Yeast species recognition from gene sequence analyses and other molecular methods

Mycoscience

Volumn 47, Issue 2, 2006, Pages 65-71

  Kurtzman, Cletus P ^a  

^a NATIONAL CENTER FOR AGRICULTURAL UTILIZATION RESEARCH   (United States)

Author keywords

Gene sequences; Molecular identification; Phylogenetic species; Rapid species identification; Yeasts

Indexed keywords

EID: 33646485558     PISSN: 13403540     EISSN: 16182545     Source Type: Journal    
DOI: 10.1007/s10267-006-0280-1     Document Type: Article

References (62)

1. C Belloch A Querol MD Garcia E Barrio 2000 Phylogeny of the genus Kluyveromyces inferred from the mitochondrial cytochrome-c oxidase II gene Int J Syst Evol Microbiol 50 405 416
2. TI Bonner DJ Brenner BR Neufeld RJ Britten 1973 Reduction in the rate of DNA reassociation by sequence divergence J Mol Biol 81 123 135
3. RJ Britten DE Graham BR Neufeld 1974 Analysis of repeating DNA sequences by reassociation L Grossman K Moldave Methods in enzymology, vol 29 Academic New York 363 418
4. GC Casey DW Dobson 2004 Potential of using real-time PCR-based detection of spoilage yeast in fruit juice: a preliminary study Int J Food Microbiol 91 327 335
5. DD Chapman DL Abercrombie CJ Douady EK Pikitch MJ Stanhopen MS Shivji 2003 A streamlined, bi-organelle, multiplex PCR approach to species identification: application to global conservation and trade monitoring of the great white shark Conserv Genet 4 415 425
6. L Cocolin A Heisey DA Mills 2001 Direct identification of the indigenous yeasts in commercial wine fermentations Am J Enol Vitic 52 49 53
7. H-M Daniel W Meyer 2003 Evaluation of ribosomal RNA and actin gene sequences for the identification of ascomycetous yeasts Int J Food Microbiol 86 71 78
8. H-M Daniel TC Sorrell W Meyer 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
9. M de Barros Lopes S Rainiere PA Henschje P Langridge 1999 AFLP fingerprinting for analysis of yeast genetic variation Int J Syst Bacteriol 49 915 924
10. MR Diaz T Boekhout B Theelen JW Fell 2000 Molecular sequence analysis of the intergenic spacer (IGS) associated with rDNA of the two varieties of the pathogenic yeast, Cryptococcus neoformans Syst Appl Microbiol 23 535 545
11. MR Diaz JW Fell 2000 Molecular analysis of ITS and IGS rDNA regions of the psychrophilic yeasts in the genus Mrakia Antonie van Leeuwenhoek 77 7 12
12. MR Diaz JW Fell 2004 High-throughput detection of pathogenic yeasts of the genus Trichosporon J Clin Microbiol 42 3696 3706
13. DE Dykhuizen L Green 1991 Recombination in Escherichia coli and the definition of biological species J Bacteriol 173 7257 7268
14. M Fan LC Chen MA Ragan R Gutell JR Warner BP Currie A Casadevall 1995 The 5S rRNA and the RNA intergenic spacer of the two varieties of Cryptococcus neoformans J Med Vet Mycol 33 215 221
15. JW Fell 1993 Rapid identification of yeast species using three primers in a polymerase chain reaction Mol Mar Biol Biotechnol 1 175 186
16. JW Fell G Blatt 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
17. JW Fell T Boekhout A Fonseca G Scorzetti A Statzell-Tallman 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
18. M Gadanho JM Almeida JP Sampaio 2003 Assessment of yeast diversity in a marine environment in the south of Portugal by microsatellite-primed PCR Antonie van Leeuwenhoek 84 217 227
19. DM Geiser JI Pitt JW Taylor 1998 Cryptic speciation and recombination in the aflatoxin-producing fungus Aspergillus flavus Proc Natl Acad Sci USA 95 388 393
20. M Goodman 1976 Protein sequences in phylogeny FJ Ayala Molecular Evolution Sinauer Sunderland, MA 141 159
21. C Groth J Hansen J Pisškur 1999 A natural chimeric yeast containing genetic material from three species Int J Syst Bacteriol 49 1933 1938
