The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts

Abstract

Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.

This is a preview of subscription content, access via your institution.

Fig. 1

References

  1. Abarenkov K, Nilsson RH, Larsson KH, Alexander IJ, Eberhardt U, Erland S, Høiland K, Kjøller R, Larsson E, Pennanen T, Sen R, Taylor AFS, Tedersoo L, Ursing BM, Vrålstad T, Liimatainen K, Peintner U, Kõljalg U (2010) The UNITE database for molecular identification of fungi—recent updates and future perspectives. New Phytol 186(2):281–285

    PubMed  Article  Google Scholar 

  2. Aime MC, Toome M, McLaughlin DJ (2014) Pucciniomycotina. In: McLaughlin DJ, Spatafora JW (eds) The Mycota VII Part A. Systematics and evolution, 2nd edn. Springer, Berlin Heidelberg, pp 271–294

    Google Scholar 

  3. Anderson JB, Ullrich RC (1979) Biological species of Armillaria mellea in North America. Mycologia 71:402–414

    Article  Google Scholar 

  4. Ariyawansa HA, Hawksworth DL, Hyde KD, Jones EBG, Maharachchikumbura SSN, Manamgoda DS, Thambugala KM, Udayanga D, Camporesi E, Daranagama A, Jayawardena R, Liu JK, McKenzie EHC, Phookamsak R, Shivas RG (2014) Epitypification and neotypification: guidelines with appropriate and inappropriate examples. Fungal Divers 69:57–91

    Article  Google Scholar 

  5. Arvanitoyannis IS (2008) Waste management for the food industries, Elsevier Inc., Oxford, p 413–452

  6. Avise JC, Ball RM Jr (1990) Principles of genealogical concordance in species concepts and biological taxonomy. In: Futuyma D, Antonovics J (eds) Oxford surveys in evolutionary biology, vol 7. Oxford University Press, Oxford, pp 45–67

    Google Scholar 

  7. Bandara AR, Rapior S, Bhat DJ, Kakumyan P, Chamyuang S, Xu J, Hyde KD (2015) Polyporus umbellatus, an edible-medicinal cultivated mushroom with multiple developed health-care products as food, medicine and cosmetics: a review. Cryptogam Mycol 36(1):3–42

    Article  Google Scholar 

  8. Barr ME (1979) A classification of Loculoascomycetes. Mycologia 71:935–957

    Article  Google Scholar 

  9. Barr ME (1987) Prodromus to class Loculoascomycetes. Newell, Amherst

    Google Scholar 

  10. Barr DJS (1992) Evolution and kingdoms of organisms from the perspective of a mycologist. Mycologia 84:1–11

    Article  Google Scholar 

  11. Bartlett JMS, Stirling D (2003) A short history of the polymerase chain reaction. PCR protocols. Methods Mol Biol 226(2):3–6

    CAS  PubMed  Google Scholar 

  12. Bates ST, Ahrendt S, Bik HM, Bruns TD, Caporaso JG, Cole J, Dwan M, Fierer N, Gu D, Houston S, Knight R, Leff J, Lewis C, Maestre JP, McDonald D, Nilsson RH, Porras-Alfaro A, Robert V, Schoch C, Scott J, Taylor DL, Parfrey LW, Stajich JE (2013) Meeting report: fungal ITS workshop. Stand Genomic Sci 8(1):118–123

    PubMed Central  PubMed  Article  Google Scholar 

  13. Bauer R, Garnica S, Oberwinkler F, Riess K, Weiß M, Begerow D (2015) Entorrhizomycota: a new fungal phylum reveals new perspectives on the evolution of fungi. PLoS ONE 10(7):e0128183. doi:10.1371/journal.pone.0128183

    PubMed Central  PubMed  Article  CAS  Google Scholar 

  14. Begerow D, Schäfer AM, Kellner R, Yurkov A, Kemler M, Oberwinkler F, Bauer R (2014) Ustilaginomycotina. In: McLaughlin DJ, Spatafora JW (eds) The Mycota VII Part A. Systematics and evolution, 2nd edn. Springer, Berlin, pp 295–330

    Google Scholar 

  15. Bellard C, Bertelsmeier C, Leadley P, Thuiller W, Courchamp F (2012) Impacts of climate change on the future of biodiversity. Ecol Lett 15:365–377

    PubMed Central  PubMed  Article  Google Scholar 

  16. Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez-García M, Ebersberger I, de Sousa F, Amend A, Jumpponen A, Unterseher M, Kristiansson E, Abarenkov K, Bertrand YJK, Sanli K, Eriksson KM, Vik U, Veldre V, Nilsson RH (2013) Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol 4(10):914–919

    Google Scholar 

  17. Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2015) GenBank. Oxf J 43(D1):30–35

    Google Scholar 

  18. Binder M, Larsson KH, Matheny PB, Hibbett DS (2010) Amylocorticiales ord. nov. and Jaapiales ord. nov.: early diverging clades of agaricomycetidae dominated by corticioid forms. Mycologia 102(4):865–880

    CAS  PubMed  Article  Google Scholar 

  19. Binder M, Justo A, Riley R, Salamov A, Lopez-Giraldez F, Sjökvist E, Copeland A, Foster B, Sun H, Larsson E, Larson K-H, Townsend J, Grigoriev IV, Hibbett DS (2013) Phylogenetic and phylogenomic overview of the Polyporales. Mycologia 105(6):1350–1373

    CAS  PubMed  Article  Google Scholar 

  20. Blackwell M (2011) The Fungi: 1, 2, 3 … 5.1 million species? Am J Bot 98:426–438

    PubMed  Article  Google Scholar 

  21. Braun U, Cook RTA (2012) Taxonomic manual of the Erysiphales (powdery mildews), vol 11, CBS biodiversity series. CBS, Utrecht

    Google Scholar 

  22. Cafaro MJ (2005) Eccrinales (Trichomycetes) are not fungi, but a clade of protists at the early divergence of animals and fungi. Mol Phylogenet Evol 35:21–34

    CAS  PubMed  Article  Google Scholar 

  23. Castlebury LA, Rossman AY, Jaklitsch WJ, Vasilyeva LN (2002) A preliminary overview of the Diaporthales based on large subunit nuclear ribosomal DNA sequences. Mycologia 94:1017–1031

    CAS  PubMed  Article  Google Scholar 

  24. Castlebury LA, Farr DF, Rossman AY, Jaklitsch WJ (2003) Diaporthe angelicae comb.nov., a modern description and placement of Diaporthopsis in Diaporthe. Mycoscience 44:203–208

