A phylogenetic study on galactose-containing Candida species based on 18S ribosomal DNA sequences

Journal of General and Applied Microbiology

Volumn 45, Issue 5, 1999, Pages 229-238

  Suzuki, Motofumi ^a   Sung Oui, Suh ^a,b   Sugita, Takashi ^a,c   Nakase, Takashi ^a  

^a RIKEN BIORESOURCE CENTER   (Japan)

^b LOUISIANA STATE UNIVERSITY   (United States)

^c MEIJI PHARMACEUTICAL UNIVERSITY   (Japan)

Author keywords

18S ribosomal DNA sequences; Galactose containing Candida species; Molecular phylogeny

Indexed keywords

FUNGAL DNA; GALACTOSE; RIBOSOME DNA; RNA 18S;

ARTICLE; CANDIDA; CANDIDA ALBICANS; CANDIDA GLABRATA; CANDIDA GUILLIERMONDII; CANDIDA KRUSEI; CANDIDA LUSITANIAE; CANDIDA PARAPSILOSIS; CANDIDA TROPICALIS; DNA SEQUENCE; FUNGAL GENETICS; GALACTOMYCES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PICHIA PASTORIS; SCHIZOSACCHAROMYCES POMBE;

APIS; ARXULA ADENINIVORANS; ARXULA TERRESTRIS; CANDIDA; CANDIDA ALBICANS; CANDIDA ANCUDENSIS; CANDIDA ANTILLANCAE; CANDIDA APICOLA; CANDIDA APIS; CANDIDA AURINGIENSIS; CANDIDA AZYMA; CANDIDA BERTAE; CANDIDA BERTAE VAR. CHILOENSIS; CANDIDA BLANKII; CANDIDA BOMBI; CANDIDA BOMBICOLA; CANDIDA BONDARZEWIAE; CANDIDA CANTARELLII; CANDIDA CASTRENSIS; CANDIDA CHIROPTERORUM; CANDIDA CIFERRII; CANDIDA DRIMYDIS; CANDIDA EDAX; CANDIDA ETCHELLSII; CANDIDA FLORICOLA; CANDIDA GALACTA; CANDIDA GEOCHARES; CANDIDA GLABRATA; CANDIDA GROPENGIESSERI; CANDIDA GUILLIERMONDII; CANDIDA HOLMII; CANDIDA INCOMMUNIS; CANDIDA INGENS; CANDIDA INSECTALENS; CANDIDA KRUSEI; CANDIDA LACTISCONDENSI; CANDIDA LUSITANIAE; CANDIDA MAGNOLIAE; CANDIDA MALTOSA; CANDIDA PALUDIGENA; CANDIDA PARAPSILOSIS; CANDIDA PARARUGOSA; CANDIDA PETROHUENSIS; CANDIDA SALMANTICENSIS; CANDIDA SANTJACOBENSIS; CANDIDA SORBOPHILA; CANDIDA SPANDOVENSIS; CANDIDA STEATOLYTICA; CANDIDA STELLATA; CANDIDA TEPAE; CANDIDA TROPICALIS; CANDIDA VACCINII; CANDIDA VALDIVIANA; CANDIDA VANDERWALTII; CANDIDA VERSATILIS; CANDIDA VINARIA; CANDIDA VISWANATHII; CLAVISPORA LUSITANIAE; DIPODASCOPSIS UNINUCLEATA; DIPODASCUS ALBIDUS; FUNGI; GALACTOMYCES; GALACTOMYCES GEOTRICHUM; GEOTRICHUM; ISSATCHENKIA ORIENTALIS; LIPOMYCES LIPOFER; MYXOGASTRIA; PICHIA GUILLIERMONDII; PICHIA PASTORIS; SACCHAROMYCES EXIGUUS; SCHIZOSACCHAROMYCES POMBE; STARMERELLA BOMBICOLA; STEPHANOASCUS CIFERRII; STEPHANOASCUS SMITHIAE; WICKERHAMIELLA DOMERCQIAE; YARROWIA LIPOLYTICA; ZYGOASCUS HELLENICUS;

