A phylogenetic study of ubiquinone Q-8 species of the genera Candida, Pichia, and Citeromyces based on 18S ribosomal DNP sequence divergence

Journal of General and Applied Microbiology

Volumn 45, Issue 5, 1999, Pages 239-246

  Suzuki, Motofumi ^a   Nakase, Takashi ^a  

^a RIKEN BIORESOURCE CENTER   (Japan)

Author keywords

18S ribosomal DNA sequences; Molecular phylogeny; Q 8 forming species of Candida

Indexed keywords

FUNGAL DNA; RIBOSOME DNA; RNA 18S; UBIQUINONE;

ARTICLE; ASCOMYCETES; CANDIDA; CITEROMYCES; DNA SEQUENCE; FUNGAL GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PICHIA; SEQUENCE HOMOLOGY;

ASCOMYCOTA; CANDIDA; CANDIDA ANATOMIAE; CANDIDA ENTOMOPHILA; CANDIDA ERNOBII; CANDIDA FENNICA; CANDIDA FRUCTUS; CANDIDA GALACTA; CANDIDA GLOBOSA; CANDIDA GOTOI; CANDIDA HOMILENTOMA; CANDIDA INCOMMUNIS; CANDIDA ISHIWADAE; CANDIDA KARAWAIEWII; CANDIDA LACTISCONDENSI; CANDIDA LUSITANIAE; CANDIDA MOLISCHIANA; CANDIDA MUSAE; CANDIDA POPULI; CANDIDA RHAGII; CANDIDA SEQUANENSIS; CANDIDA SILVANORUM; CANDIDA STELLATA; CITEROMYCES; CITEROMYCES MATRITENSIS; CLAVISPORA LUSITANIAE; FRUCTUS; FUNGI; MYXOGASTRIA; PICHIA; PICHIA BURTONII; PICHIA CAPSULATA; PICHIA CELLOBIOSA; PICHIA HOLSTII; PICHIA METHANOLICA; PICHIA PASTORIS; WILLIOPSIS SALICORNIAE;

EID: 0033506310     PISSN: 00221260     EISSN: None     Source Type: Journal    
DOI: 10.2323/jgam.45.239     Document Type: Article

References (47)

