Phylogeny of yeasts and related filamentous fungi within Pucciniomycotina determined from multigene sequence analyses

Studies in Mycology

Volumn 81, Issue , 2015, Pages 27-53

  Wang, Q M ^a   Groenewald, M ^b   Takashima, M ^c   Theelen, B ^b   Han, P J ^a   Liu, X Z ^a   Boekhout, T ^a,b,d   Bai, F Y ^a,b  

^a INSTITUTE OF MICROBIOLOGY   (China)

^b CBS KNAW FUNGAL BIODIVERSITY CENTRE   (Netherlands)

^c RIKEN BIORESOURCE CENTER   (Japan)

^d SECOND MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

Basidiomycota; Fungi; Multigene phylogeny; Pucciniomycotina; Yeasts

Indexed keywords

EID: 84958253794     PISSN: 01660616     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.simyco.2015.08.002     Document Type: Article

References (86)

1. Aime MC, Matheny PB, Henk DA, et al. (2006). An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences. Mycologia 98: 896-905.
2. Aime MC, Toome M, McLaughlin DJ (2014). Pucciniomycotina. In: The mycota, Vol. VII, Part A: Systematics and evolution (McLaughlin DJ, Spatafora JW, eds), 2nd edn. Springer-Verlag, Berlin: 271-294.
3. Bandoni RJ (1998). On some species of Mycogloea. Mycoscience 39: 31-36.
4. Bandoni RJ, Boekhout T (2011). Agaricostilbum Wright (1970). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1375-1378.
5. Bauer R, Begerow D, Sampaio JP, et al. (2006). The simple-septate basidiomycetes:a synopsis. Mycological Progress 5: 41-66.
6. Bauer R, Metzler B, Begerow D, et al. (2009). Cystobasidiopsis nirenbergiae, a new agaricostilbomycete (Pucciniomycotina). Mycological Research 113:960-966.
7. Bauer R, Oberwinkler F, Vánky K (1997). Ultrastructural markers and systematics in smut fungi and allied taxa. Canadian Journal of Botany 75: 1273-1314.
8. Biswas SK, Wang L, Yokoyama K, et al. (2005). Molecular phylogenetics of the genus Trichosporon inferred from mitochondrial cytochrome b gene sequences. Journal of Clinical Microbiology 43: 5171-5178.
9. Biswas SK, Yokoyama K, Nishimura K, et al. (2001). Molecular phylogenetics of the genus Rhodotorula and related basidiomycetous yeasts inferred from the mitochondrial cytochrome b gene. International Journal of Systematic and Evolutionary Microbiology 51: 1191-1199.
10. Boekhout T (1991). A revision of ballistoconidia-forming yeasts and fungi. Studies in Mycology 33: 1-194.
11. Boekhout T, Fonseca A, Sampaio JP, et al. (2011). Discussion of teleomorphic and anamorphic basidiomycetous yeasts. In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam:1339-1372.
12. de García V, Coelho MA, Maia TM, et al. (2015). Sex in the cold: taxonomic reorganization of psychrotolerant yeasts in the order Leucosporidiales. FEMS Yeast Research 15: fov019. http://dx.doi.org/10.1093/femsyr/fov019.
13. Fell JW (1966). Sterigmatomyces, a new fungal genus from marine areas. Antonie Van Leeuwenhoek 32: 99-104.
14. Fell JW (2011a). Sterigmatomyces Fell (1966). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1991-1994.
15. Fell JW (2011b). Sakaguchia Y. Yamada, Maeda & Mikata (1994). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1541-1544.
16. Fell JW, Boekhout T, Fonseca A, et al. (2000a). Basidiomycetous yeasts. In: The mycota VII, Systematic and evolution part B (Esser K, Lemke PA, eds). Springer-Verlag, Berlin: 3-35.
17. Fell JW, Boekhout T, Fonseca A, et al. (2000b). Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis. International Journal of Systematic and Evolutionary Microbiology 50: 1351-1371.
18. Fell JW, Statzell-Tallman A (1998). Rhodosporidium Banno. In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, eds), 4th edn. Elsevier, Amsterdam:678-692.
19. Golubev WI (1999). Mastigobasidium, a new teleomorphic genus for the perfect state of ballistosporous yeast Bensingtonia intermedia. International Journal of Systematic Bacteriology 49: 1301-1305.
20. Gochenaur SE (1981). Cyrenella elegans gen. et sp. nov., a dikaryotic anamorph. Mycotaxon 13: 267-277.