EID: 0342314496     PISSN: 00221260     EISSN: None     Source Type: Journal    
DOI: 10.2323/jgam.45.229     Document Type: Article

References (67)

1. Asao, Y., Sakasai, T., and Yokotsuka, T. (1967) Shoyu koumiseibun ni kansuru kenkyu (XXVI). Shoyukoubo niyoru koumi no seisei (2) (Studies of the flavorous substances in shoyu. Part XXVI. Flavorous components produced by yeast fermentation (2)). Nippon Nôgeikagaku Kaishi, 41, 411-434 (in Japanese).
2. Barnett, J. A., Payne, R. W., and Yarrow, D. (1990) Yeasts: Characteristics and Identification, 2nd ed., Cambridge University Press, Cambridge.
3. Barns, S. M., Lane, D. J., Sogin, M. L., Bibeau, C., and Weisburg, W. G. (1991) Evolutionary relationships among pathogenic Candida species and relatives. J. Bacteriol., 173, 2250-2255.
4. Cai, J., Roberts, I. N., and Collins, M. D. (1996) Phylogenetic relationships among members of the ascomycetous yeast genera Brettanomyces, Debaryomyces, Dekkera, and Kluyveromyces deduced by small-subunit rRNA gene sequences. Int. J. Syst. Bacteriol., 46, 542-549.
5. De Hoog, G. S., Guého, E., and Smith, M. Th. (1997) Nomenclatural notes on some arthroconidial yeasts. Mycotaxon, 63, 345-347.
6. De Hoog, G. S., Smith, M. Th., and Guého, E. (1986) A revision of the genus Geotrichum and its teleomorphs. Stud. Mycol., 29, 1-131.
7. Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39, 783-791.
8. Giaménez-Jurado, G., Cidadão, A. J., and Beijn-van der Waaij, A. (1994) A novel heterothallic ascomycetous yeast species: Stephanoascus smithiae, teleomorph of Candida edax. Syst. Appl. Microbiol., 17, 237-246.
9. Golubev, W. I., Blagodatskaya, V. M., Suetin, S. O., and Trotsenko, R.Sh. (1981) Pichia inositovora and Candida paludigena, two new species of yeasts isolated from peat. Int. J. Syst. Bacteriol., 31, 91-96.
10. Gorin, P. A. J. and Spencer, J. F. T. (1970) Proton magnetic resonance spectroscopy - An aid in identification and chemotaxonomy of yeasts. Adv. Appl. Microbiol., 13, 25-89.
11. Goto, S. and Takami, H. (1986) Classification of ascoideaceous yeasts based on the electrophoretic comparison of enzymes and coenzymes Q systems. J. Gen. Appl. Microbiol., 32, 271-282.
12. Grinbergs, J. and Yarrow, D. (1970) Two new Candida species: Candida chilensis sp.n. and Candida valdiviana sp.n. Antonie Leeuwenhoek, 36, 143-148.
13. Hendriks, L., Goris, A., Van de Peer, Y., Neefs, J.-M., Vancanneyt, M., Kersters, K., Berny, J.-F., Hennebert, G. L., and De Wachter, R. (1992) Phylogenetic relationships among ascomycetes and ascomycete-like yeasts as deduced from small ribosomal subunit RNA sequences. Syst. Appl. Microbiol., 15, 98-104.
14. Hendriks, L., Goris, A., Van de Peer, Y., Neefs, J., Vancanneyt, M., Kersters, K., Hennebert, G. L., and De Wachter, R. (1991) Phylogenetic analysis of five medically important Candida species as deduced on the basis of small ribosomal subunit RNA sequences. J. Gen. Microbiol., 137, 1223-1230.
15. Kimura, M. (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol., 16, 111-120
16. Kurtzman, C. P. (1993) Systematics of the ascomycetous yeasts assessed from ribosomal RNA sequence divergence. Antonie Leeuwenhoek, 63, 165-174.
