Genomics to study basal lineage fungal biology: Phylogenomics suggests a common origin

Fungal Genomics, 2nd Edition

Volumn 13, Issue , 2014, Pages 31-60

  Shelest, Ekaterina ^a   Voigt, Kerstin ^a,b  

^a HANS KNÖLL INSTITUTE   (Germany)

^b FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85003850845     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-642-45218-5_2     Document Type: Chapter

References (151)

1. Abe A, Oda Y, Asano K, Sone T (2007) Rhizopus delemar is the proper name for Rhizopus oryzae fumaric-malic acid producers. Mycologia 99:714-722
2. Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, Barta JA, Bowser SS, Bragerolle G, Fensome RA, Fredericq S, James TY, Karpov S, Kugrens P, Krug J, Lane CE, Lewis LA, Lodge J, Lynn DH, Mann DG, McCourt RM, Mendoza L, Moestrup O, Mozley-Standridge SE, Nerad TA, Shearer CA, Smirnov AV, Spiegel FW, Taylor MFJR (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol 52:399-451
3. Alastruey-Izquierdo A, Hoffmann K, De Hoog GS, Rodriguez-Tudela JL, Voigt K et al (2010) Species recognition and clinical relevance of the zygomy-cetous genus Lichtheimia (syn. Absidia pro parte, Mycocladus). J Clin Microbiol 48:2154-2170
4. Alexopoulos CJ, Mims CW, Blackwell M (1996) Introductory mycology, 4th edn. Wiley, New York
5. Alvarez E, Sutton DA, Cano J, Fothergill AW, Stchigel A, Rinaldi MG, Guarro J (2009) Spectrum of zygomycete species identified in clinically significant specimens in the United States. J Clin Microbiol 47:1650-1656
6. An Z, Wang C, Liu X, Bennett JW (2010) China’s fungal genomics initiative: a whitepaper. Mycology 1:1-8
7. Arroyo-Begovich A, Crabez-Trejo A (1982) Location of chitin in the cyst wall of Entamoeba invadens with colloidal gold racers. J Parasitol 68:253-258
8. Bacchi CJ, Weiss LM, Lane S, Frydman B, Valasinas A, Reddy V, Sun JS, Marton LJ, Khan IA, Moretto M, Yarlett N, Wittner M (2002) Novel synthetic polyamines are effective in the treatment of experimental microsporidiosis, an opportunistic AIDS-associated infection. Antimicrob Agents Chemother 46:55-61
9. Baldauf SL, Palmer JD (1993) Animals and fungi are each other’s closest relatives: congruent evidence from multiple proteins. Proc Natl Acad Sci U S A 90:11558-11562
10. Barr DJS (1978) Taxonomy and phylogeny of chytrids. Biosystems 10:153-165
11. Barr DJS (1980) An outline for the reclassification of the Chytridiales, and for a new order, the Spizellomy-cetales. Can J Bot 58:2380-2394
12. Barr DJS (1984) Cytological variation in zoospores of Spizellomyces (Chytridiomycetes). Can J Bot 62:1202-1208
13. Barr DJS (2001) Chytridiomycota. In: McLaughlin DJ, McLaughlin EG, Lemke PA (eds) The mycota VII Part A. Systematics and evolution. Springer, Berlin, pp 93-112
14. Barron GL (1987) The gun cell of Haptoglossa mirabilis. Mycologia 79:877-883
15. Bartnicki-Garcia S (1970) Cell wall composition and other biochemical markers in fungal phylogeny. In: Harbone JB (ed) Phytochemical phylogeny. Academic, London, pp 81-103
16. Bartnicki-Garcia S (1987) The cell wall in fungal evolution. In: Rayner ADM, Brasier CM, Moore D (eds) Evolutionary biology of the fungi. Cambridge University Press, New York, pp 389-403
17. Bastidas RJ, Shertz CA, Lee SC, Heitman J, Cardenas ME (2012) Rapamycin exerts antifungal activity in vitro and in vivo against Mucor circi-nelloides via FKBP12-dependent inhibition of Tor. Eukaryot Cell 11:270-281
18. Bennett JW (2000) Filamentous fungi. In: Encyclopedia of microbiology. Academic, San Diego, pp 468-477
19. Besl H, Bresinsky A (1997) Chemosystematics of Suil-laceae and Gomphidiaceae (suborder Suillineae). Plant Syst Evol 206:223-242
