Taxonomy and phylogenetic diversity among the yeasts

  • Cletus P. KurtzmanEmail author
  • Jure Piškur
Part of the Topics in Current Genetics book series (TCG, volume 15)


Yeasts are among the economically and scientifically most important eukaryotic microorganisms known. At present, there are 1,500 recognized species, which are distributed between the ascomycetes and the basidiomycetes, but only a small fraction of these species have undergone extensive genetic analyses. In this chapter, we discuss application of molecular methods for identification of species and for their classification from phylogenetic analysis of gene sequences. The resulting phylogeny is considered in the context of comparative genomics and evolution, and provides a useful background for selection of additional species for whole genome sequencing as well as for new biotechnological applications.


Yeast Species Phylogenetic Diversity Amplify Fragment Length Polymorphism Basidiomycetous Yeast Ascomycetous Yeast 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1. Andreasen AA, Stier TJB (1953) Anaerobic nutrition of Saccharomyces cerevisiae. I. Ergosterol requirement for the growth in a defined medium. J Cell Comp Physiol 41:23-36CrossRefGoogle Scholar
  2. 2. Bak AL, Stenderup A (1969) Deoxyribonucleic acid homology in yeasts. Genetic relatedness within the genus Candida. J Gen Microbiol 59:21-30PubMedGoogle Scholar
  3. 3. Belloch C, Querol A, Garcia MD, Barrio E (2000) Phylogeny of the genus Kluyveromyces inferred from the mitochondrial cytochrome-c oxidase II gene. Int J Syst Evol Microbiol 50:405-416PubMedGoogle Scholar
  4. 4. Berbee ML, Taylor JW (2001) Fungal molecular evolution: gene trees and geologic time. In: McLaughlin DJ, McLaughlin E, Lemke P (eds) The Mycota VII, Part B. Springer-Verlag, Berlin, pp 231-245Google Scholar
  5. 5. Bonner TI, Brenner DJ, Neufeld BR, Britten RJ (1973) Reduction in the rate of DNA reassociation by sequence divergence J Mol Biol 81:123-135Google Scholar
  6. 6. Britten RJ, Graham DE, Neufeld BR (1974) Analysis of repeating DNA sequences by reassociation. In: Grossman L, Moldave K (eds) Methods in Enzymology, Vol 29. Academic Press, NY, pp 363-418Google Scholar
  7. 7. Butler G, Kenny C, Fagan A, Kurischko C, Gaillardin C, Wolfe KH (2004) Evolution of the MAT locus and its Ho endonuclease in yeast species. Proc Natl Acad Sci USA 101:1632-1637PubMedCrossRefGoogle Scholar
  8. 8. Cain RF (1972) Evolution of the fungi. Mycologia 64:1-14Google Scholar
  9. 9. Daniel H-M, Meyer W (2003) Evaluation of ribosomal RNA and actin gene sequences for the identification of ascomycetous yeasts. Int J Food Microbiol 86:61-78PubMedCrossRefGoogle Scholar
  10. 10. Daniel H-M, Sorrell TC, 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 51:1593-1606PubMedGoogle Scholar
  11. 11. De Barros Lopes M, Rainiere S, Henschje PA, Langridge P (1999) AFLP fingerprinting for analysis of yeast genetic variation. Int J Syst Bacteriol 49:915-924Google Scholar
  12. 12. Delneri D, Colson I, Grammenoudi S, Roberts IN, Louis, EJ, Oliver SG (2003) Engineering evolution to study speciation in yeasts. Nature 422:68-72PubMedCrossRefGoogle Scholar
  13. 13. Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S, Mohr C, Pohlmann R, Luedi P, Choi S, Wing RA, Flavier A, Gaffney TD, Philippsen P (2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304:304-307PubMedCrossRefGoogle Scholar
