1887

Abstract

Detection, identification and classification of yeasts have undergone a major transformation in the past decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined gene sequences from domains 1 and 2 (D1/D2) of large subunit rRNA and from the internal transcribed spacer (ITS) now permits many laboratories to identify species accurately and this has led to a doubling in the number of known species of yeasts over the past decade. Phylogenetic analysis of gene sequences has resulted in major revision of yeast systematics, resulting in redefinition of nearly all genera. Future work calls for application of genomics to refine our understanding of the species concept and to provide a better understanding of the boundaries of genera and higher levels of classification. This increased understanding of phylogeny is expected to allow prediction of the genetic potential of various clades and species for biotechnological applications and adaptation to environmental changes.

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2014-02-01
2019-10-17
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References

  1. Berbee M. L. , Taylor J. W. . ( 1993; ). Ascomycete relationships: dating the origin of asexual lineages with 18S ribosomal RNA gene sequence data. . In The Fungal Holomorph: Mitotic, Meiotic and Pleomorphic Speciation in Fungal Systematics, pp. 67–78. Edited by Reynolds D. R. , Taylor J. W. . . Wallingford:: CAB International;.
    [Google Scholar]
  2. Boekhout T. , Fonseca Á. , Sampaio J. P. , Bandoni R. J. , Fell J. W. , Kwon-Chung K. J. . ( 2011; ). Discussion of teleomorphic and anamorphic basidiomycetous yeasts. . In The Yeasts, a Taxonomic Study, , 5th edn., pp. 1339–1372. Edited by Kurtzman C. P. , Fell J. W. , Boekhout T. . . Amsterdam:: Elsevier;. [CrossRef]
    [Google Scholar]
  3. Cain R. F. . ( 1972; ). Evolution of the fungi. . Mycologia 64:, 1–14. [CrossRef]
    [Google Scholar]
  4. Cregg J. M. , Madden K. R. . ( 1988; ). Development of the methylotrophic yeast, Pichia pastoris, as a host system for the production of foreign proteins. . Dev Ind Microbiol 29:, 33–41.
    [Google Scholar]
  5. Daniel H. M. , Sorrell T. C. , Meyer W. . ( 2001; ). Partial sequence analysis of the actin gene and its potential for studying the phylogeny of Candida species and their teleomorphs. . Int J Syst Evol Microbiol 51:, 1593–1606.[PubMed]
    [Google Scholar]
  6. Fell J. W. , Boekhout T. , Fonseca Á. , Scorzetti G. , Statzell-Tallman A. . ( 2000; ). Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis. . Int J Syst Evol Microbiol 50:, 1351–1371. [CrossRef] [PubMed]
    [Google Scholar]
  7. Fitzpatrick D. A. , Logue M. E. , Stajich J. E. , Butler G. . ( 2006; ). A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. . BMC Evol Biol 6:, 99–113. [CrossRef] [PubMed]
    [Google Scholar]
  8. Fonseca Á. , Boekhout T. , Fell J. W. . ( 2011; ). Cryptococcus Vuillemin (1901). . In The Yeasts, a Taxonomic Study, , 5th edn., pp. 1661–1737. Edited by Kurtzman C. P. , Fell J. W. , Boekhout T. . . Amsterdam:: Elsevier;. [CrossRef]
    [Google Scholar]
  9. Groth C. , Hansen J. , Piskur J. . ( 1999; ). A natural chimeric yeast containing genetic material from three species. . Int J Syst Bacteriol 49:, 1933–1938. [CrossRef] [PubMed]
    [Google Scholar]