1. Boidin, J., Pignal, M.-C., Lehodey, Y., Vey, A., and Abadie, F. (1964) Le genre Pichia sensu lato (Premiere Contribution). Bull. Soc. Mycol. France, 80, 396-438.
2. Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39, 783-791.
3. 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.
4. 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.
5. Hagler, A. N., Mendonça-Hagler, L. C., and Phaff, H. J. (1989) Candida populi, a new species of yeast occurring in exudates of Populus and Betula species. Int. J. Syst. Bacteriol., 39, 97-99.
6. James, S. A., Roberts, I. N., and Collins, M. D. (1998) Phylogenetic heterogeneity of the genus Williopsis as revealed by 18S rRNA gene sequences. Int. J. Syst. Bacteriol.,48, 591-596.
7. 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.
8. Kreger-van Rij, N. J. W. (1970) Endomycopsis Dekker. In The Yeasts: A Taxonomic Study, 2nd ed., ed. by Lodder, J., North-Holland, Amsterdam, pp. 166-208.
9. Kurtzman, C. P. (1984) Citeromyces Santa Maria. In The Yeasts: A Taxonomic Study, 3rd ed., ed. by Kreger-van Rij, N. J. W., Elsevier Science Publishers B. V., Amsterdam, pp. 117-119.
10. Kurtzman, C. P. (1992) DNA relatedness among phenotypically similar species of Pichia. Mycologia, 84, 72-76.
11. Kurtzman, C. P. (1993) Systematics of the ascomycetous yeasts assessed from ribosomal RNA sequence divergence. Antonie Leeuwenhoek, 63, 165-174.
12. Kurtzman, C. P. (1998) Pichia E. C. Hansen emend. Kurtzman. In The Yeasts: A Taxonomic Study, 4th ed., ed. by Kurtzman, C. P. and Fell, J. W., Elsevier Science B. V., Amsterdam, pp. 273-352.
13. 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.
14. Kurtzman, C. P. and Robnett, C. J. (1995) Molecular relationships among hyphal ascomycetous yeasts and yeastlike taxa. Can. J. Bot., 73, S824-S830.
15. 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.
16. 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.
17. Lee, J.-D. and Komagata, K. (1983) Further taxonomic study of methanol-assimilating yeasts with special reference to electrophoretic comparison of enzymes. J. Gen. Appl. Microbiol., 29, 395-416.
18. Makimura, K., Murayama, Y. S., and Yamaguchi, H. (1994) Detection of a wide range of medically important fungal species by polymerase chain reaction (PCR). J. Med. Microbiol., 40, 358-364.
19. Meyer, S. A. and Ahearn, D. G. (1983) Validation of the names of some Candida species. Mycotaxon, 17, 297-298.
20. 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.
21. Nakase, T. and Suzuki, M. (1997) Candida gotoi, new species of anamorphic yeast isolated from insect frass in bark of Japanese maple. Microbiol. Cult. Collect., 13, 109-112.
22. Nishida, H. and Sugiyama, J. (1994) Phylogeny and molecular evolution among higher fungi. Nippon Nôgeikagaku Kaishi, 68, 54-57.
23. Phaff, H. J., Miranda, M., Starmer, W. T., Tredick, J., and Barker, J. S. F. (1986) Clavispora opuntiae, a new heterothallic yeast occurring in necrotic tissue of Opuntia species. Int. J. Syst. Bacteriol., 36, 372-379.
24. Phaff, H. J. and Starmer, W. T. (1987) Yeasts associated with plants, insects and soil. In The Yeasts, Vol. 1, Biology of Yeasts, 2nd ed., ed. by Rose, A. H. and Harrison, J. S., Academic Press, London, pp. 123-180.
25. 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.
26. Saitou, N. and Nei, M. (1987) The neighbour-joining method: A new method for reconstruction phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
27. Smith, M. Th., van der Walt, J. P., Yamada, Y., and Batenburg-van der Vegte, W. H. (1989) Zygozyma suomiensis, sp. nov. (Lipomycetaceae), a new species from Finland. Antonie Leeuwenhoek, 56, 283-288.
28. Sonck, C. E. and Yarrow, D. (1969) Two new yeast species isolated in Finland. Antonie Leeuwenhoek, 35, 172-177.
29. Suzuki, M. and Nakase, T. (1998) Cellular neutral sugar compositions and ubiquinone systems of the genus Candida. Microbiol. Cult. Collect., 14, 49-62.
30. 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.
31. Van der Walt, J. P. and Scott, D. B. (1971) The yeast genus Saccharomycopsis Schiönning. Mycopathol. Mycol. Appl., 43, 279-288.
32. Van der Walt, J. P., von Arx, J. A., Ferreira, N. P., and Richards, P. D. G. (1987) Zygozyma gen. nov., a new genus of the Lipomycetaceae. Syst. Appl. Microbiol., 9, 115-120.
33. Van Uden, N. and Vidal-Leiria, M. (1970) Torulopsis Berlese. In The Yeasts: A Taxonomic Study, 2nd ed., ed. by Lodder, J., North-Holland, Amsterdam, pp. 1235-1308.
34. Von Arx, J. A. and van der Walt, J. P. (1976) The ascigerous state of Candida chodatii. Antonie Leeuwenhoek, 42, 309-314.
35. 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.
36. Wickerham, L. J. (1958) Sexual agglutination of heterothallic yeasts in diverse taxonomic areas. Science, 128, 1504-1505.
37. Wickerham, L. J. (1970a) Citeromyces Santa Maria. In The Yeasts: A Taxonomic Study, 2nd ed., ed. by Lodder, J., North-Holland, Amsterdam, pp. 121-127.
38. Wickerham, L. J. (1970b) Hansenula H. et P. Sydow. InThe Yeasts: A Taxonomic Study, 2nd ed., ed. by Lodder, J., North-Holland, Amsterdam, pp. 226-315.
39. Wickerham, L. J. and Burton, K. A. (1952) Occurrence of yeast mating types in nature. J. Bacteriol., 63, 449-451.
40. 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.
41. Yamada, Y., Maeda, K., and Mikata, K. (1994) The phylogenetic relationships of the hat-shaped ascospore-forming, nitrate-assimilating Pichia species, formerly classified in the genus Hansenula Sydow et Sydow, based on the partial sequences of 18S and 26S ribosomal RNAs (Saccharomycetaceae): The proposals of three new genera, Ogataea, Kuraishia, and Nakazawaea. Biosci. Biotechnol. Biochem., 58, 1245-1257.
42. Yamada, Y., Matsuda, M., Maeda, K., and Mikata, K. (1993) The phylogenetic relationships of species of the ascomycetous teleomorphic yeast genera Citeromyces, Pachysolen, Wingea, Lodderomyces, Pichia, Arxiozyma, Pachytichospora, and Clavispora and the anamorphic yeast genus Trigonopsis based on the partial sequences of 18S and 26S ribosomal RNAs. Bull. JFCC, 9, 79-94.
43. Yamada, Y., Matsuda, M., Maeda, K., and Mikata, K. (1995a) The phylogenetic relationships of methanol-assimilating yeasts based on the partial sequences of 18S and 26S ribosomal RNAs: The proposal of Komagataella gen. nov. (Saccharomycetaceae). Biosci. Biotechnol. Biochem., 59, 439-444.
44. Yamada, Y. and Nogawa, C. (1995) The phylogeny of the Lipomycetaceous yeasts based on the partial sequences of 18S and 26S ribosomal RNAs. Bull. Fac. Agric. Shizuoka Univ., 45, 13-23.
45. 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.
46. Yamada, Y., Okada, T., Ueshima, O., and Kondo, K. (1973) Coenzyme Q system in the classification of the ascosporogenous yeast genera Hansenula and Pichia. J. Gen. Appl. Microbiol., 19, 189-208.
47. Yamada, Y., Yano, J., Matsuda, M., Higashi, T., and Mikata, K. (1995b) The phylogeny of Williopsis salicorniae Hinzelin, Kurtzman et Smith based on the partial sequences of 18S and 26S ribosomal RNAs (Saccharomycetaceae). Biosci. Biotechnol. Biochem., 59, 945-948.