  14. 14. Dobzhansky T (1976) Organismic and molecular aspects of species formation. In: Molecular Evolution, Ayala FJ (ed), Sinauer Assoc. Sunderland, Massachusetts, pp 95-105Google Scholar
  15. 15. Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuveglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisrame A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wesolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL (2004) Genome Evolution in Yeast. Nature 430:35-44PubMedCrossRefGoogle Scholar
  16. 16. Fan M, Chen LC, Ragan MA, Gutell R, Warner JR, Currie BP, Casadevall, A (1995) The 5S rRNA and the RNA intergenic spacer of the two varieties of Cryptococcus neoformans. J Med Vet Mycol 33:215-221PubMedGoogle Scholar
  17. 17. Fell JW (1993) Rapid identification of yeast species using three primers in a polymerase chain reaction. Mol Mar Biol Biotechnol 1:175-186Google Scholar
  18. 18. Fell JW, 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 21:677-681CrossRefGoogle Scholar
  19. 19. Fell JW, Boekhout T, Fonseca A, 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 50:1351-1371PubMedGoogle Scholar
  20. 20. Fischer G, James SA, Roberts IN, Oliver SG, Louis DJ (2000) Chromosomal evolution in Saccharomyces. Nature 405:451-454PubMedCrossRefGoogle Scholar
  21. 21. Fuson GB, Price CW, Phaff HJ (1979) Deoxyribonucleic acid sequence relatedness among some members of the yeast genus Hansenula. Int J Syst Bacteriol 29:64-69Google Scholar
  22. 22. Gadanho M, Almeida JM, Sampaio JP (2003) Assessment of yeast diversity in a marine environment in the south of Portugal by microsatellite-primed PCR. Antonie van Leeuwenhoek 84:217-227PubMedCrossRefGoogle Scholar
  23. 23. Geiser DM, Pitt JI, Taylor JW (1998) Cryptic speciation and recombination in the aflatoxin-producing fungus Aspergillus flavus. Proc Natl Acad Sci USA 95:388-393PubMedCrossRefGoogle Scholar
  24. 24. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG (1996) Life with 6000 genes. Science 274:563-567CrossRefGoogle Scholar
  25. 25. Gojkovic Z, Knecht W, Zameitat E, Warneboldt J, Coutelis J-B, Pynyaha Y, Neuveglise C, Moller K, Loffler M, Piškur J (2004) Horizontal gene transfer promoted the evolution of the yeast ability to propagate under anaerobic conditions. Mol Gen Genomics 271:387-393CrossRefGoogle Scholar
  26. 26. Graur D, Martin W (2004) Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet 20:80-86PubMedCrossRefGoogle Scholar
  27. 27. Groth C, Hansen J, Piškur J (1999) A natural chimeric yeast containing genetic material from three species. Int J Syst Bacteriol 49:1933-1938PubMedGoogle Scholar
  28. 28. Haber, JE (1998) Mating-type gene switching in Saccharomyces cerevisiae. Annu Rev Genet 32:561-599 PubMedCrossRefGoogle Scholar
  29. 29. Hausner G, Reid J, Klassen GR (1992) Do galeate-ascospore members of the Cephaloascaceae, Endomycetaceae and Ophiostomataceae share a common phylogeny? Mycologia 84:870-881Google Scholar
  30. 30. Hendriks L, Goris A, Van de Peer Y, Neefs J-M, Vancanneyt M, Kersters K, Berny J-F, Hennebert GL, De Wachter R (1992) Phylogenetic relationships among ascomycetes and ascomycete-like yeasts as deduced from small ribosomal subunit RNA sequences. Syst Appl Microbiol 15:98-104Google Scholar