20. Bidartondo MI, Read DJ, Trappe JM, Merckx V, Ligrone R, Duckett JG (2011) The dawn of symbiosis between plants and fungi. Biol Lett 7:574-577
21. Birren B, Fink G, Lander E (2002) The fungal genome initiative. Paper of the Whitehead Institute Center for Genome Research developed by the Fungal Research Community. http://www.broadinstitute.org/annotation/fungi/fgi/FGI_01_whitepa-per_2002.pdf. Accessed 19 Oct 2010
22. Bohne W, Ferguson DJP, Kohler K, Gross U (2000) Developmental expression of a tandemly repeated, glycine- and serine-rich spore wall protein in the microsporidian pathogen Encephalitozoon cuni-culi. Infect Immun 68:2268-2275
23. Brakhage AA, Schroeckh V (2011) Fungal secondary metabolites—strategies to activate silent gene clusters. Fungal Genet Biol 48:15-22
24. Briggs CJ, Knapp R, Vrendenburg VT (2010) Enzootic and epizootic dynamics of the chytrid fungal pathogen of amphibians. Proc Natl Acad Sci U S A 107:9695-9700
25. Brown MW, Spiegel FW, Silberman JD (2009) Phylogeny of the ‘forgotten’ cellular slime mold, Fonti-cula alba, reveals a key evolutionary branch within Opisthokonta. Mol Biol Evol 26:2699-2709
26. Brunner E, Richthammer P, Ehrlich H, Paasch S, Simon P, Ueberlein S, van Pee K-H (2009) Chitin-based organic networks: an integral part of cell wall biosilica in the diatom Thalassiosira pseudonana. Angew Chem Int Ed Engl 48:9724-9727
27. Campos-Goengora E, Ebert F, Willhoeft U, Said-Fernn-dez S, Tannich E (2004) Characterization of chitin synthases from Entamoeba. Protist 155:323-330
28. Capella-Gutierrez S, Marcet-Houben M, Gabaldon T (2012) Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi. BMC Biol 10:47. doi:10.1186/1741-7007-10-47
29. Cavalier-Smith T (1981) Eukaryote kingdoms: seven or nine? BioSystems 14:461-481
30. Chakrabarti A, Das A, Mandal J, Shivaprakash MR, George VK, Tarai B, Rao P, Panda N, Verma SC, Sakhuja V (2006) The rising trend of invasive zygomycosis in patients with uncontrolled diabetes mellitus. Med Mycol 44:335-342
31. Collins JP (2013) History, novelty, and emergence of an infectious amphibian disease. Proc Natl Acad Sci USA 110:9193-9194
32. Cornely OA, Vehreschild JJ, Rüping MJGT (2009) Current experience in treating invasive zygomycosis with posaconazole. Treatment options for zygo-mycosis. Clin Microbiol 15:77-81
33. Cornman RS, Chen YP, Schatz MC, Street C, Zhao Y, Desany B, Egholm M, Hutchison S, Pettis JS, Lipkin WI, Evans JD (2009) Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees. PLoS Pathog 5:e1000466
34. Corradi N et al (2010) The complete sequence of the smallest known nuclear genome from the micro-sporidian Encephalitozoon intestinalis. Nat Commun 1:77
35. Cuomo CA, Desjardins CA, Bakowski MA, Goldberg J, Ma AT, Becnel JJ, Didier ES, Fan L, Heiman DI, Levin JZ, Young S, Zeng Q, Troemel ER (2012) Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth. Genome Res 22:2478-2488
36. Daszak P, Berger L, Cunningham AA, Hyatt AD, Green DE, Speare R (1999) Emerging infectious diseases and amphibian population declines. Emerg Infect Dis 5:735-748
37. De Hoog GS, Guarro J, Gene J, Figueras M (2000) Atlas of clinical fungi, 2nd edn. Centraalbureau voor Schimmelcultures, Utrecht. http://books.google.de/books?id=clv_CWVR1GoC
38. De Santiago AALCM, Hoffmann K, Lima DX, de Oliviera RJV, Vieira HEE, Malosso E, Maia LC, da Silva GA (2013) A new species of Lichtheimia (Mucoromycotina, Mucorales) isolated from Brazilian soil. Mycol Prog. doi:10.1007/s11557-113-0920-8
39. Delbac F, Peuvel I, Metenier G, Peyretaillade E, Vivares CP (2001) Microsporidian invasion apparatus: identification of a novel polar tube protein and evidence for clustering of ptp1 and ptp2 genes in three Encephalitozoon species. Infect Immun 69:1016-1024