21. Hamamoto M (2011). Erythrobasidium Hamamoto, Sugiyama & Komagata (1991). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1433-1435.
22. Hamamoto M, Boekhout T, Nakase T (2011). Sporobolomyces Kluyver & van Niel (1924). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1929-1990.
23. Hamamoto M, Nakase T (2000). Phylogenetic analysis of the ballistoconidiumforming yeast genus Sporobolomyces based on 18S rDNA sequences. International Journal of Systematic and Evolutionary Microbiology 50:1373-1380.
24. Hamamoto M, Sugiyama J, Komagata K (1988). Transfer of Rhodotorula hasegawae to a new basidiomycetous genus Erythrobasidium as Erythrobasidium hasegawae comb. nov. The Journal of General and Applied Microbiology 34: 279-287.
25. Hamamoto M, Thanh VN, Nakase T (2002). Bannoa hahajimensis gen. nov., sp. nov., and three related anamorphs, Sporobolomyces bischofiae sp. nov., Sporobolomyces ogasawarensis sp. nov. and Sporobolomyces syzygii sp. nov., yeasts isolated from plants in Japan. International Journal of Systematic and Evolutionary Microbiology 52: 1023-1032.
26. Hauerslev K (1999). New and rare species of Heterobasidiomycetes. Mycotaxon 72: 465-486.
27. Hawksworth DL (2011). A new dawn for the naming of fungi: impacts of decisions made in Melbourne in July 2011 on the future publication and regulation of fungal names. MycoKeys 1: 7-20.
28. Hibbett DS, Binder M, Bischoff JF, et al. (2007). A higher-level phylogenetic classification of the Fungi. Mycological Research 111: 509-547.
29. James TY, Kauff F, Schoch CL, et al. (2006). Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443: 818-822.
30. Kachalkin AV (2014). Yeasts of the White Sea intertidal zone and description of Glaciozyma litorale sp. nov. Antonie Van Leeuwenhoek 105: 1073-1083.
31. Kirschner R, Sampaio JP, Begerow D, et al. (2003). Mycogloea nipponica - the first known teleomorph in the heterobasidiomycetous yeast genus Kurtzmanomyces. Antonie Van Leeuwenhoek 84: 109-114.
32. Kurtzman CP, Fell JW, Boekhout T (2011). The yeasts: a taxonomic study, 5th edn. Elsevier, Amsterdam.
33. Kwon-Chung KJ (2011). Chinonosphaera Cox (1976). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1395-1401.
34. Laich F, Chávez R, Vaca I (2014). Leucosporidium escuderoi f.a., sp. nov., a basidiomycetous yeast associated with an Antarctic marine sponge. Antonie Van Leeuwenhoek 105: 593-601.
35. Manohar CS, Boekhout T, Müller WH, et al. (2014). Tritirachium candoliense sp. nov., a novel basidiomycetous fungus isolated from the anoxic zone of the Arabian Sea. Fungal Biology 118: 139-149.
36. Margesin R, Fonteyne PA, Schinner F, et al. (2007). Rhodotorula psychrophila sp. nov., Rhodotorula psychrophenolica sp. nov. and Rhodotorula glacialis sp. nov., novel psychrophilic basidiomycetous yeast species isolated from alpine environments. International Journal of Systematic and Evolutionary Microbiology 57: 2179-2184.
37. McNeill J, Barrie FR, Buck WR, et al. (2012). International Code of Nomenclature for algae, fungi, and plants (Melbourne Code). Regnum Vegetabile 154. A.R.G. Gantner Verlag KG, Ruggell, Liechtenstein, ISBN 978-3-87429-425-6. Available at: http://www.iapt-taxon.org/nomen/main.php.
38. Nagahama T, Hamamoto M, Nakase T, et al. (2006). Phylogenetic relationship within the Erythrobasidium clade: molecular phylogenies, secondary structure, and intron positions inferred from partial sequences of ribosomal DNA and elongation factor-1a genes. The Journal of General and Applied Microbiology 52: 37-45.
39. Nakase T (2000). Expanding world of ballistosporous yeasts: distribution in the phyllosphere, systematics and phylogeny. The Journal of General and Applied Microbiology 46: 189-216.
40. Nakase T, Bai FY, Boekhout T (2011). Bensingtonia Ingold emend. Nakase & Boekhout (1986). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1607-1622.
41. Nakase T, Itoh M, Sugiyama J (1989). Bensingtonia ingoldii sp. nov., a ballistospore-forming yeast isolated from Knightia excelsa collected in New Zealand. The Journal of General and Applied Microbiology 35: 53-58.