17. Kurtzman, C. P. (1998) Yarrowia van der Walt & von Arx. In The Yeasts: A Taxonomic Study, 4th ed., ed. by Kurtzman, C. P. and Fell, J. W., Elsevier Science B. V., Amsterdam, pp. 420-421
18. Kurtzman, C. P. and Robnett, C. J. (1994) Orders and families of ascosporogenous yeasts and yeast-like taxa compared from ribosomal RNA sequence similarities. In Ascomycete Systematics: Problems and Perspectives in the Nineties, ed. by Hawksworth, D. L., Plenum Press, New York, pp. 249-258.
19. Kurtzman, C. P. and Robnett, C. J. (1995) Molecular relationships among hyphal ascomycetous yeasts and yeastlike taxa. Can. J. Bot., 73, S824-S830.
20. Kurtzman, C. P. and Robnett, C. J. (1997) Identification of clinically important ascomycetous yeasts based on nucleotide divergence in the 5′ end of the large-subunit (26S) ribosomal DNA gene. J. Clin. Microbiol., 35, 1216-1223.
21. Kurtzman, C. P. and Robnett, C. J. (1998) Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie Leeuwenhoek, 73, 331-371.
22. Lee, F.-L., Lee, C.-F., Okada, S., Uchimura, T., Komagata, K., and Kozaki, M. (1993) Candida galacta comb, nov., a new combination for Candida apis var. galacta. Int. J. Syst. Bacteriol., 43, 183-184.
23. Meyer, S. A., Ahearn, D. G., and Yarrow, D. (1984) Candida Berkhout. In The Yeasts: A Taxonomic Study, 3rd revised and enlarged ed., ed. by Kreger-van Rij, N. J. W., Elsevier Science Publishers B. V., Amsterdam, pp. 585-844.
24. Meyer, S. A., Payne, R. W., and Yarrow, D. (1998) Candida Berkhout. In The Yeasts: A Taxonomic Study, 4th ed., ed. by Kurtzman, C. P. and Fell, J. W., Elsevier Science B. V., Amsterdam, pp. 454-573.
25. Middelhoven, W. J. (1993) Catabolism of benzene compounds by ascomycetous and basidiomycetous yeasts and yeastlike fungi. A literature review and an experimental approach. Antonie Leeuwenhoek, 63, 125-144.
26. Montrocher, R. (1980) Significance of immunoprecipitation in yeast taxonomy: Antigenic analyses of some species within the genus Candida. Cell. Mol. Biol., 26, 293-302.
27. Montrocher, R. (1984) Etude des affinites interspecifiqes dans le genre Candida (Levures asporogenes). Approches serologique, biochimique et mathematique. These.
28. Montrocher, R., Billon-Grand, G., and Claisse, M. (1990) Analysis of cytochromes aid co-enzymes Q in the yeast genus Candida. J. Gen. Appl. Microbiol., 36, 151-161.
29. Nakase, T. and Komagata, K. (1971) Significance of DNA base composition in the classification of yeast genus Candida. J. Gen. Appl. Microbiol., 17, 259-279.
30. Nakase, T. and Suzuki, M. (1985) Taxonomic studies on Debaryomyces hansenii (Zopf) Lodder et Kreger-van Rij and related species. I. Chemotaxonomic investigations. J. Gen. Appl. Microbiol., 31, 49-69.
31. Nishida, H. and Sugyama, J. (1994) Phylogeny and molecular evolution among higher fungi. Nippon Nôgeikagaku Kaishi, 68, 54-57.
32. Onishi, H. (1957) Studies on osmophilic yeasts. Part III. Classification of osmophilic soy and miso yeasts. Bull. Agric. Chem. Soc. Jpn., 21, 151-156.
33. Prillinger, H., Oberwinkler, F., Umile, C., Tlachac, K., Bauer, R., Dörfler, C., and Taufratzhofer, E. (1993) Analysis of cell wall carbohydrates (neutral sugars) from ascomycetous and basidiomycetous yeasts with and without derivatization. J. Gen. Appl. Microbiol., 39, 1-34.
