) from ascomycetous and basidiomycetous yeasts with and without derivatization. J Gen Appl Microbiol 39, 1-14.
51. Roeijmans, H., Prillinger, H., Umile, C., Sugiyama, J., Nakase, T. & Boekhout, T. (1998). Analysis of carbohydrate composition of cell walls and extracellular carbohydrates. In The Yeasts, a Taxonomic Study, 4th edn, pp. 99-101. Edited by C. P. Kurtzman & J. W. Fell. Amsterdam: Elsevier.
52. Sampaio, J. P. & Fonseca, A. (1995). Physiological aspects in the systematics of heterobasidiomycetous yeasts. Stud Mycol 38, 29-46.
53. Sampaio, J. P., Bauer, R., Begerow, D. & Oberwinkler, F. (1999). Occultifur externus sp. nov., a new species of simple-pored auricularioid heterobasidiomycete from plant litter in Portugal. Mycologia 91, 1094-1104.
54. Shinoda, T., Ikeda, R., Nishikawa, A. & Fukazawa, Y. (1980). The serological, chemical and physiochemical analyses of cryptococcal capsular polysaccharides. Jpn J Med Mycol 21, 230-238.
55. Simmons, R. B. & Ahearn, D. G. (1987). Cell wall ultrastructure and diazonium blue B reaction of Sporopachydermia quercuum, Bullera tsugae, and Malassezia spp. Mycologia 79, 38-43.
56. Statzell-Tallman, A. & Fell, J. W. (1998). Leucosporidium Fell et al. In The Yeasts, a Taxonomic Study, 4th edn, pp. 670-675. Edited by C. P. Kurtzman & J. W. Fell. Amsterdam: Elsevier.
57. Sugita, T., Nishikawa, A. & Shinoda, T. (1992). DNA relatedness among three varieties of Cryptococcus albidus. J Gen Appl Microbiol 38, 83-86.
58. Sugiyama, J. & Suh, S.-O. (1993). Phylogenetic analysis of basidiomycetous yeasts inferred from small subunit ribosomal DNA sequence. J Gen Microbiol 139, 1595-1598.
59. Suh, S.-O. & Nakase, T. (1995). Phylogenetic analysis of the ballistosporogenous anamorphic genera Udeniomyces and Bullera, and related basidiomycetous yeasts, based on 18S rDNA sequence. Microbiology 141, 901-906.
60. Suh, S.-O. & Sugiyama, J. (1993). Phylogeny among the basidiomycetous yeasts inferred from small subunit ribosomal DNA sequence. J Gen Microbiol 139, 1595-1598.
61. Swann, E. A. & Taylor, J. W. (1995a). Phylogenetic diversity of yeast-producing basidiomycetes. Mycol Res 99, 1205-1210.
62. Swann, E. A. & Taylor, J. W. (1995b). Toward a phylogenetic systematics of the Basidiomycota: integrating yeasts and filamentous basidiomycetes using 18S rRNA gene sequences. Stud Mycol 38, 147-162.
63. Swann, E. A. & Taylor, J. W (1995c). Phylogenetic perspectives on basidiomycete systematics: evidence from the 18S rRNA gene. Can J Bot (suppl. 1) 73, S862-S868.
64. Swann, E. C., Frieders, E. M. & McLaughlin, D. J. (1999). Microbotryum, Kriegeria and the changing paradigm in basidiomycete classification. Mycologia 91, 51-66.
65. Vancanneyt, M., Coopman, R., Tytgat, R., Hennebert, G. L. & Kersters, K. (1994). Whole-cell protein patterns, DNA base compositions and coenzyme Q types in the yeast genus Cryptococcus Kützing and related taxa. Syst Appl Microbiol 17, 65-75.
66. Van de Peer, Y., Hendriks, L., Goris, A., Neefs, J. M., Vancanneyt, M., Kersters, K., Berny, J. F., Hennebert, G. L. & De Wachter, R. (1992). Evolution of basidiomycetous yeasts as deduced from small ribosomal subunit RNA sequences. Syst Appl Microbiol 15, 250-258.
67. Vaughan-Martini, A. (1991). Intraspecific discontinuity within the yeast species Cryptococcus albidus as revealed by nDNA/nDNA reassociation. Exp Mycol 15, 140-145.
68. Walsh, T. J., Francesconi, A., Kasai, M. & Chanock, S. J. (1995). PCR and single-strand conformational polymorphism for recognition of medically important opportunistic fungi. J Clin Microbiol 33, 3216-3220.
69. Weijman, A. C. M. & Golubev, W. I. (1987). Carbohydrate patterns and taxonomy of yeasts and yeast-like fungi. Stud Mycol 30, 361-371.
70. Wells, K. (1994). Jelly fungi, then and now! Mycologia 86, 18-48.
71. Yamada, Y. & Kawasaki, H. (1989). The molecular phylogeny of the Q8-equipped basidiomycetous yeasts genera Mrakia Yamada et Komagata and Cystofilobasidum Oberwinkler et Bandoni based on the partial sequences of 18S and 26S ribosomal ribonucleic acids. J Gen Appl Microbiol 35, 173-183.
72. Yamada, Y. & Nakagawa, Y. (1992). The phylogenetic relationships of some heterobasidiomycetous yeast species based on the partial sequences of 18S and 26S ribosomal RNAs. J Gen Appl Microbiol 38, 559-565.