42. Nishida H, Ando K, Ando Y, et al. (1995). Mixia osmundae: transfer from the Ascomycota to the Basidiomycota based on evidence from molecules and morphology. Canadian Journal of Botany 73: S660-S666.
43. Nishida H, Robert V, Sugiyama J (2011). Mixia C.L. Kramer emend. H. Nishida, K. Ando, Y. Ando, Hirata & Sugiyama (1995). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1499-1502.
44. Oberwinkler F (1990). New genera of auricularioid heterobasidiomycetes. Report of Tottori Mycology Institute 28: 113-127.
45. Pohl CH, Smit MS, Albertyn J (2011). Rhodotorula bloemfonteinensis sp. nov., Rhodotorula eucalyptica sp. nov., Rhodotorula orientis sp. nov. and Rhodotorula pini sp. nov., yeasts isolated from monoterpene-rich environments. International Journal of Systematic and Evolutionary Microbiology 61:2320-2327.
46. Pore RS, Fell JW (2011). Reniforma Pore & Sorenson (1990). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1869-1872.
47. Pore RS, Sorenson WG (1990). Reniforma strues, a new yeast from wastewater. Mycologia 82: 549-553.
48. Posada D, Crandall KA (1998). Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817-818.
49. Roberts P (1996). Heterobasidiomycetes from Majorca & Cabrera (Balearic Islands). Mycotaxon 60: 111-124.
50. Roberts P (1997). New heterobasidiomycetes from Great Britain. Mycotaxon 63:195-216.
51. Ronquist F, Teslenko M, van der Mark P, et al. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539-542.
52. Sampaio JP (2011a). Rhodotorula Harrison (1928). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1873-1927.
53. Sampaio JP (2011b). Kurtzmanomyces Y. Yamada, M, Itoh, Kawasaki, Banno & Nakase (1988). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1795-1800.
54. Sampaio JP (2011c). Cyrenella Gochenaur (1981). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1743-1745.
55. Sampaio JP (2011d). Leucosporidium Fell, Statzell, I.L. Hunter & Phaff (1969). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1485-1494.
56. Sampaio JP (2011e). Curibasidium Sampaio & Golubev (2004). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1413-1418.
57. Sampaio JP, Bauer R, Begerow D, et al. (1999). Occultifur externus sp. nov., a new species of simple-pored auricularioid heterobasidiomycetes from plant litter in Portugal. Mycologia 91: 1094-1101.
58. Sampaio JP, Chen CJ (2011). Naohidea Oberwinkler (1990). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1511-1513.
59. Sampaio JP, Gadanho M, Bauer R, et al. (2003). Taxonomic studies in the Microbotryomycetidae: Leucosporidium golubevii sp. nov., Leucosporidiella gen. nov. and the new orders Leucosporidiales and Sporidiobolales. Mycological Progress 2: 53-68.
60. Sampaio JP, Golubev WI, Fell JW, et al. (2004). Curvibasidium cygneicollum gen. nov., sp. nov. and Curvibasidium pallidicorallinum sp. nov., novel taxa in the Microbotryomycetidae (Urediniomycetes), and their relationship with Rhodotorula fujisanensis and Rhodotorula nothofagi. International Journal of Systematic and Evolutionary Microbiology 54: 1401-1407.
61. Sampaio JP, Kirschner R, Oberwinkler F (2011). Colacogloea Oberwinkler (1990). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1403-1408.
62. Sampaio JP, Oberwinkler F (2011). Cystobasidium (Lagerheim) Neuhoff (1924). In: The yeasts, a taxonomic study (Kurtzman CP, Fell JW, Boekhout T, eds), 5th edn. Elsevier, Amsterdam: 1419-1422.
63. Schell WA, Lee AG, Aime MC (2011). A new lineage in Pucciniomycotina: class Tritirachiomycetes, order Tritirachiales, family Tritirachiaceae. Mycologia 103: 1331-1340.
64. Scorzetti G, Fell JW, Fonseca A, et al. (2002). Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions. FEMS Yeast Research 2: 495-517.
65. Shivas RG, Rodrigues de Miranda L (1983). Two new species of the genus Sporobolomyces and a new Rhodotorula species from leaf surfaces. Antonie Van Leeuwenhoek 49: 159-166.
66. Stamatakis A (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