34. Ramírez, C. and González, A. (1984a) Two new species and one variety of nitrate-utilizing mycelial Candida isolated from decayed wood in the evergreen rainy Valdivian forest of southern Chile. Mycopathologia, 88, 55-60.
35. Ramírez, C. and González, A. (1984b) Five new filamentous, glucose-fermenting Candida isolated from decayed wood in the evergreen rainy Valdivian forest of southern Chile. Mycopathologia, 88, 83-92.
36. Ramírez, C. and González, A. (1984c) Three new filamentous, fermenting Candida isolated from decayed wood in the evergreen rainy Valdivian forest of southern Chile. Mycopathologia, 88, 93-98.
37. Ramírez, C. and González, A. (1984d) Two new amycelial Candida isolated from decayed wood in the evergreen rainy Valdivian forest of southern Chile. Mycopathologia, 88, 99-103.
38. Ramírez, C. and González, A. (1984e) Candida santjacobensis and Candida ancudensis, two new species of yeasts isolated from decayed wood in the evergreen rainy Valdivian forest of southern Chile. Mycopathologia, 88, 105-109.
39. Ramírez, C. and González, A. (1984f) Two new filamentous, non fermenting Candida and a new Schizoblastosporion isolated from decayed wood in the evergreen rainy Valdivian forest of southern Chile. Mycopathologia, 88, 165-171.
40. Ramírez, C. and González, A. (1984g) Three new, non-fermenting, and nitrate-negative Candida species isolated from decayed wood in the evergreen rainy Valdivian forest of southern Chile. Mycopathologia, 88, 175-180.
41. Saitou, N. and Nei, M. (1987) The neighbour-joining method: A new method for reconstruction phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
42. Smith, M. Th. (1986) Zygoascus hellenicus gen. nov., sp. nov., the teleomorph of Candida hellenica (=C. inositophila-C. steatolytica). Antonie Leeuwenhoek, 52, 25-37.
43. Spencer, J. F. T. and Gorin, P. A. J. (1969) Systematics of the genus Candida Berkhout: Proton magnetic resonance spectra of the mannans and riannose-containing polysaccharides as an aid in classification. Antonie Leeuwenhoek, 35, 33-44.
44. Spencer, J. F. T. and Gorin, P. A. J. (1970) Systematics of the genus Torulopsis: Proton magnetic resonance spectra of the mannose-containing polysaccharides as an aid in classification. Antonie Leeuwenhoek, 36, 509-524.
45. Spencer, J. F. T. and Gorin, P. A. J. (1971) Systematics of the genus Candida Berkhout: Proton magnetic resonance spectra of the mannose-containing polysaccharides of some further species of Candida as an aid in classification. Antonie Leeuwenhoek, 37, 75-88.
46. Suzuki, M. and Nakase, T. (1998) Cellular neutral sugar compositions and ubiquinone systems of the genus Candida. Microbiol. Cult. Collect., 14, 49-62.
47. Suzuki, M., Nakase, T., Mori, H., Toriumi, H., and Kurtzman, C. P. (1992) Chemotaxonomic study on halophilic/halotolerant yeasts in the matured soy sauce mashes. Bull. JFCC, 8, 18-27.
48. Takashima, M., Suh, S.-O., and Nakase, T. (1995) Phylogenetic relationships among species of the genus Bensingtonia and related taxa based on the small subunit ribosomal DNA sequences. J. Gen. Appl. Microbiol., 41, 131-141.
49. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
50. Tokuoka, K., Ishitani, T., Goto, S., and Komagata, K. (1985) Identification of yeasts isolated from high-sugar foods. J. Gen. Appl. Microbiol., 31, 411-427.