40. Doweld A (2001) Prosyllabus tracheophytorum— Tentamen systematis plantarum vascularium (Tracheophyta). Goes mMi, Moscow, pp 1-111
41. Durkin CA, Mock T, Armbrust EV (2009) Chitin in diatoms and its association with the cell wall. Eukaryot Cell 8:1038-1050
42. Ebersberger I, Gube M, Strauss S, Kupczok A, Eckart M, Voigt K, Kothe E, von Haeseler A (2009a) A stable backbone for the fungi. Nat Precedings. hdl:10101/npre.2009.2901.1. Accessed 19 Sept 2012
43. Ebersberger I, Strauss S, von Haeseler A (2009b) HaMStR: profile hidden Markov model based. BMC Evol Biol 9:157
44. Ebersberger I, de Matos SR, Kupczok A, Gube M, Kothe E, Voigt K, von Haeseler A (2012) A consistent phylogenetic backbone for the fungi. Mol Biol Evol 29:1319-1334
45. Eckart M, Eckart M, Fliegerova K, Hoffmann K, Voigt K (2010) Molecular identification of anaerobic rumen fungi. In: Gherbawy Y, Voigt K (eds) Molecular identification of fungi: Part I. Springer, Berlin, pp 297-313
46. Fast NM, Keeling PJ (2001) Alpha and beta subunits of pyruvate dehydrogenase E1 from the microspor-idian Nosema locustae: mitochondrion-derived carbon metabolism in microsporidia. Mol Biochem Parasitol 117:201-209
47. Fisher MC, Garner TWJ, Walker SF (2009) Global emergence of Batrachochytrium dendrobatidis and amphibian chytridiomycosis in space, time, and host. Annu Rev Microbiol 63:291-310
48. Frisvad JC, Filtenborg O (1990) Secondary metabolites as consistent criteria in Penicillium taxonomy and a synoptic key to Penicillium subgenus Penicil-lium. In: Samson RA, Pitt JI (eds) Modern concepts in Penicillium and Aspergillus classification. Plenum Press, New York, pp 373-384
49. Gherbawy Y, Voigt K (eds) (2010) Molecular identification of fungi. Springer, Berlin, Heidelberg, New York: 1st edition, March 2010, vol XXI, 501 p. 87 illus., 39 in colour. Hardcover, ISBN 978-3-64205041-1
50. Glockling SL, Beakes GW (2002) Ultrastructural morphogenesis of dimorphic arcuate infection (gun) cells of Haptoglossa erumpens an obligate parasite of Bunonema nematodes. Fungal Genet Biol 37:250-262
51. 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 6,000 genes. Science 274(546):563-567
52. Greco N, Bussers JC, Van Daele Y, Goffinet G (1990) Ultrastructural localization of chitin in the cystic wall of Euplotes muscicola Kahl (Ciliata, Hypotri-chia). Eur J Protistol 26:75-80
53. Griffith GW, Baker S, Fliegerova K, Liggenstoffer A, van der Giezen M, Voigt K, Beakes G (2010) Anaerobic fungi: Neocallimastigomycota. IMA Fungus 1:181-185
54. Grigoriev IV, Cullen D, Goodwin SB, Hibbett D, Jeffries TW, Kubicek CP, Kuske C, Magnuson JK, Martin F, Spatafora JW, Tsang A, Baker SE (2011) Fueling the future with fungal genomics. Mycology 3:192-209
55. Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, Kuo A, Minovitsky S, Nikitin R, Ohm RA, Otillar R, Poliakov A, Ratnere I, Riley R, Smirnova T, Rokhsar D, Dubchak I (2012) The genome portal of the Department of Energy Joint Genome Research. Nucleic Acids Res 40(1):D26-D32
56. Gryganskyi AP, Lee SC, Litvintseva AP, Smith ME, Bonito G, Porter T, Anishchenko IM, Heitman J, Vilgalys R (2010) Structure, function, and phylog-eny of the mating locus in the Rhizopus oryzae complex. PLoS One 5(12):e15273. doi:10.1371/journal.pone.0015273
57. Hashimoto T, Snchez LB, Shirakura T, Müller M, Hasegawa M (1998) Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phy-logeny. Proc Natl Acad Sci USA 95:6860-6865
58. 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
59. Hawksworth DL (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105:1422-1432
60. Hawksworth DL, Rossman AY (1997) Where are all the undescribed fungi? Phytopathology 87:888-891