  31. 31. James SA, Collins MD, Roberts IN (1996) Use of an rRNA internal transcribed spacer region to distinguish phylogenetically closely related species of the genera Zygosaccharomyces and Torulaspora. Int J Syst Bacteriol 46:189-194PubMedGoogle Scholar
  32. 32. Johnston M (1999) Feasting, fasting and fermenting. Glucose sensing in yeast and other cells. Trends Genet 15:29-33PubMedCrossRefGoogle Scholar
  33. 33. Keeling PJ, Roger AJ (1995) The selfish pursuit of sex. Nature 375:283PubMedCrossRefGoogle Scholar
  34. 34. Kellis M, Birren BW, Lander, ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617-624PubMedCrossRefGoogle Scholar
  35. 35. Kurtzman CP (1984a) Synonymy of the yeast genera Hansenula and Pichia demonstrated through comparisons of deoxyribonucleic acid relatedness. Antonie van Leeuwenhoek 50:209-217PubMedCrossRefGoogle Scholar
  36. 36. Kurtzman CP (1984b) Resolution of varietal relationships within the species Hansenula anomala, Hansenula bimundalis, and Pichia nakazawae through comparisons of DNA relatedness. Mycotaxon 19:271-279Google Scholar
  37. 37. Kurtzman CP (1987) Prediction of biological relatedness among yeasts from comparisons of nuclear DNA complementarity. In: de Hoog GS, Smith MTh, Weijman ACM (eds) The Expanding Realm of Yeast-like Fungi. Elsevier, Amsterdam, pp 459-468Google Scholar
  38. 38. Kurtzman CP (1990a) Candida shehatae - genetic diversity and phylogenetic relationships with other xylose-fermenting yeasts. Antonie van Leeuwenhoek 57:215-222PubMedCrossRefGoogle Scholar
  39. 39. Kurtzman CP (1990b) DNA relatedness among species of Sterigmatomyces and Fellomyces. Int J Syst Bacteriol 40:56-59Google Scholar
  40. 40. Kurtzman CP (1993a) DNA-DNA hybridization approaches to species identification in small genome organisms. In: Zimmer EA, White TJ, Cann RL, Wilson AC (eds) Methods in Enzymology, Vol 224. Academic Press, New York, pp 335-348Google Scholar
  41. 41. Kurtzman CP (1993b) Systematics of the ascomycetous yeasts assessed from ribosomal RNA sequence divergence. Antonie van Leeuwenhoek 63:165-174PubMedCrossRefGoogle Scholar
  42. 42. Kurtzman CP (2003) Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora. FEMS Yeast Res 4:233-245PubMedCrossRefGoogle Scholar
  43. 43. Kurtzman CP, Fell JW (1998) The Yeasts, A Taxonomic Study, 4th edn, Elsevier Science BV, Amsterdam, pp 1055Google Scholar
  44. 44. Kurtzman CP, Robnett CJ (1994) Orders and families of ascosporgenous yeasts and yeast-like taxa compared from ribosomal RNA sequence similarities. In: Hawksworth DL (ed) Ascomycete systematics, problems and perspectives in the nineties. Plenum Press, New York, pp 249-258Google Scholar
  45. 45. Kurtzman CP, Robnett CJ (1995) Molecular relationships among hyphal ascomycetous yeasts and yeastlike taxa. Can J Bot 73 (Suppl 1):S824-S830Google Scholar
  46. 46. Kurtzman CP, Robnett CJ (1998) Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek 73:331-371PubMedCrossRefGoogle Scholar
  47. 47. Kurtzman CP, Robnett CJ (2003) Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses. FEMS Yeast Res 3:417-432PubMedCrossRefGoogle Scholar
  48. 48. Kurtzman CP, Sugiyama J (2001) Ascomycetous yeasts and yeastlike taxa. In: McLaughlin DJ, McLaughlin E, Lemke P (eds) The Mycota VII, Part A. Springer-Verlag, Berlin, pp 179-200Google Scholar
  49. 49. Kurtzman CP, Johnson CJ, Smiley MJ (1979) Determination of conspecificity of Candida utilis and Hansenula jadinii through DNA reassociation. Mycologia 71:844-847Google Scholar