    Article  Google Scholar 

  25. Chomnunti P, Hongsanan S, Aguirre-Hudson B, Tian Q, Peršoh D, Dhami MK, Alias AS, Xu JC, Liu XZ, Stadler M, Hyde KD (2014) The sooty moulds. Fungal Divers 66:1–36

    Article  Google Scholar 

  26. Cracraft J, Donoghue MJ (eds) (2004) Assembling the tree of life. Oxford University Press, New York

    Google Scholar 

  27. Crous PW, Gams W, Stalpers JA, Robert V, Stegehuis G (2004a) An online database of names and descriptions as an alternative to registration. Mycol Res 108:1236–1238

    Article  Google Scholar 

  28. Crous PW, Gams W, Stalpers JA, Robert V, Stegehuis G (2004b) MycoBank: an online initiative to launch mycology into the 21st century. Stud Mycol 50:19–22

    Google Scholar 

  29. Cummins GB, Hiratsuka Y (2003) Illustrated genera of rust fungi, 3rd edn. Am Phytopathol Soc, St. Paul

  30. Dentinger BTM, Gaya E, O’ Brien H, Suz LM, Lachlan R, Díaz-Valderrama JR, Koch RA, Aime MC (2015) Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life. Biol J Linn Soc. doi:10.1111/bij.12553

  31. Dettman JR, Jacobson DJ, Taylor JW (2003) A multilocus genealogical approach to phylogenetic species recognition in themodel eukaryote Neurospora. Evolution 57:2703–2720

    PubMed  Article  Google Scholar 

  32. Diba K, Kordbacheh P, Mirhendi SH, Rezaie S, Mahmoudi M (2007) Identification of Aspergillus species using morphological characteristics. Pak J Med Sci 23:867–872

    Google Scholar 

  33. Dupis JR, Roe AD, Fah S (2012) Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Mol Ecol 21:4422–4436

    Article  Google Scholar 

  34. Duránad N, Teixeirab MFS, Contia RD, Espositocd E (2002) Ecological-friendly pigments from fungi. Crit Rev Food Sci Nutr 42(1):53–66

    Article  Google Scholar 

  35. Eggins HOW, Pugh GJF (1962) Isolation of cellulose-decomposing fungi from the soil. Nature 193:94–95

    Article  Google Scholar 

  36. Ertz D, Diederich P (2015) Dismantling Melaspileaceae: a first phylogenetic study of Buelliella, Hemigrapha, Karschia, Labrocarpon and Melaspilea. Fungal Divers 71:141–164. doi:10.1007/s13225-015-0321-1

    Article  Google Scholar 

  37. Ertz D, Lawrey JD, Common RS, Diederich P (2013) Molecular data resolve a new order of Arthoniomycetes sister to the primarily lichenized Arthoniales and composed of black yeasts, lichenicolous and rock-inhabiting species. Fungal Divers 66:113–137. doi:10.1007/s13225-013-0250-9

    Article  Google Scholar 

  38. Espinoza JG, Briceno EX, Keith LM, Latorre BA (2008) Canker and twig dieback of blueberry caused by Pestalotiopsis spp. and a Truncatella sp. in Chile. Plant Dis 92:1407–1414

    Article  Google Scholar 

  39. Fiore-Donno AM, Nikolaev SI, Nelson M, Pawlowski J, Cavalier-Smith T, Baldauf SL (2010) Deep phylogeny and evolution of slime moulds (Mycetozoa). Protist 161:55–70

    CAS  PubMed  Article  Google Scholar 

  40. Fischer AL, Moncalvo JM, Klironomos JN, Malcolm JR (2012) Fruiting body and molecular rDNA sampling of fungi in woody debris from logged and unlogged boreal forests in Northeastern Ontario. Ecoscience 19:374–390

    Article  Google Scholar 

  41. Freeman K, Martin A, Karki D, Lyncha RC, Mittera MS, Meyera AF, Longcorec JE, Simmonsc DR, Schmidta SK (2009) Evidence that chytrids dominate fungal communities in high-elevation soils. Proc Natl Acad Sci U S A 106:18315–18320

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  42. Gargas A, Taylor JW (1992) Polymerase chain reaction (pcr) primers for amplifying and sequencing nuclear 18 s rdna from lichenized fungi. Mycologia 84(4):589–592

    CAS  Article  Google Scholar 

  43. Gherbawy Y, Voigt K (2010) Molecular identification of fungi. Springer, Berlin, pp vii–xi

    Google Scholar 

  44. Giraud T, Refregier G, de Vienne DM, Hood ME (2008) Speciation in fungi. Fungal Genet Biol 45:791–802

    CAS  PubMed  Article  Google Scholar 

  45. Gottlieb AM, Lichtwardt RW (2001) Molecular variation within and among species of Harpellales. Mycologia 93:66–81

    CAS  Article  Google Scholar 

  46. Gregory TR, Nicol JA, Tamm H, Kullman B, Kullman K, Leitch IJ, Murray BG, Kapraun DF, Greilhuber J, Bennett MD (2007) Eukaryotic genome size databases. Oxf J 35:332–338

    Google Scholar 

  47. Groenewald JZ, Nakashima C, Nishikawa J, Shin HD, Park JH, Jama AN, Groenewald M, Braun U, Crous PW (2013) Species concepts in Cercospora: spotting the weeds among the roses. Stud Mycol 75:115–170

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  48. Guarro J, Gene J, Stchigel AM (1999) Developments in fungal taxonomy. Clin Microbiol Rev 12:454–500

    PubMed Central  CAS  PubMed  Google Scholar 

  49. Gupta VK, Sreenivasaprasad S, Mach RL (2015) Fungal bio-molecules: sources, applications and recent developments. Science p 424

  50. 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

    Article  Google Scholar 

  51. Hawksworth DL (2015) Naming fungi involved in spoilage of food, drink, and water. Food Mycol 5:23–28

    Google Scholar 

  52. Heffer V, Johnson KB, Powelson ML, Shishkoff N (2006) Identification of powdery mildew fungi. The American Phytopathological Society Laboratory Exercises in Plant Pathology series. The Plant Health Instructor. doi: 10.1094/PHI-I-2006-0706-01

  53. Hennebert GL (1987) Pleoanamorphy and its nomenclatural problem. In: Sugiyama J (ed) Pleomorphic fungi: the diversity and its taxonomic implications. Kodansha, Tokyo, pp 263–290

    Google Scholar 

  54. Hennebert GL, Weresub LK (1977) Terms for states and forms of fungi, their names and types. Mycotaxon 6:207–211

    Google Scholar 

  55. Hibbett DS, Taylor JW (2013) Fungal systematics: is a new age of enlightenment at hand? Nat Rev Microbiol 11:129–133

    CAS  PubMed  Article  Google Scholar 

  56. Hibbett DS, Pine EM, Langer G, Langer E, Donoghue MJ (1997) Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences. Proc Natl Acad Sci U S A 94:12002–12006