61. Hawksworth DL, Kirk PM, Sutton BC, Pegler DN (1995) Ainsworth and Bisby’s dictionary of the fungi, 8th edn. International Mycological Institute, Kew, London
62. Heckman DS, Geiser DM, Eidell BR, Stauffer RL, Kardos NL, Hedges SB (2001) Molecular evidence for the early colonization of land by fungi and plants. Science 293:1129-1133
63. Herth W, Kuppel A, Schnepf E (1977) Chitinous fibrils in the lorica of the flagellate chrysophyte Poterio-chromonas stipitata(syn. Ochromonas malhamen-sis). J Cell Biol 73:311-321
64. Hibbett DS, Taylor JW (2013) Fungal systematics: is a new age of enlightenment at hand? Nat Rev Microbiol 11:129-133
65. Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson O, Huhndorf S, James T, Kirk PM, Liicking R, Lumbsch T, Lutzoni F, Matheny PB, McLaughlin DJ, Powell MJ, Redhead S, Schoch CL, Spatafora JW, Stalpers JA, Vilgalys R, Aime MC, Aptroot A, Bauer R, Begerow D, Benny GL, Castlebury LA, Crous PW, Dai Y-C, Gams W, Geiser DM, Griffith GW, Gueidan C, Hawksworth DL, Hestmark G, Hosaka K, Humber RA, Hyde K, Koljalb U, Kurtzman CP, Larsson K-H, Lichtwardt R, Longcore J, Miadlikowska J, Miller A, Moncalvo J-M, Mozley-Standridge S, Oberwinkler F, Parmasto R, Reeb V, Rogers JD, Roux C, Ryvarden L, Sampaio JP, Schuessler A, Sugiyama J, Thorn RG, Tibell L, Untereiner WA, Walker C, Wang A, Weir A, Weiss M, White M, Winka K, Yao Y-J, Zhang N (2007) A higher-level phylogenetic classification of the Fungi. Mycol Res 111:509-547
66. Hibbett DS, Ohman A, Kirk PM (2009) Fungal ecology catches fire. New Phytol 184:279-282
67. Hijri M, Redecker D, MacDonald-Comber Petetot JA, Voigt K, Wostemeyer J, Sanders IR (2002) Identification and isolation of two ascomycete fungi from spores of the arbuscular mycorrhizal fungus Scutellospora castanea. Appl Environ Microbiol 68:4567-4573
68. Hirt RP, Healy B, Vossbrinck CR, Canning EU, Embley TM (1997) A mitochondrial Hsp70 orthologue in Vairimorpha necatrix: molecular evidence that microsporidia once contained mitochondria. Curr Biol 7:995-998
69. Hoffmann K, Telle S, Walther G, Eckart M, Kirchmair M, Prillinger HJ, Prazenica A, Newcombe G, Dolz F, Papp T, Vgvolgyi C, de Hoog S, Olsson L, Voigt K (2009) Diversity, genotypic identification, ultrastructural and phylogenetic characterization of zygomycetes from different ecological habitats and climatic regions: limitations and utility of nuclear ribosomal DNA barcode markers. In: Gherbawy Y, Mach RL, Rai M (eds) Current advances in molecular mycology. Nova Science, New York, pp 263-312
70. Hoffmann K, Voigt K, Kirk PM (2011) Mortierellomy-cotina subphyl. nov. based on multi-gene genealogies. Mycotaxon 115:353-363
71. Humber RA (2012) Entomophthoromycota: a new phylum and reclassification for entomophthoroid fungi. Mycotaxon 120:477-492
72. James TY, Berbee ML (2011) No jacket required—new fungal lineage defies dress code: recently described zoosporic fungi lack a cell wall during trophic phase. Bioessays 34:94-102
73. James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung GH, Johnson D, O’Rourke B, Crockett M, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schüler A, Longcore JE, O’Donnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Humber RA, Morton JB, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lucking R, Büdel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, Vilgalys R (2006a) Reconstructing the early evolution of the fungi using a six-gene phylogeny. Nature 443:818-822
74. James TY, Letcher PM, Longcore JE, Mozley-Strandridge SE, Porter D, Powell MJ, Griffith GW, Vilgalys R (2006b) A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomy-cota). Mycologia 98:860-871