  10. Guilliermond A. . ( 1912; ). Les Levures. Encyclopédie Scientifique. Paris:: O. Doin et Fils;.
    [Google Scholar]
  11. Hawksworth D. L. , Crous P. W. , Redhead S. A. , Reynolds D. R. , Samson R. A. , Seifert K. A. , Taylor J. W. , Wingfield M. J. , Abaci O. . & other authors ( 2011; ). The Amsterdam declaration on fungal nomenclature. . IMA Fungus 2:, 105–112. [CrossRef] [PubMed]
    [Google Scholar]
  12. James T. Y. , Kauff F. , Schoch C. L. , Matheny P. B. , Hofstetter V. , Cox C. J. , Celio G. , Gueidan C. , Fraker E. . & other authors ( 2006; ). Reconstructing the early evolution of Fungi using a six-gene phylogeny. . Nature 443:, 818–822. [CrossRef] [PubMed]
    [Google Scholar]
  13. Johnson E. A. , Echavarri-Erasun C. . ( 2011; ). Yeast Biotechnology. . In The Yeasts, a Taxonomic Study, , 5th edn., pp. 21–44. Edited by Kurtzman C. P. , Fell J. W. , Boekhout T. . . Amsterdam:: Elsevier;. [CrossRef]
    [Google Scholar]
  14. Kluyver A. J. , van Niel C. B. . ( 1924; ). Über Spiegelbilder erzeugende Hefenarten und die neue Hefengattung Sporobolomyces . . Zentralbl Bakteriol Parasitenkd (Abt. II) 63:, 1–20.
    [Google Scholar]
  15. Kluyver A. J. , van Niel C. B. . ( 1927; ). Sporobolomyces: ein Basidiomyzet?. Ann Mycol 25:, 389–394.
    [Google Scholar]
  16. Kuramae E. E. , Robert V. , Snel B. , Boekhout T. . ( 2006a; ). Conflicting phylogenetic position of Schizosaccharomyces pombe . . Genomics 88:, 387–393. [CrossRef] [PubMed]
    [Google Scholar]
  17. Kuramae E. E. , Robert V. , Snel B. , Weiß M. , Boekhout T. . ( 2006b; ). Phylogenomics reveal a robust fungal tree of life. . FEMS Yeast Res 6:, 1213–1220. [CrossRef] [PubMed]
    [Google Scholar]
  18. Kurtzman C. P. . ( 2011; ). Discussion of teleomorphic and anamorphic ascomycetous yeasts and yeast-like taxa. . In The Yeasts, a Taxonomic Study, , 5th edn., pp. 293–307. Edited by Kurtzman C. P. , Fell J. W. , Boekhout T. . . Amsterdam:: Elsevier;. [CrossRef]
    [Google Scholar]
  19. Kurtzman C. P. . ( 2012; ). Citeromyces hawaiiensis sp. nov., an ascosporic yeast associated with Myoporum sandwicense . . Int J Syst Evol Microbiol 62:, 1215–1219. [CrossRef] [PubMed]
    [Google Scholar]
  20. Kurtzman C. P. , 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, pp. 249–258. Edited by Hawksworth D. L. . . New York:: Plenum Press;.[CrossRef]
    [Google Scholar]
  21. Kurtzman C. P. , Robnett C. J. . ( 1998; ). Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. . Antonie van Leeuwenhoek 73:, 331–371. [CrossRef] [PubMed]
    [Google Scholar]
  22. Kurtzman C. P. , Robnett C. J. . ( 2003; ). Phylogenetic relationships among yeasts of the ‘Saccharomyces complex’ determined from multigene sequence analyses. . FEMS Yeast Res 3:, 417–432. [CrossRef] [PubMed]
    [Google Scholar]
  23. Kurtzman C. P. , Robnett C. J. . ( 2007; ). Multigene phylogenetic analysis of the Trichomonascus, Wickerhamiella and Zygoascus yeast clades, and the proposal of Sugiyamaella gen. nov. and 14 new species combinations. . FEMS Yeast Res 7:, 141–151. [CrossRef] [PubMed]
    [Google Scholar]
  24. Kurtzman C. P. , Robnett C. J. . ( 2010; ). Systematics of methanol assimilating yeasts and neighboring taxa from multigene sequence analysis and the proposal of Peterozyma gen. nov., a new member of the Saccharomycetales . . FEMS Yeast Res 10:, 353–361. [CrossRef] [PubMed]
    [Google Scholar]
  25. Kurtzman C. P. , Robnett C. J. . ( 2013; ). Relationships among genera of the Saccharomycotina (Ascomycota) from multigene phylogenetic analysis of type species. . FEMS Yeast Res 13:, 23–33. [CrossRef] [PubMed]