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  57. Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE, Huhndorf S, James T, Kirk PM, Lücking R, Lumbsch HT, Lutzoni F, Mathenya 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, Dair YC, Gams W, Geisers DM (2007) A higher-level phylogenetic classification of the fungi. Mycol Res 111(5):509–547

    PubMed  Article  Google Scholar 

  58. Hibbett DS, Ohmana A, Glotzera D (2011) Progress in molecular and morphological taxon discovery in fungi and options for formal classification of environmental sequences. Fungal Biol Rev 25:38–47

    Article  Google Scholar 

  59. Hibbett DS, Stajich JE, Spatafora JW (2013) Towards genome-enabled mycology. Mycologia 105(6):1339–1349

    PubMed  Article  Google Scholar 

  60. Hibbett DS, Bauer R, Binder M, Giachini AJ, Hosaka K, Justo A, Larsson E, Larsson KH, Lawrey JD, Miettinen O, Nagy LG, Nilsson RH, Weiss M, Thorn RG (2014) In: McLaughlin DJ, Spatafora JW (eds) The Mycota VII Part A. Systematics and evolution, 2nd edn. Springer, Berlin, pp 373–429

    Google Scholar 

  61. Hongsanan S, Li YM, Liu JK, Hofmann T, Piepenbring M, Bhat JD, Boonmee S, Doilom M, Singtripop C, Tian Q, Mapook A, ZengXY BAH, Xu JC, Mortimer PE, Wu HX, Yang JB, Hyde KD (2014) Revision of genera in Asterinales. Fungal Divers 68(1):1–68

    Article  Google Scholar 

  62. Huang F, Hou X, Dewdney MM, Fu Y, Chen G, Hyde KD, Li H (2013) Diaporthe species occurring on Citrus in China. Fungal Divers 61:237–250

    Article  Google Scholar 

  63. Hutchings JA, Côté IM, Dodson JJ, Fleming IA, Jennings S, Mantua NJ, Peterman RM, Riddell BE, Weaveri AJ (2012) Climate change, fisheries, and aquaculture: trends and consequences for Canadian marine biodiversity. Environ Rev 20:220–311

    Article  Google Scholar 

  64. Hyde KD, Bahkali AH, Moslem MA (2010a) Fungi—an unusual source for cosmetics. Fungal Divers 43:1–9

    Article  Google Scholar 

  65. Hyde KD, Chomnunti P, Crous PW, Groenewald JZ, Damm U, Ko TWK, Shivas RG, Summerell BA, Tan YP (2010b) A case for re-inventory of Australia’s plant pathogens. Persoonia 25:50–60. doi:10.3767/003158510X548668

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  66. Hyde KD, Jones EBG, Liu JK, Ariyawansa H, Boehm E, Boonmee S, Braun U, Chomnunti P, Crous PW, Dai DQ, Diederich P, Dissanayake A, Doilom M, Doveri F, Hongsanan S, Jayawardena R, Lawrey JD, Li YM, Liu YX, Lücking R, Monkai J, Muggia L, Nelsen MP, Pang KL, Phookamsak R, Senanayake I, Shearer CA, Suetrong S, Tanaka K, Thambugala KM, Wijayawardene NN, Wikee S, Wu HX, Zhang Y, Aguirre-Hudson B, Alias SA, Aptroot A, Bahkali AH, Bezerra JL, Bhat DJ, Camporesi E, Chukeatirote E, Gueidan C, Hawksworth DL, Hirayama K, Hoog SD, Kang JC, Knudsen K, Li WJ, Li XH, Liu ZY, Mapook A, McKenzie EHC, Miller AN, Mortimer PE, Phillips AJL, Raja HA, Scheuer C, Schumm F, Taylor JE, Tian Q, Tibpromma S, Wanasinghe DN, Wang Y, Xu JC, Yan JY, Yacharoen S, Zhang M (2013a) Families of Dothideomycetes. Fungal Divers 63:1–313

    Article  Google Scholar 

  67. Hyde KD, Udayanga D, Manamgoda DS, Tedersoo L, Larsson E, Abarenkov K, Bertrand YJK, Oxelman B, Hartmann M, Kauserud H, Ryberg M, Kristiansson E, Nilsson RH (2013b) Incorporating molecular data in fungal systematics: a guide for aspiring researchers. Curr Res Environ Appl Mycol 3:1–32

    Google Scholar 

  68. Inui T, Takeda Y, Iizuka H (1965) Taxonomical studies on genus Rhizopus. J Gen Appl Microbiol 11:1–121

    Article  Google Scholar 

  69. James TY, Porter D, Leander CA, Vilgalys R, Longcore JE (2000) Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics. Can J Bot 78:336–350

    CAS  Google Scholar 

  70. James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox C, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold EA, Amtoft A, Stajich JE, Hosaka K, Sung G-H, Johnson D, O’Rourke B, Crockett M, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schüßler 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 J, 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, Lücking R, Büdel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin D, Spatafora J, Vilgalys R (2006) Reconstructing the early evolution of the fungi using a six gene phylogeny. Nature 443:818–822

    CAS  PubMed  Article  Google Scholar 

  71. Jeewon R, Liew ECY, Hyde KD (2002) Phylogenetic relationships of Pestalotiopsis and allied genera inferred from ribosomal DNA sequences and morphological characters. Mol Phylogenet Evol 25:378–392

    CAS  PubMed  Article  Google Scholar 

  72. Jensen AB, Gargas A, Eilenberg J, Rosendahl S (1998) Relationships of the insect-pathogenic order Entomophthorales (Zygomycota, Fungi) based on phylogenetic analyses of nuclear small subunit ribosomal DNA sequences (SSU rDNA). Fungal Genet Biol 24:325–334

    CAS  PubMed  Article  Google Scholar 

  73. Jones MDM, Forn I, Gadelha C, Egan MJ, Bass D, Massana R, Richards TA (2011) Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474:200–203

    CAS  PubMed  Article  Google Scholar 

  74. Jones G, Aydin Z, Oxelman B (2014) DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Oxf J 31(7):991–998

    Google Scholar 

  75. Judd WS, Campbell CS, Kellogg, Stevens PF, Donoghue MJ (2002) Plant systematics: a phylogenetic approach, vol 2. Sinauer Associates, Sunderland, pp 1–39

    Google Scholar 

  76. Kendrick B (ed) (1979) The whole fungus: the sexual-asexual synthesis, vol 1–2. National Museums of Canada, Ottawa

    Google Scholar 

  77. Kendrick B (1985) The fifth kingdom. Mycologue Publications, Canada p vii + p 363

  78. Kirk PM, Cannon PF, David JC, Stalpers JA (2001) Ainsworth & Bisby’s dictionary of the fungi, 9th edn. CAB International, Wallingford