75. Jany JL, Pawlowska TE (2010) Multinucleate spores contribute to evolutionary longevity of asexual glomeromycota. Am Nat 175:424-435. doi:10.1086/650725
76. Johnson DL, Garnow RI (1971) The avoidance response in Phycomyces. J Gen Physiol 57:41-49
77. Jones MDM, Forn I, Gadelha C, Egan MJ, Bass D, Massana R, Richards TA (2011a) Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474:200-203
78. Jones MDM, Richards TA, Hawksworth DL, Bass D (2011b) Validation and justification of the phylum name Cryptomycota phyl. nov. IMA Fungus 2:173-175
79. Joneson S, Stajich JE, Shiu S-H, Rosenblum EB (2011) Genomic transition to pathogenicity in chytrid tungi. PLoS Pathog 7(11):e1002338
80. Kamaishi T, Hashimoto T, Nakamura Y, Nakamura F, Murata S, Okada N, Okamoto KI, Shimizu M, Hasegawa M (1996) Protein phylogeny of translation elongation factor EF-1a suggests microspor-idians are extremely ancient eukaryotes. J Mol Evol 42:257-263
81. Karpov SA, Mikhailov KV, Mirzaeva GS, Mirabdullaev IM, Mamkaeva KA, Titova NN, Aleoshin VV (2013) Obligately phagotrophic aphelids turned out to branch with the earliest-diverging Fungi. Protist 164:195-205
82. Katinka MD, Duprat S, Cornillot E, Meeteenier G, Thomarat F, Prenier G, Barbe V, Peyretaillade E, Brottier P, Wincker P, Delbac F, El Alaoui H, Peyret P, Saurin W, Gouy M, Weissenbach J, Vivares CP (2001) Genome sequence and gene compaction of the eukaryote parasite Encephalito-zoon cuniculi. Nature 414:450-453
83. Keeling PJ, Slamovits CH (2004) Simplicity and complexity of Microsporidian genomes. Eukaryot Cell 3:1363-1369
84. Kneipp LF, Andrade AF, de Souza W, Angluster J, Alviano CS, Travassos LR (1998) Trichomonas vaginalis and Tritrichomonas foetus: expression of chitin at the cell surface. Exp Parasitol 89:195-204
85. Lang BF, O’Kelly C, Nerad T, Gray MW, Burger G (2002) The closest unicellular relatives of animals. Curr Biol 12:1773-1778
86. Lanternier F, Dannaoui E, Morizot G, Elie C, Huerre M et al (2012) A global analysis of mucormycosis in France: the RetroZygo Study (2005-2007). Clin Infect Dis 54:35-43. doi:10.1093/cid/cir880
87. Lara E, Moreira D, Lopez-Garcia P (2010) The environmental clade LKM11 and Rozella form the deepest branching clade of fungi. Protist 161:116-121
88. Lee SC, Li A, Calo S, Heitman J (2013) Calcineurin plays key roles in the dimorphic transition and virulence of the human pathogenic zygomycete Mucor circi-nelloides. PLoS Pathog 9(9):e1003625. doi:10.1371/journal.ppat.1003625
89. Li CH, Cervantes M, Springer DJ, Boekhout T, Ruiz-Vazquez RM, Torres-Martinez SR, Lee SC (2011) Sporangiospore size dimorphism is linked to virulence of Mucor circinelloides. PLoS Pathog 7 (6):e1002086. doi:10.1371/journal.ppat.1002086
90. Liggenstoffer AS, Youssef NH, Couger MB, Elshahed MS (2010) Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores. ISME J 4:1225-1235
91. Liu YJ, Hodson MC, Hall BD (2006) Loss of the flagel-lum happened only once in the fungal lineage: phylogenetic structure of kingdom Fungi inferred from RNA polymerase II subunit genes. BMC Evol Biol 6:74. doi:10.1186/1471-2148-6-74
92. Longcore JE, Pessier AP, Nichols DK (1999) Batracho-chytrium dendrobatidis gen. et sp. nov., a chytrid pathogenic to amphibians. Mycologia 91:219-227
93. Ma LJ, Ibrahim AS, Skory C, Grabherr MG, Burger G et al (2009) Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genet 5:e1000549. doi:10.1371/journal.pgen.1000549
94. Marano AV, Gleason FH, Barlocher F, Pires-Zottarelli CL, Lilje O, Schmidt SK, Rasconi S, Kagami M, Barrera MD, Sime-Ngando T, Boussiba S, de Souza JI, Edwards JE (2012) Quantitative methods for the analysis of zoosporic fungi. J Microbiol Methods 89:22-33
