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Fungal Diversity

, Volume 74, Issue 1, pp 3–18 | Cite as

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

  • Subashini C. Jayasiri
  • Kevin D. Hyde
  • Hiran A. Ariyawansa
  • Jayarama Bhat
  • Bart Buyck
  • Lei Cai
  • Yu-Cheng Dai
  • Kamel A. Abd-Elsalam
  • Damien Ertz
  • Iman Hidayat
  • Rajesh Jeewon
  • E. B. Gareth Jones
  • Ali H. Bahkali
  • Samantha C. Karunarathna
  • Jian-Kui Liu
  • J. Jennifer Luangsa-ard
  • H. Thorsten Lumbsch
  • Sajeewa S. N. Maharachchikumbura
  • Eric H. C. McKenzie
  • Jean-Marc Moncalvo
  • Masoomeh Ghobad-Nejhad
  • Henrik Nilsson
  • Ka-Lai Pang
  • Olinto L. Pereira
  • Alan J. L. Phillips
  • Olivier Raspé
  • Adam W. Rollins
  • Andrea I. Romero
  • Javier Etayo
  • Faruk Selçuk
  • Steven L. Stephenson
  • Satinee Suetrong
  • Joanne E. Taylor
  • Clement K. M. Tsui
  • Alfredo Vizzini
  • Mohamed A. Abdel-Wahab
  • Ting-Chi Wen
  • Saranyaphat Boonmee
  • Dong Qin Dai
  • Dinushani A. Daranagama
  • Asha J. Dissanayake
  • Anusha H. Ekanayaka
  • S. C. Fryar
  • Sinang Hongsanan
  • Ruvishika S. Jayawardena
  • Wen-Jing Li
  • Rekhani H. Perera
  • R. Phookamsak
  • Nimali I. de Silva
  • Kasun M. Thambugala
  • Qing Tian
  • Nalin N. Wijayawardene
  • Rui-Lin Zhao
  • Qi Zhao
  • Ji-Chuan Kang
  • Itthayakorn PromputthaEmail author
Article

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.

Keywords

Classification Database FacesofFungi Fungi Phylogeny Taxonomy 

Notes

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.