    Google Scholar 

  79. Knorr D (1998) Technology aspects related to microorganisms in functional foods. Trends Food Sci Technol p 295–306

  80. Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Scott JA, Senés C, Smith ME, Suija A, Taylor DL, Telleria MT, Weiss M, Larsson KH (2013) Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 22(21):5271–5277

    PubMed  Article  CAS  Google Scholar 

  81. Kumar TKA, Blackwell M, Letcher PM, Roberson RW, McLaughlin DJ (2013) Research and teaching with the AFTOL SBD: an informatics resource for fungal subcellular and biochemical data. IMA Fungus 4(2):259–263

    Article  Google Scholar 

  82. Laitila A, Alakomi HL, Raaska L (2002) Antifungal activities of two Lactobacillus plantarum strains against Fusarium moulds in vitro and in malting of barley. J Appl Microbiol 93:566–576

    CAS  PubMed  Article  Google Scholar 

  83. Lange L (2010) The importance of fungi for a more sustainable future on our planet. Fungal Biol Rev 24:90–92

    Article  Google Scholar 

  84. Lange L (2014) The importance of fungi and mycology for addressing major global challenges. IMA Fungus 5:463–471

    PubMed Central  PubMed  Article  Google Scholar 

  85. Lange L, Bech L, Busk PK, Grell MN, Huang Y, Lange M, Linde T, Pilgaard B, Roth TX (2012) The importance of fungi and of mycology for a global development of the bioeconomy. IMA Fungus 3:87–92

    PubMed Central  PubMed  Article  Google Scholar 

  86. Leavitt SD, Esslinger TL, Divakar PK, Lumbsch HT (2012) Miocene divergence, phenotypically cryptic lineages, and contrasting distribution patterns in common lichen-forming fungi (Ascomycota: Parmeliaceae). Biol J Linn Soc 107:920–937. doi:10.1111/j.1095-8312.2012.01978.x

    Article  Google Scholar 

  87. Leavitt SD, Esslinger TL, Spribille T, Divakar PK, Lumbsch HT (2013) Multilocus phylogeny of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota): Insights on diversity, distributions, and a comparison of species tree and concatenated topologies. Mol Phylogenet Evol 66:138–152. doi:10.1016/j.ympev.2012.09.013

    PubMed  Article  Google Scholar 

  88. Leavitt SD, Moreau SD, Lumbsch HT (2015) The dynamic discipline of species delimitation: progress toward effectively recognizing species boundaries in natural populations. In: Upreti DK, Divakar PK, Shukla V, Bajapi R (eds) Recent advances in lichenology. Springer, Delhi, pp 11–44

    Google Scholar 

  89. Liew EC, Aptroot A, Hyde KD (2000) Phylogenetic significance of the pseudoparaphyses in Loculoascomycete taxonomy. Mol Phylogenet Evol 16:392–402

    CAS  PubMed  Article  Google Scholar 

  90. Lindahl BD, Nilsson RH, Tedersoo L, Abarenkov K, Carlsen T, Kjøller R, Kauserud H (2013) Fungal community analysis by high-throughput sequencing of amplified markers—a user’s guide. New Phytol 199(1):1288–1299

  91. Liu YJ, Hodson MC, Hall BD (2006) Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of kingdom Fungi inferred from RNA polymerase II subunit genes. BMC Evol Biol 6: 74. www.biomedcentral.com/1471-2148/6/74

  92. Lumbsch HT, Huhndorf SM (2010) Myconet volume 14. Part one. Outline of Ascomycota – (2009) Part two. Notes on ascomycete systematics. Nos. 4751–5113. Fieldiana Life Earth Sci 1:1–64

    Article  Google Scholar 

  93. Lutzoni F, Kauff F, Cox CJ, McLaughlin D, Celio G, Dentinger B, Padamsee M, Hibbett DS, James TY, Baloch E, Grube M, Reeb V, Hofstetter V, Schoch C, Arnold AE, Miadlikowska J, Spatafora J, Johnson D, Hambleton S, Crockett M, Shoemaker R, Sung G-H, Luücking R, Lumbsch T, O’Donnell K, Binder M, Diederich P, Ertz D, Gueidan C, Hansen K, Harris RC, Hosaka K, Lim Y-W, Matheny B, Nishida H, Pfister D, Rogers J, Rossman A, Schmitt I, Sipman H, Stone J, Sugiyama J, Yahr R, Vilgalys R (2004) Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am J Bot 91:1446–1480

    PubMed  Article  Google Scholar 

  94. Maharachchikumbura SSN, Guo LD, Chukeatirote E, Bahkali AH, Hyde KD (2011) Pestalotiopsis–morphology, phylogeny, biochemistry and diversity. Fungal Divers 50:167–187

    Article  Google Scholar 

  95. Maharachchikumbura SSN, Guo LD, Cai L, Chukeatirote E, Wu WP, Sun X, Crous PW, Bhat DJ, McKenzie EHC, Bahkali AH, Hyde KD (2012) A multi-locus backbone tree for Pestalotiopsis, with a polyphasic characterization of 14 new species. Fungal Divers 56:95–129

    Article  Google Scholar 

  96. Maharachchikumbura SSN, Guo LD, Chukeatirote E, Hyde KD (2013a) Improving the backbone tree for the genus Pestalotiopsis; addition of P. steyaertii and P. magna sp. nov. Mycol Prog. doi:10.1007/s11557-013-0944-0

    Google Scholar 

  97. Maharachchikumbura SSN, Guo LD, Chukeatirote E, McKenzieI EHC, Hyde KD (2013b) A destructive new disease of Syzygium samarangense in Thailand caused by the new species Pestalotiopsiss amarangensis. Trop Plant Pathol 38:227–235

    Article  Google Scholar 

  98. Maharachchikumbura SSN, Chukeatirote E, Guo LD, Crous PW, Mckenzie EHC, Hyde KD (2013c) Pestalotiopsis species associated with Camellia sinensis (tea). Mycotaxon 123:47–61

    Article  Google Scholar 

  99. Maharachchikumbura SSN, Hyde KD, Jones EGB, McKenzie EHC, Huang SK, Abdel-Wahab MA, Daranagama DA, Dayarathne M, D’souza MJ, Goonasekara ID, Hongsanan S, Jayawardena RS, Kirk PM, Konta S, Liu JK, Liu ZY, Norphanphoun C, Pang KL, Perera RH, Senanayake IC, Shang Q, Shenoy BD, Xiao Y, Bahkali AH, Kang J, Somrothipol S, Suetrong S, Wen T, Xu J (2015) Towards a natural classification and backbone tree for Sordariomycetes. Fungal Divers 72:199–301