95. Marcet-Houben M, Marceddu G, Gabaldon T (2009) Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence. BMC Evol Biol 9:295
96. Martel A, Spitzen-van der Sluijs A, Blooi M, Bert W, Ducatelle R, Woeltjes A, Bosman W, Chiers K, Bossuyt F, Pasmans F (2013) Batrachochytrium salamandrivorans sp. nov. causes lethal chytridio-mycosis in amphibians. Proc Natl Acad Sci USA 110:15325-15329
97. Martin F, Gianinazzi-Pearson V, Hijri M, Lammers P, Requena N, Sanders IR, Sachar-Hill Y, Tuskan GA, Young JPW (2008) The long hard road to a completed Glomus intraradices genome. New Phytol 180:747-750
98. Maxson LR, Maxson RD (1990) Immunological techniques. In: Hillis DM, Moritz C (eds) Molecular systematics. Sinauer, Sunderland, pp 127-155
99. McNeill J, Barrie FR, Buck WR, Demoulin V, Greuter W, Hawksworth DL, Herendeen PS, Knapp S, Marhold K, Prado J, Prud’ Homme vanReine WF, Smith GF, Wiersema JH, Turland NJ (2012) International Code of Nomenclature for algae, fungi, and plants (Melbourne Code). Regnum vegetabile 154. Adopted by the Eighteenth International Bot-nical Congress Melbourne, Australia, July 2011. Koeltz Scientific Books, Koenigstein
100. Mehrotra RS, Aneja KR (1990) An introduction to Mycology, 1st edn. New Age (P) Ltd. Publishers, New Delhi, pp 141-143
101. Mendoza L, Taylor JW, Ajello L (2002) The class Meso-mycetozoea: a heterogenous group of microorganisms at the animal-fungal boundary. Annu Rev Microbiol 56:315-344
102. Mulisch M (1993) Chitin in protistan organisms: distribution, synthesis and deposition. Eur J Protistol 29:1-18
103. Noha H, Youssef NH, Couger MB, Struchtemeyer CG, Liggenstoffer AS, Prade RA, Najar FZ, Atiyeh HK, Wilkins MR, Mostafa S, Elshahed MS (2013) The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader. Appl Environ Microbiol 79:4620-4634. doi:10.1128/AEM.00821-13
104. Paterson RRM, Bridge PD (1994) Biochemical techniques for filamentous fungi. CAB International, Wallingford
105. Patterson DJ (1999) The diversity of eukaryotes. Am Nat 154:S96-S124
106. Patterson DJ, Zolffel M (1991) Heterotrophic flagellates of uncertain taxonomic position. In: Patterson DJ, Larsen J (eds) The biology of free-living heterotro-phic flagellates, vol 45, Systematics Association Special Volume. Clarendon, Oxford, pp 427-447
107. Peyretaillade E, Biderre C, Peyret P, Duffieux F, Mete-nier G, Gouy M, Michot B, Vivares CP (1998a) Microsporidian Encephalitozoon cuniculi, a unicellular eukaryote with an unusual chromosomal dispersion of ribosomal genes and a LSU rRNA reduced to the universal core. Nucleic Acids Res 26:3513-3520
108. Peyretaillade E, Broussolle V, Peyret P, Meeteenier G, Gouy M, Vivares CP (1998b) Microsporidia, ami-tochondrial protists, possess a 70-kDa heat shock protein gene of mitochondrial evolutionary origin. Mol Biol Evol 15:683-689
109. Philipps BL, Puschendorf R (2013) Do pathogens become more virulent as they spread? Evidence from the amphibian declines in Central America. Proc Biol Sci 280:20131290
110. Pirozynski KA, Malloch DW (1975) The origin of land plants: a matter of mycotrophism. Biosystems 6:153-164
111. Pitt JI (1979) The genus Penicillium and its teleo-morphic states Eupenicillium and Talaromyces. Academic, London
112. Popescu T, Roessler A, Fukshansky L (1989) A novel effect in Phycomyces phototropism. Plant Physiol 91:1586-1593
113. Ragan MA, Murphy CA, Rand TG (2003) Are Ichthyos-porea animals or fungi? Bayesian phylogenetic analysis of elongation factor 1a of Ichthyophonus irregularis. Mol Phylogent Evol 29:550-562
114. Redecker D, Kodner R, Graham LE (2000) Glomalean fungi from the Ordovician. Science 289:1920-1921