22. SA James MD Collins IN Roberts 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 46 189 194
23. CP Kurtzman 1984a Synonymy of the yeast genera Hansenula and Pichia demonstrated through comparisons of deoxyribonucleic acid relatedness Antonie van Leeuwenhoek 50 209 217
24. CP Kurtzman 1984b Resolution of varietal relationships within the species Hansenula anomala, Hansenula bimundalis, and Pichia nakazawae through comparisons of DNA relatedness Mycotaxon 19 271 279
25. CP Kurtzman 1987 Prediction of biological relatedness among yeasts from comparisons of nuclear DNA complementarity GS De Hoog MT Smith ACM Weijman The expanding realm of yeast-like Fungi Elsevier Amsterdam 459 468
26. CP Kurtzman 1990 Candida shehatae: genetic diversity and phylogenetic relationships with other xylose-fermenting yeasts Antonie van Leeuwenhoek 57 215 222
27. CP Kurtzman 1993 DNA-DNA hybridization approaches to species identification in small genome organisms EA Zimmer TJ White RL Cann AC Wilson Methods in enzymology, vol 224 Academic Press New York 335 348
28. CP Kurtzman 2005 New species and new combinations in the yeast genera Kregervanrija gen. nov., Saturnispora and Candida FEMS Yeast Res 4 233 245
29. CP Kurtzman JW Fell 1998 The yeasts, a taxonomic study 4th edn. Elsevier Amsterdam
30. CP Kurtzman HJ Phaff 1987 Molecular taxonomy AH Rose JS Harrison The yeasts, vol 1 2nd edn. Academic London 63 94
31. CP Kurtzman CJ Robnett 1998 Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences Antonie van Leeuwenhoek 73 331 371
32. CP Kurtzman CJ Robnett 2003 Phylogenetic relationships among yeasts of the "Saccharomyces complex" determined from multigene sequence analyses FEMS Yeast Res 3 417 432
33. CP Kurtzman CJ Robnett JN Ward C Brayton P Gorelick TJ Walsh 2005 Multigene phylogenetic analysis of pathogenic Candida species in the Kazachstania (Arxiozyma) telluris complex and description of their ascosporic states as Kazachstania bovina sp. nov., K. heterogenica sp. nov., K. pintolopesii sp. nov., and K. slooffiae sp. nov J Clin Microbiol 43 101 111
34. CP Kurtzman MJ Smiley CJ Johnson LJ Wickerham GB Fuson 1980a Two new and closely related heterothallic species, Pichia amylophila and Pichia mississippiensis: characterization by hybridization and deoxyribonucleic acid reassociation Int J Syst Bacteriol 30 208 216
35. CP Kurtzman MJ Smiley CJ Johnson 1980b Emendation of the genus Issatchenkia Kudriavsev and comparison of species by deoxyribonucleic acid reassociation, mating reaction, and ascospore ultrastructure Int J Syst Bacteriol 30 503 513
36. MA Lachance HM Daniel W Meyer GS Prasad SP Gautam K Boundy-Mills 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
37. BM Mannarelli CP Kurtzman 1998 Rapid identification of Candida albicans and other human pathogenic yeasts by using short oligonucleotides in a PCR J Clin Microbiol 36 1634 1641
38. A Martini HJ Phaff 1973 The optical determination of DNA-DNA homologies in yeasts Ann Microbiol 23 59 68
39. W Masoud LB Cesar L Jespersen M Jakobsen 2004 Yeast involved in fermentation of Coffea arabica in East Africa determined by genotyping and by direct denaturing gradient gel electrophoresis Yeast 21 549 556
40. CB Meroth WP Hammes C Hertel 2003 Identification and population dynamics of yeasts in sourdough fermentation processes by PCR-denaturing gradient gel electrophoresis Appl Environ Microbiol 69 7453 7461
41. G Muyzer K Smalla 1998 Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology Antonie van Leeuwenhoek 73 127 141
42. T Nakase K Komagata 1968 Taxonomic significance of base composition of yeast DNA J Gen Appl Microbiol 14 345 357
43. GI Naumov SA James ES Naumova EJ Louis IN Roberts 2000 Three new species in the Saccharomyces sensu stricto complex: Saccharomyces cariocanus, Saccharomyces kudriavzevii and Saccharomyces mikatae Int J Syst Evol Microbiol 50 1931 1942