    Article  Google Scholar 

  100. Manamgoda DS, Udayanga D, Cai L, Chukeatirote E, Hyde KD (2013) Endophytic Colletotrichum from tropical grasses with a new species C. endophytica. Fungal Divers 61:107–115

    Article  Google Scholar 

  101. Martins CVB, da Silva DL, Neres ATM et al (2009) Curcumin as a promising antifungal of clinical interest. J Antimicrob Chemother 63:337–339

    CAS  PubMed  Article  Google Scholar 

  102. Matheny PB, Liu YJ, Ammirati JF, Hall BD (2001) Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales). Am J Bot 89(4):688–698

    Article  Google Scholar 

  103. Matheny PB, Wang Z, Binder M, Curtis JM, Lim YW, Nilsson RH, Hughes KW, Hofstetter V, Ammirati JF, Schoch CL, Langer E, Langer G, McLaughlin DJ, Wilson AW, Frøslev T, Ge ZW, Kerrigan RW, Slot JC, Yang ZL, Baroni TJ, Fischer M, Hosaka K, Matsuura K, Seidl MT, Vauras J, Hibbett DS (2007) Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Mol Phylogenet Evol 43(2):430–451

    CAS  PubMed  Article  Google Scholar 

  104. McLaughlin DJ, Frieders EM, Haisheng L (1995) A microscopist’s view of heterobasidiomycete phylogeny. Stud Mycol 38:91–109

    Google Scholar 

  105. McLaughlin, David, Spatafora, Joseph W (2015) Systematics and evolution (Eds.) The Mycota, Springer-Verlag Berlin Heidelberg 7B:1–311

  106. McNeill J, Turland NJ (2011) Synopsis of proposals on botanical nomenclature—Melbourne 2011: a review of the proposals concerning the International Code of Botanical Nomenclature submitted to the XVIII International Botanical Congress. Taxon 60:243–286

    Google Scholar 

  107. McNeill J, Barrie FR, Buck WR, Demoulin V, Greuter W, Hawksworth DL, Herendeen PS, Knapp S, Marhold K, Prado J, van Reine WF P’h, Smith GE, Wiersema JH, Turland NJ (eds) (2012) International Code of Nomenclature for algae, fungi, and plants (Melbourne Code) adopted by the Eighteenth International Botanical Congress Melbourne, Australia, July 2011. [Regnum Vegetabile No. 154.]. Koeltz Scientific Books, Königsten

    Google Scholar 

  108. Mesirov JP (2010) Accessible reproducible research. Science 327(5964):415–416

    CAS  PubMed  Article  Google Scholar 

  109. Moncalvo JM, Buchanan PK (2008) Molecular evidence for long distance dispersal across the Southern Hemisphere in the Ganoderma applanatum-australe species complex (Basidiomycota). Mycol Res 112:425–436

    CAS  PubMed  Article  Google Scholar 

  110. Moncalvo JM, Lutzoni FM, Rehner SA, Johnson J, Vilgalys R (2000) Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. Syst Biol 49:278–305

    CAS  PubMed  Article  Google Scholar 

  111. Moncalvo JM, Vilgalys R, Redhead SA, Johnson JE, James TY, Aime MC, Hofstetter V, Verduin DJW, Larsson E, Baroni TJ, Thorn RG, Jacobsson S, Clémençon H, Miller OK (2002) One hundred and seventeen clades of Euagarics. Mol Phylogenet Evol 23:357–400

    CAS  PubMed  Article  Google Scholar 

  112. Mori Y, Sato Y, Takamatsu S (2000) Evolutionary analysis of the powdery mildew fungi using nucleotide sequences of the nuclear ribosomal DNA. Mycologia 92:74–93

    CAS  Article  Google Scholar 

  113. Muzzarelli RAA, Boudrant J, Meyer D (2012) Current views on fungal chitin/chitosan, human chitinases, food preservation, glucans, pectins and inulin: A tribute to Henri Braconnot, precursor of the carbohydrate polymers science, on the chitin bicentennial. Carbohydr Polym 87:995–1012

    CAS  Article  Google Scholar 

  114. Nakamura Y, Cochrane G, Karsch-Mizrachi I (2013) The international nucleotide sequence database collaboration. Nucleic Acids Res 41:D21–D24

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  115. Nguyen NH, Songb Z, Batesb ST, Brancoc S, Tedersood L, Menkea J, Schillinge JS, Kennedya PG (2015) FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol (in press)

  116. Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson KH (2008) Intraspecific ITS variability in the kingdom fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinformatics Online 4:193–201

    Google Scholar 

  117. Nilsson RH, Hyde KD, Pawłowska J, Ryberg M, Tedersoo L, Aas AB, Alias SA, Alves A, Anderson CL, Antonelli A, Arnold AE, Bahnmann B, Bahram M, Bengtsson-Palme J, Berlin A, Branco S, Chomnunti P, Dissanayake A, Drenkhan R, Friberg H, Frøslev TG, Halwachs B, Hartmann M, Henricot M, Jayawardena R, Jumpponen A, Kauserud H, Koskela S, Kulik T, Liimatainen K, Lindahl BD, Lindner D, Liu JK, Maharachchikumbura S, Manamgoda D, Martinsson S, Neves MA, Niskanen T, Nylinder S, Pereira OL, Pinho DB, Porter TM, Queloz V, Riit T, Sánchez-García M, de Sousa F, Stefańczyk E, Tadych M, Takamatsu S, Tian Q, Udayanga D, Unterseher M, Wang Z, Wikee S, Yan J, Larsson E, Larsson KH, Kõljalg U, Abarenkov K (2014) Improving ITS sequence data for identification of plant pathogenic fungi. Fungal Divers 67(1):11–19

    Article  Google Scholar 

  118. Nilsson RH, Tedersoo L, Ryberg M, Kristiansson E, Hartmann M, Unterseher M, Porter TM, Bengtsson-Palme J, Walker DM, de Sousa F, Gamper HA, Larsson E, Larsson KH, Kõljalg U, Edgar RC, Abarenkov K (2015) A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts. Microbes Environ 30(2):140–150

    Article  Google Scholar 

  119. O’Donnell K (1979) Zygomycetes in culture, vol 2, Palfrey contributions in botany. Department of Botany, University of Georgia, Athens, p 257

    Google Scholar 

  120. Oberwinkler F (1987) Heterobasidiomycetes with ontogenetic yeast-stages—systematic and phylogenetic aspects. Stud Mycol 30:61–74