51. Tokuoka, K., Ishitani, T., Goto, S., and Komagata, K. (1987) Four new yeast species belonging to the genus Candida. J. Gen. Appl. Microbiol., 33, 1-10.
52. Tsuchiya, T., Fukazawa, Y., and Kawakita, S. (1965) Significance of serological studies on yeasts. Mycopathol. Mycol. Appl., 26, 1-15.
53. Van der Walt, J. P. and Liebenberg, N. V. D. W. (1973) The yeast genus Wickerhamiella gen. nov. (Ascomycetes). Antonie Leeuwenhoek, 39, 121-128.
54. Van der Walt, J. P., Smith, M. Th., and Yamada, Y. (1990) Arxula gen. nov. (Candidaceae), a new anamorphic, arthroconidial yeast genus. Antonie Leeuwenhoek, 57, 59-61.
55. Van der Walt, J. P. and van Kerken, A. E. (1961) Candida ingens nov. spec. Antonie Leeuwenhoek, 27, 284-286.
56. Viljoen, B. C. and Kock, J. L. F. (1989) A taxonomic study of the yeast genus Candida Berkhout. Syst. Appl. Microbiol., 12, 91-102.
57. Von Arx, J. A. and Weijman, A. C. M. (1979) Conidiation and carbohydrate composition in some Candida and Torulopsis species. Antonie Leeuwenhoek, 45, 547-555.
58. Weijman, A. C. M. (1977) Carbohydrate composition and taxonomy of the genus Dipodascus. Antonie Leeuwenhoek, 43, 323-331.
59. Weijman, A. C. M. (1979) Carbohydrate composition and taxonomy of Geotrichum, Trichosporon and allied genera. Antonie Leeuwenhoek, 45, 119-127.
60. Weijman, A. C. M. and Rodrigues de Miranda, L. (1988) Carbohydrate patterns of Candida, Cryptococcus and Rhodotorula species. Antonie Leeuwenhoek, 54, 535-543.
61. Weijman, A. C. M., Rodrigues de Miranda, L., and van der Walt, J. P. (1988) Redefinition of Candida Berkhout and the consequent emendation of Cryptococcus Kützing and Rhodotorula Harrison. Antonie Leeuwenhoek, 54, 545-553.
62. Weijman, A. C. M. and van der Walt, J. P. (1989) Carbohydrate profiles and the taxonomic concept of the Lipomycetaceae. Stud. Mycol., 31, 193-199.
63. Wilmotte, A., Van de Peer, Y., Goris, A., Chapelle, S., De Baere, R., Nelissen, B., Neefs, J.-M., Hennebert, G. L., and De Wachter, R. (1993) Evolutionary relationships among higher fungi inferred from small ribosomal subunit RNA sequence analysis. Syst. Appl. Microbiol., 16, 436-444.
64. Yamada, Y. and Kondo, K. (1972) Taxonomic significance of coenzyme Q system in yeasts and yeast-like fungi (1). In Yeasts. Models in Science and Technics. Proc. 1st Spec. Int. Symp. on Yeasts, ed. by Kocková-Kratochvilová, A. and Minarik, E., Slovak Academy of Sciences, Bratislava, pp. 363-372.
65. Yamada, Y. and Nogawa, C. (1990) The molecular phylogeny of the ascomycetous anamorphic yeast genus Arxula van der Walt, Smith et Yamada based on the partial sequences of 18S and 26S ribosomal ribonucleic acids. J. Gen. Appl. Microbiol., 36, 425-434.
66. Yamada, Y., Nojiri, M., Matsuyama, M., and Kondo, K. (1976) Coenzyme Q system in the classification of the ascosporogenous yeast genera Debaryomyces, Saccharomyces, Kluyveromyces, and Endomycopsis. J. Gen. Appl. Microbiol., 22, 325-337.
67. Yamada, Y., Yano, J., Matsuda, M., and Mikata, K. (1994) The phylogeny of anamorphic yeast species classified in the genus Candida Berkhout based on the partial sequences of 18S and 26S ribosomal RNAs. Bull. Fac. Agric. Shizuoka Univ., 44, 21-28.