    [Google Scholar]
  26. Kurtzman C. P. , Suzuki M. . ( 2010; ). Phylogenetic analysis of ascomycete yeasts that form coenzyme Q-9 and the proposal of the new genera Babjeviella, Meyerozyma, Millerozyma, Priceomyces and Scheffersomyces . . Mycoscience 51:, 2–14. [CrossRef]
    [Google Scholar]
  27. Kurtzman C. P. , Albertyn J. , Basehoar-Powers E. . ( 2007; ). Multigene phylogenetic analysis of the Lipomycetaceae and the proposed transfer of Zygozyma species to Lipomyces and Babjevia anomala to Dipodascopsis . . FEMS Yeast Res 7:, 1027–1034. [CrossRef] [PubMed]
    [Google Scholar]
  28. Kurtzman C. P. , Robnett C. J. , Basehoar-Powers E. . ( 2008; ). Phylogenetic relationships among species of Pichia, Issatchenkia and Williopsis determined from multigene phylogenetic analysis and the proposal of Barnettozyma gen. nov., Lindnera gen. nov. and Wickerhamomyces gen. nov.. FEMS Yeast Res 8:, 939–954. [CrossRef] [PubMed]
    [Google Scholar]
  29. Kurtzman C. P. , Fell J. W. , Boekhout T. . (editors) ( 2011; ). The Yeasts: a Taxonomic Study, , 5th edn.. Amsterdam:: Elsevier;.
    [Google Scholar]
  30. Lachance M. A. , Kurtzman C. P. . ( 2013; ). The yeast genus Tortispora gen. nov., description of Tortispora ganteri sp. nov., Tortispora mauiana f. a., sp. nov., Tortispora agaves f. a., sp. nov., Tortispora sangerardonensis f. a., sp. nov., Tortispora cuajiniquilana f. a., sp. nov., Tortispora starmeri f. a., sp. nov. and Tortispora phaffii f. a., sp. nov., reassignment of Candida caseinolytica to Tortispora caseinolytica f. a., comb. nov., emendation of Botryozyma, and assignment of Botryozyma, Tortispora gen. nov. and Trigonopsis to the family Trigonopsidaceae fam. nov.. Int J Syst Evol Microbiol 63:, 3104–3114. [CrossRef] [PubMed]
    [Google Scholar]
  31. Lachance M. A. , Pang W. M. . ( 1997; ). Predacious yeasts. . Yeast 13:, 225–232. [CrossRef] [PubMed]
    [Google Scholar]
  32. Lachance M. A. , Pupovac-Velikonja A. , Natarajan S. , Schlag-Edler B. . ( 2000; ). Nutrition and phylogeny of predacious yeasts. . Can J Microbiol 46:, 495–505. [CrossRef] [PubMed]
    [Google Scholar]
  33. Lachance M. A. , Daniel H. M. , Meyer W. , Prasad G. S. , Gautam S. P. , Boundy-Mills K. . ( 2003; ). The D1/D2 domain of the large-subunit rDNA of the yeast species Clavispora lusitaniae is unusually polymorphic. . FEMS Yeast Res 4:, 253–258. [CrossRef] [PubMed]
    [Google Scholar]
  34. Lachance M. A. , Boekhout T. , Scorzetti G. , Fell J. W. , Kurtzman C. P. . ( 2011; ). Candida Berkhout. . In The Yeasts, a Taxonomic Study, , 5th edn., pp. 987–1278. Edited by Kurtzman C. P. , Fell J. W. , Boekhout T. . . Amsterdam:: Elsevier;. [CrossRef]
    [Google Scholar]
  35. Liu Y. , Leigh J. W. , Brinkmann H. , Cushion M. T. , Rodriguez-Ezpeleta N. , Philippe H. , Lang B. F. . ( 2009; ). Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts. . Mol Biol Evol 26:, 27–34. [CrossRef] [PubMed]
    [Google Scholar]
  36. McCormick S. P. , Price N. P. J. , Kurtzman C. P. . ( 2012; ). Glucosylation and other biotransformations of T-2 toxin by yeasts of the Trichomonascus clade. . Appl Environ Microbiol 78:, 8694–8702. [CrossRef] [PubMed]
    [Google Scholar]
  37. McNeill J. , Barrie F. R. , Buck W. R. , Demoulin V. , Greuter W. , Hawkworth D. L. , Herendeen P. S. , Knapp S. , Marhold K. . & other authors ( 2012; ). International Code of Nomenclature for Algae, Fungi, and Plants (Melbourne Code). Regnum Veg, 154. Koenigstein, Germany:: Gantner Verlag;.