67. Standley K (2013). MAFFT multiple sequence alignment software version 7:improvements in performance and usability. Molecular Biology and Evolution 30: 772-780.
68. Swofford DL (2002). PAUP*. Phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland MA.
69. Takashima M, Suh SO, Nakase T (1995). Bensingtonia musae sp. nov. isolated from a dead leaf of Musa paradisiaca and its phylogenetic relationship among basidiomycetous yeasts. The Journal of General and Applied Microbiology 41: 143-151.
70. Taylor JW (2011). One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR. IMA Fungus 2: 113-120.
71. Toome M, Roberson RW, Aime MC (2013). Meredithblackwellia eburnea gen. et sp. nov., Kriegeriaceae fam. nov. and Kriegeriales ord. nov. - toward resolving higher-level classification in Microbotryomycetes. Mycologia 105: 486-495.
72. Trichiés G (2006). Hétérobasidiomycétes inusuels ou nouveaux découverts en France. Bulletin de la Société Mycologique de France 122: 29-60.
73. Turchetti B, Thomas Hall SR, Connell LB, et al. (2011). Psychrophilic yeasts from Antarctica and European glaciers: description of Glaciozyma gen. nov., Glaciozyma martinii sp. nov. and Glaciozyma watsonii sp. nov. Extremophiles 15: 573-586.
74. Vánky K (2002). Illustrated genera of smut fungi, 2nd edn. APS Press, St. Paul, MN.
75. Wang QM, Bai FY (2004). Four new yeast species of the genus Sporobolomyces from plant leaves. FEMS Yeast Research 4: 579-586.
76. Wang QM, Bai FY (2008). Molecular phylogeny of basidiomycetous yeasts in the Cryptococcus luteolus lineage (Tremellales) based on nuclear rDNA and mitochondrial cytochrome b gene sequence analyses: proposal of Derxomyces gen. nov. and Hannaella gen. nov., and description of eight novel Derxomyces species. FEMS Yeast Research 8: 799-814.
77. Wang QM, Bai FY, Zhao JH, et al. (2003). Bensingtonia changbaiensis sp. nov. and Bensingtonia sorbi sp. nov., novel ballistoconidium-forming yeast species from plant leaves. International Journal of Systematic and Evolutionary Microbiology 53: 2085-2089.
78. Wang QM, Boekhout T, Bai FY (2012). Bensingtonia rectispora sp. nov. and Bensingtonia bomiensis sp. nov., novel ballistoconidium-forming yeast species from plant leaves collected in Tibet. International Journal of Systematic and Evolutionary Microbiology 62: 2039-2044.
79. Wang QM, Theelen B, Groenewald M, et al. (2014). Moniliellomycetes and Malasseziomycetes, two new classes in Ustilaginomycotina. Persoonia 33: 41-47.
80. Wright JE (1970). Agaricostilbum, a new genus of Deuteromycetes on palm spathes from Argentina. Mycologia 62: 679-682.
81. Wright JE, Bandoni RJ, Oberwinkler F (1981). Agaricostilbum: an auricularioid basidiomycete. Mycologia 73: 880-886.
82. Yamada Y, Kondo K (1973). Coenzyme Q system in the classification of the yeast genera Rhodotorula and Cryptococcus, and the yeast-like genera Sporobolomyces and Rhodosporidium. The Journal of General and Applied Microbiology 19: 59-77.
83. Yamada Y, Maeda K, Mikata K (1994). The phylogenetic relationships of Rhodosporidium dacryoideum Fell, Hunter et Tallman based on the partial sequences of 18S and 26S ribosomal RNAs: the proposal of Sakaguchia gen. nov., a heterobasidiomycetous yeast genus. Bioscience, Biotechnology and Biochemistry 58: 99-103.
84. Yokoyama K (2005). Phylogenetic relationship of the genus Malassezia based on mitochondrial cytochrome b gene. Japanese Journal of Medical Mycology 46: 151-156.
85. Yurkov AM, Kachalkin AV, Daniel HM, et al. (2015). Two yeast species Cystobasidium psychroaquaticum f.a. sp. nov. and Cystobasidium rietchieii f.a. sp. nov. isolated from natural environments, and the transfer of Rhodotorula minuta clade members to the genus Cystobasidium. Antonie Van Leeuwenhoek 107: 173-185.
86. Yurkov AM, Schäfer AM, Begerow D (2012). Leucosporidium drummii sp. nov., a member of the Microbotryomycetes isolated from soil. International Journal of Systematic and Evolutionary Microbiology 62: 728-734.