    Google Scholar 

  121. Oberwinkler F (2014) Dacrymycetes. In: McLaughlin DJ, Spatafora JW (eds) The Mycota VII Part A. Systematics and evolution, 2nd edn. Springer, Berlin, pp 357–372

    Google Scholar 

  122. Parnmen S, Rangsiruji A, Mongkolsuk P, Boonpragob K, Nutakki A, Lumbsch HT (2012) Using phylogenetic and coalescent methods to understand the species diversity in the Cladia aggregata complex (Ascomycota, Lecanorales). PLoS ONE 7(12):e52245. doi:10.1371/journal.pone.0052245

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  123. Petrini LE, Petrini O (2013) Identifying moulds a practical guide. J. Cramer: VII (191):37

  124. Phillips AJL, Alves A, Abdollahzadeh J, Slippers B, Wingfield MJ, Groenewald JZ, Crous PW (2013) The Botryosphaeriaceae: genera and species known from culture. Stud Mycol 76:51–167

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  125. Photita W, Taylor PWJ, Ford R, Hyde KD, Lumyong S (2005) Morphological and molecular characterization of Colletotrichum species from herbaceous plants in Thailand. Fungal Divers 18:117–133

    Google Scholar 

  126. Porter TM, Schadt CW, Rizvi L, Martin AP, Schmidt SK, Scott-Denton L, Vilgalys R, Moncalvo JM (2008) Widespread occurrence and phylogenetic placement of a soil clone group add a prominent new branch to the fungal tree of life. Mol Phylogenet Evol 46:635–644

    CAS  PubMed  Article  Google Scholar 

  127. Prillinger H, Dörfler C, Laaser G, Hauska G (1990) A contribution to the systematics and evolution of higher fungi: yeast-types in the basidiomycetes. Part III: Ustilago-type. Z Mycol 56:251–278

    Google Scholar 

  128. Prillinger H, Laaser G, Dörfler C, Ziegler K (1991) A contribution to the systematics and evolution of higher fungi: yeast-types in the basidiomycetes. Part IV: Dacrymyces-type, Tremella-type. Sydowia 43:170–218

    Google Scholar 

  129. Promputtha I, Jeewon R, Lumyong S, McKenzie EHC, Hyde KD (2005) Ribosomal DNA fingerprinting in the identification of non-sporulating endophytes from Magnolia liliifera (Magnoliaceae). Fungal Divers 20:167–186

    Google Scholar 

  130. Promputtha I, Lumyong S, Vijaykrishna D, McKenzie EHC, Hyde KD, Jeewon R (2007) A phylogenetic evaluation of whether endophytes become saprotrophs at host senescence. Microb Ecol 53:579–590

    PubMed  Article  Google Scholar 

  131. Rehner SA, Uecker FA (1994) Nuclear ribosomal internal transcribed spacer phylogeny and host diversity in the coelomycete Phomopsis. Can J Bot 72:166–167

    Article  Google Scholar 

  132. Reynolds DR, Taylor JW (eds) (1993) The fungal holomorph: mitotic, meiotic and pleomorphic speciation in fungal systematics. CAB International, Oxon

    Google Scholar 

  133. Roderic DM (2005) A taxonomic search engine: federating taxonomic databases using web services. BMC Bioinfomatics 6:48

    Article  CAS  Google Scholar 

  134. Rossman AY, Farr DF, Castlebury LA (2007) A review of the phylogeny and biology of the Diaporthales. Mycoscience 48:135–144

    Article  Google Scholar 

  135. Salgado-Salazar C, Rossman AY, Chaverri P (2013) Not as ubiquitous as we thought: taxonomic crypsis, hidden diversity and cryptic speciation in the cosmopolitan fungus Thelonectria discophora (Nectriaceae, Hypocreales, Ascomycota). PLoS ONE 8(10):e76737. doi:10.1371/journal.pone.0076737

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  136. Sánchez-Ramírez S, Tulloss RE, Cifuentes-Blanco J, Guzmán-Dávalos L, Valenzuela R, Estrada-Torres A, Ruán-Soto F, Díaz-Moreno R, Hernández-Rico N, Torres-Gómez M, León H, Moncalvo JM (2015) In and out of refugia: historical patterns of diversity and demography in the North American Caesar’s mushroom species complex. Mol Ecol 24(19):4809–5074. doi:10.1111/mec.13413

    Article  Google Scholar 

  137. Santos JM, Phillips AJL (2009) Resolving the complex of Diaporthe (Phomopsis) species occurring on Foeniculum vulgare in Portugal. Fungal Divers 34:111–125

    Google Scholar 

  138. Santos JM, Vrandečić K, Ćosić J, Duvnjak T, Phillips AJL (2011) Resolving the Diaporthe species occurring on soybean in Croatia. Persoonia 27:9–19

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  139. Schadt CW, Martin AP, Lipson DA, Schmidt SK (2003) Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science 301:1359–1361

    CAS  PubMed  Article  Google Scholar 

  140. Schesser K, Luder A, Henson JM (1991) Use of polymerase chain reaction to detect the take-all fungus, Gaeumannomyces graminis, in infected wheat plants. Appl Environ Microbiol 57(2):553–556

    PubMed Central  CAS  PubMed  Google Scholar 

  141. Schoch CL, Shoemaker RA, Seifert KA, Hambleton S, Spatafora JW, Crous PW (2006) A multigene phylogeny of Dothideomycetes using four nuclear loci. Mycologia 98:1041–1052

    CAS  PubMed  Article  Google Scholar 

  142. Schoch CL, Robbertse B, Robert V, Vu D, Cardinali G, Irinyi L, Meyer W, Nilsson RH, Hughes K, Miller AN, Kirk PM, Abarenkov K, Aime MC, Ariyawansa HA, Bidartondo M, Boekhout T, Buyck B, Cai Q, Chen J, Crespo A, Crous PW, Damm U, De Beer ZW, Dentinger BT, Divakar PK, Dueñas M, Feau N, Fliegerova K, García MA, Ge ZW, Griffith GW, Groenewald JZ, Groenewald M, Grube M, Gryzenhout M, Gueidan C, Guo L, Hambleton S, Hamelin R, Hansen K, Hofstetter V, Hong SB, Houbraken J, Hyde KD, Inderbitzin P, Johnston PR, Karunarathna SC, Kõljalg U, Kovács GM, Kraichak E, Krizsan K, Kurtzman CP, Larsson KH, Leavitt S, Letcher PM, Liimatainen K, Liu JK, Lodge DJ, Luangsa-ard JJ, Lumbsch HT, Maharachchikumbura SS, Manamgoda D, Martín MP, Minnis AM, Moncalvo JM, Mulè G, Nakasone KK, Niskanen T, Olariaga I, Papp T, Petkovits T, Pino-Bodas R, Powell MJ, Raja HA, Redecker D, Sarmiento-Ramirez JM, Seifert KA, Shrestha B, Stenroos S, Stielow B, Suh SO, Tanaka K, Tedersoo L, Telleria MT, Udayanga D, Untereiner WA, Diéguez Uribeondo J, Subbarao KV, Vágvölgyi C, Visagie C, Voigt K, Walker DM, Weir BS, Weiß M, Wijayawardene NN, Wingfield MJ, Xu JP, Yang ZL, Zhang N, Zhuang WY, Federhen S (2014) Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database. doi:10.1093/database/bau061