    [Google Scholar]
  38. Middelhoven W. J. , Kurtzman C. P. . ( 2003; ). Relation between phylogeny and physiology in some ascomycetous yeasts. . Antonie van Leeuwenhoek 83:, 69–74. [CrossRef] [PubMed]
    [Google Scholar]
  39. Nakase T. , Itoh M. , Takematsu A. , Komagata K. . ( 1988; ). Candida tanzawaensis, a new species of yeast isolated from moss collected in Japan. . Trans Mycol Soc Japan 29:, 331–338.
    [Google Scholar]
  40. Nguyen N. H. , Suh S. O. , Marshall C. J. , Blackwell M. . ( 2006; ). Morphological and ecological similarities: wood-boring beetles associated with novel xylose-fermenting yeasts, Spathaspora passalidarum gen. sp. nov. and Candida jeffriesii sp. nov.. Mycol Res 110:, 1232–1241. [CrossRef] [PubMed]
    [Google Scholar]
  41. Nyland G. . ( 1949; ). Studies on some unusual Heterobasidiomycetes from Washington State. . Mycologia 41:, 686–701. [CrossRef]
    [Google Scholar]
  42. Péter G. , Dlauchy D. , Price N. P. , Kurtzman C. P. . ( 2012; ). Diddensiella caesifluorescens gen. nov., sp. nov., a riboflavin-producing yeast species of the family Trichomonascaceae. . Int J Syst Evol Microbiol 62:, 3081–3087. [CrossRef] [PubMed]
    [Google Scholar]
  43. Peterson S. W. , Kurtzman C. P. . ( 1991; ). Ribosomal RNA sequence divergence among sibling species of yeasts. . Syst Appl Microbiol 14:, 124–129. [CrossRef]
    [Google Scholar]
  44. Rokas A. , Williams B. L. , King N. , Carroll S. B. . ( 2003; ). Genome-scale approaches to resolving incongruence in molecular phylogenies. . Nature 425:, 798–804. [CrossRef] [PubMed]
    [Google Scholar]
  45. Rosling A. , Cox F. , Cruz-Martinez K. , Ihrmark K. , Grelet G.-A. , Lindahl B. D. , Menkis A. , James T. Y. . ( 2011; ). Archaeorhizomycetes: unearthing an ancient class of ubiquitous soil fungi. . Science 333:, 876–879. [CrossRef] [PubMed]
    [Google Scholar]
  46. Rozpędowska E. , Piškur J. , Wolfe K. H. . ( 2011; ). Genome sequences of Saccharomycotina: resources and applications in phylogenomics. . In The Yeasts, a Taxonomic Study, , 5th edn., pp. 145–157. Edited by Kurtzman C. P. , Fell J. W. , Boekhout T. . . Amsterdam:: Elsevier;. [CrossRef]
    [Google Scholar]
  47. Sampaio J. P. . ( 2011; ). Rhodotorula Harrison (1928). . In The Yeasts, a Taxonomic Study, , 5th edn., pp. 1873–1927. Edited by Kurtzman C. P. , Fell J. W. , Boekhout T. . . Amsterdam:: Elsevier;. [CrossRef]
    [Google Scholar]
  48. Schoch C. L. , Sung G. H. , López-Giráldez F. , Townsend J. P. , Miadlikowska J. , Hofstetter V. , Robbertse B. , Matheny P. B. , Kauff F. . & other authors ( 2009; ). The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. . Syst Biol 58:, 224–239. [CrossRef] [PubMed]
    [Google Scholar]
  49. Schoch C. L. , Seifert K. A. , Huhndorf S. , Robert V. , Spouge J. L. , Levesque C. A. , Chen W. . Fungal Barcoding Consortium ( 2012; ). Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. . Proc Natl Acad Sci U S A 109:, 6241–6246. [CrossRef] [PubMed]
    [Google Scholar]