44. GI Naumov ES Naumova PD Sniegowski 1998 Saccharomyces paradoxus and Saccharomyces cerevisiae are associated with exudates of North American oaks Can J Microbiol 44 1045 1050
45. H-V Nguyen A Lepingle C Gaillardin 2000 Molecular typing demonstrates homogeneity of Saccharomyces uvarum strains and reveals the existence of hybrids between S. uvarum and S. cerevisiae, including the S. bayanus type strain CBS 380 Syst Appl Microbiol 23 71 85
46. T Nilsson-Tillgren C Gjermansen MC Kielland-Brandt JGL Petersen S Holmberg 1981 Genetic differences between Saccharomyces carlsbergensis and S. cerevisiae. Analysis of chromosome III by single chromosome transfer Carlsberg Res Commun 46 65 76
47. K O'Donnell HC Kistler BK Tacke HH Casper 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 7910
48. BT Page CP Kurtzman 2005 Rapid identification of Candida and other clinically important yeast species by flow cytometry J Clin Microbiol 43 4507 4514
49. SW Peterson CP Kurtzman 1991 Ribosomal RNA sequence divergence among sibling species of yeasts Syst Appl Microbiol 14 124 129
50. CJ Prakitchaiwattana GH Fleet GM Heard 2004 Application and evaluation of denaturing gradient gel electrophoresis to analyse the yeast ecology of wine grapes FEMS Yeast Res 4 865 877
51. CW Price GB Fuson HJ Phaff 1978 Genome comparison in yeast systematics: delimitation of species within the genera Schwanniomyces, Saccharomyces, Debaryomyces, and Pichia Microbiol Rev 42 161 193
52. S Rigby GW Procop G Haase D Wilson G Hall C Kurtzman K Oliveira S Von Oy JJ Hyldig-Nielsen J Coull H Stender 2002 Fluorescence in situ hybridization with peptide nucleic acid probes for rapid identification of Candida albicans directly from blood culture bottles J Clin Microbiol 40 2182 2186
53. G Scorzetti JW Fell A Fonseca A Statzell-Tallman 2002 Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions FEMS Yeast Res 2 495 517
54. MT Smith V Robert GA Poot W Epping AWAM de Cock 2005 Taxonomy and phylogeny of the ascomycetous yeast genus Zygoascus, with proposal of Zygoascus meyerae sp. nov. and related anamorphic varieties Int J Syst Evol Microbiol 55 1353 1363
55. PD Sniegowski PG Dombrowski E Fingerman 2002 Saccharomyces cerevisiae and Saccharomyces paradoxus coexist in a natural woodland site in North America and display different levels of reproductive isolation from European conspecifics FEMS Yeast Res 1 299 306
56. M Špírek J Yang C Groth RF Petersen RB Langkjær ES Naumova P Sulo GI Naumov J Piškur 2003 Saccharomyces sensu lato chromosomes are highly dynamic FEMS Yeast Res 3 363 373
57. H Stender C Kurtzman JJ Hyldig-Nielsen D Sørensen A Broomer K Oliveira H Perry-O'Keefe A Sage B Young J Coull 2001 Identification of Dekkera bruxellensis (Brettanomyces) from wine by fluorescence in situ hybridization using peptide nucleic acid probes Appl Environ Microbiol 67 938 941
58. JW Taylor DJ Jacobson S Kroken T Kasuga DM Geiser DS Hibbett MC Fisher 2000 Phylogenetic species recognition and species concepts in fungi Fungal Genet Biol 31 21 32
59. A Vaughan-Martini CP Kurtzman 1985 Deoxyribonucleic acid relatedness among species of the genus Saccharomyces sensu stricto Int J Syst Bacteriol 35 508 511
60. A Vaughan-Martini CP Kurtzman SA Meyer EB O'Neill 2005 Two new species in the Pichia guilliermondii clade: Pichia caribbica sp. nov., the ascosporic state of Candida fermentati, and Candida carpophila comb. nov FEMS Yeast Res 5 463 469
61. A Vaughan-Martini A Martini 1987 Three newly delimited species of Saccharomyces sensu stricto Antonie van Leeuwenhoek 53 77 84
62. Y Yamada K Mikata I Banno 1993 Reidentification of 121 strains of the genus Saccharomyces Bull Jpn Fed Cult Coll 9 95 119