    PubMed Central  PubMed  Google Scholar 

  143. Seif E, Leigh J, Liu Y, Roewer I, Forget L, Lang BF (2005) Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms. Nucleic Acid Res 33:734–744

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  144. Seifert KA, Gams W, Crous PW, Samuels GJ (2000) Molecules, morphology and classification: towards monophyletic genera in the Ascomycetes. Stud Mycol 45:1–231

    Google Scholar 

  145. Seifert K, Morgan-Jones G, Gams W, Kendrick B (2011) The genera of Hyphomycetes. CBS-KNAW Fungal Biodiversity Centre, Utrecht

    Google Scholar 

  146. Senanayake IC, Maharachchikumbura SSN, Hyde KD, Bhat JD, Jones EBG, McKenzie EHC, Dai DQ, Daranagama DA, Dayarathne MC, Goonasekara ID, Konta S, Li WJ, Shang QJ, Stadler M, Wijayawardene NN, Xiao YP, Norphanphoun C, Li Q, Liu XZ, Bahkali AH, Kang JC, Wang Y, Wen TC, Wendt L, Xu JC, Camporesi E (2015) Towards unraveling relationships in Xylariomycetidae (Sordariomycetes). Fungal Divers 73(1):1–85. doi:10.1007/s13225-015-0340-y

    Article  Google Scholar 

  147. Shenoy BD, Jeewon R, Hyde KD (2007) Impact of DNA sequence-data on the taxonomy of anamorphic fungi. Fungal Divers 26:1–54

    Google Scholar 

  148. Smil V (2003) The earth’s biosphere: evolution, dynamics, and change. Massachusetts Institute of Technology, 1st edn. MIT press, p 181

  149. Steenkamp ET, Wright J, Baldauf SL (2006) The protistan origins of animals and fungi. Mol Biol Evol 23:93–106

    CAS  PubMed  Article  Google Scholar 

  150. Stephenson SL (2011) From morphological to molecular: studies of myxomycetes since the publication of the Martin and Alexopoulos monograph. Fungal Divers 50:21–34

    Article  Google Scholar 

  151. Sugiyama J (ed) (1987) Pleomorphic fungi: the diversity and its taxonomic implications. Kodansha, Tokyo, pp 1–325

    Google Scholar 

  152. Sugiyama J (1998) Relatedness, phylogeny, and evolution of the fungi. Mycoscience 39:487–511

    Article  Google Scholar 

  153. Swann EC, Taylor JW (1993) Higher taxa of basidiomycetes: an 18S rRNA gene perspective. Mycologia 85:923–936

    CAS  Article  Google Scholar 

  154. Swann EC, Taylor JW (1995) Phylogenetic perspectives on basidiomycete systematics: evidence from the 18S rRNA gene. Can J Bot 73:S862–S868

    CAS  Article  Google Scholar 

  155. Swann EC, Frieders EM, McLaughlin DJ (1999) Microbotryum, Kriegeria and the changing paradigm in basidiomycete classification. Mycologia 91:51–66

    Article  Google Scholar 

  156. Talbot PHB (1971) Principles of fungal taxonomy, Macmillan, London, p 274

  157. Tan YP, Edwards J, Grice KRE, Shivas RG (2013) Molecular phylogenetic analysis reveals six new Diaporthe species from Australia. Fungal Divers 61:251–260

    Article  Google Scholar 

  158. Tanabe Y, O’Donnell K, Saikawa M, Sugiyama J (2000) Molecular phylogeny of parasitic Zygomycota (Dimargaritales, Zoopagales) based on nuclear small subunit ribosomal DNA sequences. Mol Phylogenet Evol 16:253–262

    CAS  PubMed  Article  Google Scholar 

  159. Tanabe Y, Saikawa M, Watanabe MM, Sugiyama J (2004) Molecular phylogeny of Zygomycota based on EF-1a and RPB1 sequences: limitations and utility of alternative markers to rDNA. Mol Phylogenet Evol 30:438–449

    CAS  PubMed  Article  Google Scholar 

  160. Tanabe Y, Watanabe MM, Sugiyama J (2005) Evolutionary relationships among basal fungi (Chytridiomycota and Zygomycota): insights from molecular phylogenetics. J Gen Appl Microbiol 51:267–276

    CAS  PubMed  Article  Google Scholar 

  161. Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibett DS, Fisher MC (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol 31:21–32

    CAS  PubMed  Article  Google Scholar 

  162. Tedersoo L, Bahram M, Põlme S, Kõljalg U, Yorou NS, Wijesundera R, Ruiz RV, Vasco-Palacios AM, Thu PQ, Suija A, Smith ME, Sharp C, Saluveer E, Saitta A, Rosas M, Riit T, Ratkowsky D, Pritsch K, Põldmaa K, Piepenbring M, Phosri C, Peterson M, Parts K, Pärtel K, Otsing E, Nouhra E, Njouonkou AL, Nilsson RH, Morgado LN, Mayor J, May TW, Majuakim L, Lodge DJ, Lee SS, Larsson KH, Kohout P, Hosaka K, Hiiesalu I, Henkel TW, Harend H, Guo L, Greslebin A, Grelet G, Geml J, Gates G, Dunstan W, Dunk C, Drenkhan R, Dearnaley J, De Kesel A, Dang T, Chen X, Buegger F, Brearley FQ, Bonito G, Anslan S, Abell S, Abarenkov K (2014) Global diversity and geography of soil fungi. Science 346(6213). doi: 10.1126/science.1256688

  163. Tedersoo L, Ramirez KS, Nilsson RH, Kaljuvee A, Kõljalg U, Abarenkov K (2015) Standardizing metadata and taxonomic identification in metabarcoding studies. Gigascience 4:34

    PubMed Central  PubMed  Article  Google Scholar 

  164. Thambugala KM, Ariyawansa HA, Li YM, Boonmee S, Hongsanan S, Tian Q, Singtripop C, Bhat DJ, Camporesi E, Jayawardena R, Liu ZY, Xu JC, Chukeatirote E, Hyde KD (2014) Dothideales. Fungal Divers 68(1):105–158