  50. 50. Kurtzman CP, Smiley MJ, Johnson CJ, Wickerham LJ, Fuson GB (1980a) Two new and closely related heterothallic species, Pichia amylophila and Pichia mississippiensis: Characterization by hybridization and deoxyribonucleic acid reassociation. Int J Syst Bacteriol 30:208-216Google Scholar
  51. 51. Kurtzman CP, Smiley MJ, Johnson CJ (1980b) Emendation of the genus Issatchenkia Kudriavsev and comparison of species by deoxyribonucleic acid reassociation, mating reaction, and ascospore ultrastructure. Int J Syst Bacteriol 30:503-513Google Scholar
  52. 52. Kwast KE, Lai L-C, Menda N, James DT III, Aref S, Burke PV (2002) Genomic analyses of anaerobically induced genes in Saccharomyces cerevisiae: functional roles of Rox1 and other factors in mediating the anoxic response. J Bacteriol 184:250-265PubMedCrossRefGoogle Scholar
  53. 53. Lachance MA, Daniel HM, Meyer W, Prasad GS, Gautam SP, 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 4:253-258PubMedCrossRefGoogle Scholar
  54. 54. Landvik S (1996) Neolecta, a fruit-body producing genus of the basal ascomycetes, as shown by SSU and LSU rDNA sequences. Mycol Res 100:199-202Google Scholar
  55. 55. Liu YJ, Whelen S, Hall BD (1999) Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Mol Biol Evol 16:1799-1808PubMedGoogle Scholar
  56. 56. Mannarelli BM, Kurtzman CP (1998) Rapid identification of Candida albicans and other human pathogenic yeasts by using short oligonucleotides in a PCR. J Clin Microbiol 36:1634-1641PubMedGoogle Scholar
  57. 57. Martini A, Phaff HJ (1973) The optical determination of DNA-DNA homologies in yeasts. Ann Microbiol 23:59-68Google Scholar
  58. 58. Meyer SA, Phaff HJ (1972) DNA base composition and DNA-DNA homology studies as tools in yeast systematics. In: Kochová-Kratochvílová A, Minarik E (eds) Yeasts as Models in Science and Technics. Publishing House of the Slovak Academy of Sciences, Bratislava, Czechoslovakia, pp 375-386Google Scholar
  59. 59. Møller K, Olsson L, Piškur J (2001) Ability for anaerobic growth is not sufficient for development of the petite phenotype in Saccharomyces kluyveri. J Bacteriol 183:2485-2489CrossRefGoogle Scholar
  60. 60. Nagy M, Lacroute F, Thomas D (1992) Divergent evolution of pyrimidine biosynthesis between anaerobic and aerobic yeasts. Proc Natl Acad Sci USA 89:8966-8970PubMedCrossRefGoogle Scholar
  61. 61. Naumov GI (2000) Saccharomyces bayanus var. uvarum comb. nov., a new variety established by genetic analysis. Mikrobiologiya 69:410-414Google Scholar
  62. 62. Naumov GI, James SA, Naumova ES, Louis EJ, Roberts IN (2000) Three new species in the Saccharomyces sensu stricto complex: Saccharomyces cariocanus, Saccharomyces kudriavzevii and Saccharomyces mikatae. Int J Syst Evol Microbiol 50:1931-1942PubMedGoogle Scholar
  63. 63. Nilsson-Tillgren T, Gjermansen C, Kielland-Brandt MC, Petersen JGL, Holmberg S (1981) Genetic differences between Saccharomyces carlsbergensis and S. cerevisiae. Analysis of chromosome III by single chromosome transfer. Carlsberg Res Commun 46:65-76CrossRefGoogle Scholar
  64. 64. Nishida H, Sugiyama J (1993) Phylogenetic relationships among Taphrina, Saitoella, and other fungi. Mol Biol Evol 12:883-886Google Scholar
  65. 65. Nishida H, Sugiyama J (1994) Archiascomycetes: detection of a major new lineage within the Ascomycota. Mycoscience 35:361-366CrossRefGoogle Scholar