115. Remy W, Taylor TN, Hass H, Kerp H (1994) Four hundred-million year-old vesicular arbuscular mycorrhizae. Proc Natl Acad Sci USA 91:11841-11843
116. Ribes JA, Vanover-Sams CL, Baker DJ (2000) Zygomycetes in human disease. Clin Microbiol Rev 13:236-301
117. Ride WDL, Cogger HG, Dupuis C, Kraus O, Minelli A, Thompson FC, Tubbs PK (2000) International code of zoological nomenclature. Adopted by the International Union of Biological Sciences. International Trust for Zoological Nomenclature 1999, London
118. Roden MM, Zaoutis TE, Buchanan WL, Knudsen TA, Sarkisova TA, Schaufele RL, Sein M, Sein T, Chiou CC, Chu JH, Kontoyiannis DP, Walsh TJ (2005) Epidemiology and outcome of zygomycosis: a review of 929 reported cases. Clin Infect Dis 41:634-653
119. Rosenblum EB, James TY, Zamudio KR, Poorten TJ, Ilut D, Rodriguez D, Eastman JM, RichardsHrdlicka K, Joneson S, Jenkinson TS, Longcore JE, Olea GP, Toledo LF, Arellano ML, Medina EM, Restrepo S, Flechas SV, Berger L, Briggs CJ, Stajich JE (2013) Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data. Proc Natl Acad Sci U S A 110:9193-9194
120. Ruiz-Trillo I, Lane CE, Archibald JM, Roger AJ (2006) Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Cap-saspora owczarzaki and Sphaeroforma arctica. J Eukaryot Microbiol 53:379-384
121. Ruiz-Trillo I, Burger G, Holland PWH, King N, Lang BF, Roger AJ, Gray MW (2007) The origins of multicellularity: a multi-taxon genome initiative. Trends Genet 23:113-118
122. Saffo MB, Fultz S (1986) Chitin in the symbiotic protist Nephromyces. Can J Bot 64:1306-1310
123. Saffo MB, McCoy AM, Rieken C, Slamovits CH (2010) Nephromyces, a beneficial apicomplexan symbiont in marine animals. Proc Natl Acad Sci U S A 107:16190-16195
124. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Fungal Barcod-ing 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
125. Schroeckh V, Scherlach K, Nützmann HW, Ekaterina S, Schmidt-Heck SJ, Martin K, Hertweck C, Brakhage AA (2009) Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans. Proc Natl Acad Sci U S A 106:14558-14563
126. Shalchian-Tabrizi K, Minge MA, Espelund M, Orr R, Ruden T, Jakobsen KS, Cavalier-Smith T (2008) Multigene phylogeny of Choanozoa and the origin of animals. PLoS ONE 3:e2098. doi:10.1371/jour-nal.pone.0002098
127. Shelest E (2008) Transcription factors in fungi. FEMS Microbiol Lett 286:145-151
128. Simon L, Bousquet J, Lévesque RC, Lalonde M (1993) Origin and diversification of endomycorrhizal fungi and co-incidence with vascular land plants. Nature 363:67-69
129. Skiada A, Pagano L, Groll A, Zimmerli S, Dupont B, Lagrou K, Lass-Florl C, Bouza E, Klimko N, Gaustad P, Richardson M, Hamal P, Akova M, Meis JF, Rodriguez-Tudela JL, Roilides E, Mitrousia-Ziouva A, Petrikkos G, European Confederation of Medical Mycology Working Group on Zygomycosis (2011) Zygomycosis in Europe: analysis of 230 cases accrued by the registry of the European Confederation of Medical Mycology (ECMM) Working Group on Zygomycosis between 2005 and 2007. Clin Microbiol Infect 17:1859-1867
130. Smith SE, Read DJ (2008) Mycorrhizal symbiosis. Academic, San Diego
131. Spatafora J (2011) 1000 fungal genomes to be sequenced. Fungi: 1000 genomes. IMA Fungus 2 (2):41
132. Steenkamp ET, Wright J, Baldauf SL (2006) The protis-tan origins of animals and fungi. Mol Biol Evol 23:93-106
133. Sugar AM (1992) Mucormycosis. Clin Infect Dis 14 (Suppl 1):S126-S129. http://www.pubmedcentral. nih.gov/articlerender.fcgi?artid=90004andtool=pm-centrezandrendertype=abstract