    Article  Google Scholar 

  165. Tian C, Beeson WT, Iavarone AT, Suna J, Marlettab MA, Cate JHD, Glassa NL (2009) Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa. Proc Natl Acad Sci U S A 106:22157–22162

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  166. Udayanga D, Liu X, McKenzie EHC, Chukeatirote E, Bahkali AHA, Hyde KD (2011) The genus Phomopsis: biology, applications, species concepts and names of common phytopathogens. Fungal Divers 50:189–225

    Article  Google Scholar 

  167. Udayanga D, Liua X, McKenzie EHC, Chukeatirote E, Hyde KD (2012a) Multilocus phylogeny of Diaporthe reveals three new cryptic species from Thailand. Cryptogam Mycol 33:295–309

    Article  Google Scholar 

  168. Udayanga D, Liu XZ, Crous PW, McKenzie EHC, Chukeatirote E, Hyde KD (2012b) A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis). Fungal Divers 56:157–171

    Article  Google Scholar 

  169. Udayanga D, Castlebury LA, Rossman AY, Chukeatirote E, Hyde KD (2014) Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex. Fungal Divers 67(1):203–229

    Article  Google Scholar 

  170. Valones MAA, Guimarães RL, Brandão LAC, de Souza PRE, Carvalho AAT, Crovela S (2009) Principles and applications of polymerase chain reaction in medical diagnostic fields: a review. Braz J Microbiol 40:1–11

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  171. van der Heijden MGA, Klironomos JN, Ursic M, Moutoglis P, Streitwolf-Engel R, Boller T, Wiemken A, Sanders IR (1998) Mycorrhizal fungal divers determines plant biodiversity, ecosystem variability and productivity. Nature 396:69–72

    Article  CAS  Google Scholar 

  172. Wehmeyer LE (1933) The genus Diaporthe Nitschke and its segregates. University of Michigan Press, Ann Arbor

    Google Scholar 

  173. Weiss M, Bauer R, Sampaio JP, Oberwinkler F (2014) In: McLaughlin DJ, Spatafora JW (eds) The Mycota VII Part A. Systematics and evolution, 2nd edn. Springer, Berlin, pp 331–356

    Google Scholar 

  174. Weresub LK, Hennebert GL (1979) Anamorph and teleomorph: terms for organs of reproduction rather than karyological phases. Mycotaxon 8:181–186

    Google Scholar 

  175. White MM (2002) Taxonomic and molecular systematic studies of the Harpellales (Trichomycetes) toward understanding the diversity, evolution and dispersal of gut fungi [Doctoral dissertation]. University of Kansas Press, p 172

  176. White MM (2006) Evolutionary implications of a rRNA based phylogeny of Harpellales. Mycol Res 110:1011–1024

    CAS  PubMed  Article  Google Scholar 

  177. White MM, Cafaro MJ, Gottlieb AM (2001) Taxonomy and systematics of Trichomycetes-past, present and future. In: Misra JK, Horn BW (eds) Trichomycetes and other fungal groups. Science Publishers, Enfield, pp 27–37

    Google Scholar 

  178. Wijayawardene NN, Crous PW, Kirk PM, Hawksworth DL, Boonmee S, Braun U, Dai DQ, D’souza MJ, Diederich P, Dissanayake A, Doilom M, Hongsanan S, Jones EBG, Groenewald JZ, Jayawardena R, Lawrey JD, Liu JK, Lücking R, Madrid H, Manamgoda DS, Muggia L, Nelsen MP, Phookamsak R, Suetrong S, Tanaka K, Thambugala KM, Wanasinghe DN, Wikee S, Zhang Y, Aptroot A, Ariyawansa HA, Bahkali AH, Bhat DJ, Gueidan C, Chomnunti P, De Hoog GS, Knudsen K, Li WJ, McKenzie EHC, Miller AN, Phillips AJL, Piątek M, Raja HA, Shivas RS, Slippers B, Taylor JE, Tian Q, Wang Y, Woudenberg JHC, Cai L, Jaklitsch WM, Hyde KD (2014) Naming and outline of Dothideomycetes–2014. Fungal Divers 69(1):1–55

    Article  Google Scholar 

  179. Woudenberg JHC, Groenewald JZ, Binder M, Crous PW (2013) Alternaria redefined. Stud Mycol 75:171–212

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  180. Zhang N, Blackwell M (2001) Molecular phylogeny of dogwood anthracnose fungus (Discula destructiva) and the Diaporthales. Mycologia 93:355–365

    CAS  Article  Google Scholar 

  181. Zhang N, Castlebury LA, Miller AN, Huhndorf SM, Schoch CL, Seifert KA, Rossman AY, Rogers JD, Kohlmeyer J, Volkmann-Kohlmeyer B, Sung GH (2006) An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny. Mycologia 98(6):1076–1087

    CAS  PubMed  Article  Google Scholar 

  182. Zinger L, Coissac E, Choler P, Geremia R (2009) Assessment of microbial communities by graph partitioning in a study of soil fungi in two alpine meadows. Appl Environ Microbiol 75:5863–5870

    PubMed Central  CAS  PubMed  Article  Google Scholar 

Download references

Acknowledgments

We acknowledge the International Highly Cited Research Group (IHCRRGP# 14-205), Deanship of Scientific Research, King Saud University, Riyadh, Kingdom of Saudi Arabia. Kevin D. Hyde thanks the Chinese Academy of Sciences for an award of Visiting Professorship for Senior International Scientists at Kunming Institute of Botany [project number 2013T2S003]. MFLU [grant number 56101020032] is thanked for supporting studies on Dothideomycetes. J.M. Moncalvo thanks the ROM Governors and NSERC for supporting fungal biodiversity studies. O.L. Pereira thanks the FAPEMIG and CNPq. T.C. Wen are grateful to The National Natural Science Foundation of China (No.31460012 & No.31200016). We are grateful to the Mushroom Research Foundation, Chiang Rai, Thailand for financing the webpage. Subashini C. Jayasiri is grateful to Mr. and (the late) Mrs. Jayasiri and S.P.R.D. Lasantha for their valuable suggestions.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Itthayakorn Promputtha.

Additional information

Database URL: www.Facesoffungi.org

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Jayasiri, S.C., Hyde, K.D., Ariyawansa, H.A. et al. The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts. Fungal Diversity 74, 3–18 (2015). https://doi.org/10.1007/s13225-015-0351-8

Download citation

Keywords

  • Classification
  • Database
  • FacesofFungi
  • Fungi
  • Phylogeny
  • Taxonomy