  66. 66. O'Donnell K, Kistler HC, Tacke BK, Casper HH (2000) Gene genealogies reveal global phylogeographic structure and reproductive isolation among lineages of Fusarium graminearum, the fungus causing wheat scab. Proc Natl Acad Sci USA 97:7905-7910CrossRefGoogle Scholar
  67. 67. Petersen RF, Marinoni G, Nielsen ML, Piškur J (2000) Molecular approaches for analyzing diversity and phylogeny among yeast species. In: Ernst JF, Schmidt A (eds) Dimorphism in Human Pathogenic and Apathogenic Yeasts. Karger, Basel, pp 15-35Google Scholar
  68. 68. Peterson SW, Kurtzman CP (1991) Ribosomal RNA sequence divergence among sibling species of yeasts. Syst Appl Microbiol 14:124-129Google Scholar
  69. 69. Piškur J, Langkjær RB (2004) Yeast genome sequencing: the power of comparative genomics. Mol Microbiol 53:381-389CrossRefGoogle Scholar
  70. 70. Price CW, Fuson GB, Phaff HJ (1978) Genome comparison in yeast systematics: Delimitation of species within the genera Schwanniomyces, Saccharomyces, Debaryomyces, and Pichia. Microbiol Rev 42:161-193PubMedGoogle Scholar
  71. 71. Redhead SA, Malloch DW (1977) The Endomycetaceae: new concepts, new taxa. Can J Bot 55:1701-1711CrossRefGoogle Scholar
  72. 72. Rokas A, Williams BL, King N, Carroll SB (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804PubMedCrossRefGoogle Scholar
  73. 73. Scorzetti G, Fell JW, 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 2:495-517PubMedGoogle Scholar
  74. 74. Sjamsuridzal W, Tajiri Y, Nishida H, Thuan TB, Kawasaki H, Hirata A, Yakota A, Sugiyama J (1997) Evolutionary relationships of members of the genera Taphrina, Protomyces, Schizosaccharomyces, and related taxa within the archiascomycetes: integrated analysis of genotypic and phenotypic characters. Mycoscience 38:267-280CrossRefGoogle Scholar
  75. 75. Špírek M, Yang J, Groth C, Petersen RF , Langkjær RB, Naumova ES, Sulo P, Naumov GI, Piškur J (2003) Saccharomyces sensu lato chromosomes are highly dynamic. FEMS Yeast Res 3:363-373CrossRefGoogle Scholar
  76. 76. Strathern JN, Herskowitz I (1979) Asymmetry and directionality in production of new cell types during clonal growth: the switching pattern of homothallic yeast. Cell 17:371-381 PubMedCrossRefGoogle Scholar
  77. 77. Sugiyama J (1998) Relatedness, phylogeny, and evolution of the fungi. Mycoscience 39:487-511CrossRefGoogle Scholar
  78. 78. Swann EC, Taylor JW (1993) Higher taxa of basidiomycetes: An 18S rRNA gene perspective. Mycologia 85:923-936Google Scholar
  79. 79. Vaughan-Martini A, Kurtzman CP (1985) Deoxyribonucleic acid relatedness among species of the genus Saccharomyces sensu stricto. Int J Syst Bacteriol 35:508-511CrossRefGoogle Scholar
  80. 80. Wilmotte A, Van de Peer Y, Goris A, Chapelle S, De Baere R, Nelissen B, Neefs J-M, Hennebert GL, De Wachter R (1993) Evolutionary relationships among higher fungi inferred from small ribosomal subunit RNA sequence analysis. Syst Appl Microbiol 16:436-444Google Scholar
  81. 81. Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713PubMedCrossRefGoogle Scholar
  82. 82. Wolfe K (2004) Evolutionary genomics: Yeasts accelerate beyond BLAST. Current Biology 14:R392-R394PubMedCrossRefGoogle Scholar

Authors and Affiliations

  1. 1.Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IllinoisUSA
  2. 2.BioCentrum-DTU, Technical University of Denmark and Cell and Organism Biology, University of LundSweden

Personalised recommendations