  50. Scorzetti G. , Fell J. W. , Fonseca A. , Statzell-Tallman A. . ( 2002; ). Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions. . FEMS Yeast Res 2:, 495–517.[PubMed] [CrossRef]
    [Google Scholar]
  51. Sugita T. , Nakajima M. , Ikeda R. , Matsushima T. , Shinoda T. . ( 2002; ). Sequence analysis of the ribosomal DNA intergenic spacer 1 regions of Trichosporon species. . J Clin Microbiol 40:, 1826–1830. [CrossRef] [PubMed]
    [Google Scholar]
  52. Sugiyama J. , Hosaka K. , Suh S. O. . ( 2006; ). Early diverging Ascomycota: phylogenetic divergence and related evolutionary enigmas. . Mycologia 98:, 996–1005. [CrossRef] [PubMed]
    [Google Scholar]
  53. Suh S. O. , McHugh J. V. , Blackwell M. . ( 2004; ). Expansion of the Candida tanzawaensis yeast clade: 16 novel Candida species from basidiocarp-feeding beetles. . Int J Syst Evol Microbiol 54:, 2409–2429. [CrossRef] [PubMed]
    [Google Scholar]
  54. Suh S. O. , Nguyen N. H. , Blackwell M. . ( 2006; ). A yeast clade near Candida kruisii uncovered: nine novel Candida species associated with basidioma-feeding beetles. . Mycol Res 110:, 1379–1394. [CrossRef] [PubMed]
    [Google Scholar]
  55. Takashima M. , Nakase T. . ( 1999; ). Molecular phylogeny of the genus Cryptococcus and related species based on the sequences of SSU rDNA and internal transcribed spacer regions. . Microbiol Cult Collect 15:, 35–47.
    [Google Scholar]
  56. Taylor J. W. , Jacobson D. J. , Kroken S. , Kasuga T. , Geiser D. M. , Hibbett D. S. , Fisher M. C. . ( 2000; ). Phylogenetic species recognition and species concepts in fungi. . Fungal Genet Biol 31:, 21–32. [CrossRef] [PubMed]
    [Google Scholar]
  57. Tomaszewski E. K. , Logan K. S. , Snowden K. F. , Kurtzman C. P. , Phalen D. N. . ( 2003; ). Phylogenetic analysis identifies the ‘megabacterium’ of birds as a novel anamorphic ascomycetous yeast, Macrorhabdus ornithogaster gen. nov., sp. nov. . Int J Syst Evol Microbiol 53:, 1201–1205. [CrossRef] [PubMed]
    [Google Scholar]
  58. von Arx J. A. , van der Walt J. P. . ( 1987; ). Ophiostomatales and Endomycetales. . Stud Mycol 30:, 167–176.
    [Google Scholar]
  59. Walker W. F. . ( 1985; ). 5S ribosomal RNA sequences from ascomycetes and evolutionary implications. . Syst Appl Microbiol 6:, 48–53. [CrossRef]
    [Google Scholar]
  60. Weiß M. , Göker M. . ( 2011; ). Molecular phylogenetic reconstruction. . In The Yeasts, a Taxonomic Study, , 5th edn., pp. 159–174. Edited by Kurtzman C. P. , Fell J. W. , Boekhout T. . . Amsterdam:: Elsevier;. [CrossRef]
    [Google Scholar]
  61. Wolfe K. H. . ( 2006; ). Comparative genomics and genome evolution in yeasts. . Philos Trans R Soc Lond B Biol Sci 361:, 403–412. [CrossRef] [PubMed]
    [Google Scholar]
  62. Yamada Y. , Banno I. , von Arx J. A. , van der Walt J. P. . ( 1987; ). Taxonomic significance of the coenzyme Q system in yeasts and yeast-like fungi. . Stud Mycol 30:, 299–308.
    [Google Scholar]
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