134. Sun HY, Aguado JM, Bonatti H, Forrest G, Gupta KL, Safdar N, John GT, Pursell KJ, Muñoz P, Patel R, Fortun J, Martin-Davila P, Philippe B, Philit F, Tabah A, Terzi N, Chatelet V, Kusne S, Clark N, Blumberg E, Julia MB, Humar A, Houston S, Lass-Florl C, Johnson L, Dubberke ER, Barron MA, Lortholary O, Singh N, Zygomycosis Transplant Study Group (2009) Pulmonary zygo-mycosis in solid organ transplant recipients in the current era. Am J Transplant 9:2166-2171
135. Tanabe Y, Watanabe MM, Sugiyama J (2002) Are Microsporidia really related to Fungi? A reappraisal based on additional gene sequences from basal fungi. Mycol Res 106:1380-1391
136. Vitale RG, de Hoog GS, Schwarz P, Dannaoui E, Deng S, Machouart M, Voigt K, van de Sande WWJ, Dolatabadi S, Meis JF, Walther G (2012) Antifungal susceptibility and phylogeny of opportunistic members of the order Mucorales. J Clin Microbiol 50:66-75
137. Voigt K (2012a) Chytridiomycota. In: Engler A, Frey W (eds) Syllabus of plant families, vol 1/1: Blue-green algae, myxomycetes and myxomycete-like organisms, phytoparqasitic protists, heterotrophic Het-erokontobionta and Fungi pp. Borntraeger, Stuttgart, pp 106-129
138. Voigt K (2012b) Zygomycota. In: Engler A, Frey W (eds) Syllabus of plant families, vol 1/1: Blue-green algae, myxomycetes and myxomycete-like organisms, phytoparqasitic protists, heterotrophic Heterokontobionta and Fungi pp. Borntraeger, Stuttgart, pp 130-162
139. Voigt K, Kirk PM (2011) Recent developments in the taxonomic affiliation and phylogenetic positioning of fungi: impact in applied microbiology and environmental biotechnology. Appl Microbiol Bio-technol 90:41-57
140. Voigt K, Marano AV, Gleason F (2013) Ecological and economical importance of parasitic and zoosporic true Fungi. In: Kempken F (ed) The Mycota vol. XI: agricultural applications, 2nd edn. Springer, Berlin, pp 243-270
141. Vossbrinck CR, Maddox JV, Friedman S, Debrunner-Vossbrinck BA, Woese CR (1987) Ribosomal RNA sequence suggests microsporidia are extremely ancient eukaryotes. Nature 326:411-414
142. Voyles J, Young S, Berger L, Campbell C, Voyles WF, Dinudom A, Cook D, Webb R, Alford RA, Skerratt LF, Speare R (2009) Pathogenesis of chytridiomy-cosis, a cause of catastrophic amphibian declines. Science 326:582-585
143. Voyles J, Vredenburg VT, Tunstall TS, Parker JM, Briggs CJ, Rosenblum EB (2012) Pathophysiology in mountain yellow-legged frogs (Rana muscosa) during a chytridiomycosis outbreak. PLoS ONE 7: e35374. doi:10.1371/journal.pone.0035374
144. Wang B, Yeun LH, Xue JY, Liu Y, Ané JM, Qiu YL (2010) Presence of three mycorrhizal genes in the common ancestor of land plants suggests a key role of mycorrhizas in the colonization of land by plants. New Phytol 186:514-525
145. Wang L, Chen W, Feng Y, Ren Y, Gu Z, Chen H, Wang H, Thomas MJ, Zhang B, Berquin IM, Li Y, Wu J, Zhang H, Song Y, Liu X, Norris JS, Wang S, Du P, Shen J, Wang N, Yang Y, Wang W, Feng L, Ratledge C, Zhang H, Chen YQ (2011) Genome characterization of the oleaginous fungus Mortier-ella alpina. PLoS ONE 6(12):e28319. doi:10.1371/journal.pone.0028319
146. Wang D, Wu R, Xu Y, Li M (2013) Draft genome sequence of Rhizopus chinensis CCTCCM201021, used for brewing traditional Chinese alcoholic beverages. Genome Announc 1(2):e0019512. doi:10.1128/genomeA.00195-12
147. Ward HHD, Alroy J, Lev BI, Keusch GT, Pereira MEA (1985) Identification of chitin as a structural component of Giardia cysts. Infect Immun 49:629-634
148. Webster J, Weber RWS (2007) Introduction to fungi. Cambridge University Press, Cambridge
149. Whittaker RH (1969) New concepts of kingdoms of organisms. Science 163:150-160
150. Zettler LA, Nerad T, O’Kelly C, Sogin M (2001) The nucleariid amoebae: more protists at the animal-fungal boundary. J Eukaryot Microbiol 48:293-297
151. Zhao Z, Huiquan Liu H, Wang C, Xu JR (2013) Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi. BMC Genomics 14:274