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):281–285PubMedCrossRefGoogle 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 271–294Google Scholar
  3. Anderson JB, Ullrich RC (1979) Biological species of Armillaria mellea in North America. Mycologia 71:402–414CrossRefGoogle 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 69:57–91CrossRefGoogle Scholar
  5. Arvanitoyannis IS (2008) Waste management for the food industries, Elsevier Inc., Oxford, p 413–452Google Scholar
  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 45–67Google 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):3–42CrossRefGoogle Scholar
  8. Barr ME (1979) A classification of Loculoascomycetes. Mycologia 71:935–957CrossRefGoogle Scholar
  9. Barr ME (1987) Prodromus to class Loculoascomycetes. Newell, AmherstGoogle Scholar
  10. Barr DJS (1992) Evolution and kingdoms of organisms from the perspective of a mycologist. Mycologia 84:1–11CrossRefGoogle Scholar
  11. Bartlett JMS, Stirling D (2003) A short history of the polymerase chain reaction. PCR protocols. Methods Mol Biol 226(2):3–6PubMedGoogle 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):118–123PubMedCentralPubMedCrossRefGoogle 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 PubMedCentralPubMedCrossRefGoogle 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 295–330Google Scholar
  15. Bellard C, Bertelsmeier C, Leadley P, Thuiller W, Courchamp F (2012) Impacts of climate change on the future of biodiversity. Ecol Lett 15:365–377PubMedCentralPubMedCrossRefGoogle 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):914–919Google Scholar
  17. Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2015) GenBank. Oxf J 43(D1):30–35Google 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):865–880PubMedCrossRefGoogle 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):1350–1373PubMedCrossRefGoogle Scholar
  20. Blackwell M (2011) The Fungi: 1, 2, 3 … 5.1 million species? Am J Bot 98:426–438PubMedCrossRefGoogle Scholar
  21. Braun U, Cook RTA (2012) Taxonomic manual of the Erysiphales (powdery mildews), vol 11, CBS biodiversity series. CBS, UtrechtGoogle 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 35:21–34PubMedCrossRefGoogle 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 94:1017–1031PubMedCrossRefGoogle 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 44:203–208CrossRefGoogle 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 66:1–36CrossRefGoogle Scholar
  26. Cracraft J, Donoghue MJ (eds) (2004) Assembling the tree of life. Oxford University Press, New YorkGoogle 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 108:1236–1238CrossRefGoogle 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 50:19–22Google Scholar
  29. Cummins GB, Hiratsuka Y (2003) Illustrated genera of rust fungi, 3rd edn. Am Phytopathol Soc, St. PaulGoogle Scholar
  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 57:2703–2720PubMedCrossRefGoogle Scholar
  32. Diba K, Kordbacheh P, Mirhendi SH, Rezaie S, Mahmoudi M (2007) Identification of Aspergillus species using morphological characteristics. Pak J Med Sci 23:867–872Google 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 21:4422–4436CrossRefGoogle Scholar
  34. Duránad N, Teixeirab MFS, Contia RD, Espositocd E (2002) Ecological-friendly pigments from fungi. Crit Rev Food Sci Nutr 42(1):53–66CrossRefGoogle Scholar
  35. Eggins HOW, Pugh GJF (1962) Isolation of cellulose-decomposing fungi from the soil. Nature 193:94–95CrossRefGoogle 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 CrossRefGoogle 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 CrossRefGoogle 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 92:1407–1414CrossRefGoogle 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 161:55–70PubMedCrossRefGoogle 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 19:374–390CrossRefGoogle 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 106:18315–18320PubMedCentralPubMedCrossRefGoogle 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):589–592CrossRefGoogle Scholar
  43. Gherbawy Y, Voigt K (2010) Molecular identification of fungi. Springer, Berlin, pp vii–xiCrossRefGoogle Scholar
  44. Giraud T, Refregier G, de Vienne DM, Hood ME (2008) Speciation in fungi. Fungal Genet Biol 45:791–802PubMedCrossRefGoogle Scholar
  45. Gottlieb AM, Lichtwardt RW (2001) Molecular variation within and among species of Harpellales. Mycologia 93:66–81CrossRefGoogle 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 35:332–338Google 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 75:115–170PubMedCentralPubMedCrossRefGoogle Scholar
  48. Guarro J, Gene J, Stchigel AM (1999) Developments in fungal taxonomy. Clin Microbiol Rev 12:454–500PubMedCentralPubMedGoogle Scholar
  49. Gupta VK, Sreenivasaprasad S, Mach RL (2015) Fungal bio-molecules: sources, applications and recent developments. Science p 424Google Scholar
  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 1:7–20CrossRefGoogle Scholar
  51. Hawksworth DL (2015) Naming fungi involved in spoilage of food, drink, and water. Food Mycol 5:23–28Google 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 263–290Google Scholar
  54. Hennebert GL, Weresub LK (1977) Terms for states and forms of fungi, their names and types. Mycotaxon 6:207–211Google Scholar
  55. Hibbett DS, Taylor JW (2013) Fungal systematics: is a new age of enlightenment at hand? Nat Rev Microbiol 11:129–133PubMedCrossRefGoogle 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 94:12002–12006PubMedCentralPubMedCrossRefGoogle 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):509–547PubMedCrossRefGoogle 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 25:38–47CrossRefGoogle Scholar
  59. Hibbett DS, Stajich JE, Spatafora JW (2013) Towards genome-enabled mycology. Mycologia 105(6):1339–1349PubMedCrossRefGoogle 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 373–429Google 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):1–68CrossRefGoogle 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 61:237–250CrossRefGoogle 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 20:220–311CrossRefGoogle Scholar
  64. Hyde KD, Bahkali AH, Moslem MA (2010a) Fungi—an unusual source for cosmetics. Fungal Divers 43:1–9CrossRefGoogle 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 PubMedCentralPubMedCrossRefGoogle 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 63:1–313CrossRefGoogle 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 3:1–32Google Scholar
  68. Inui T, Takeda Y, Iizuka H (1965) Taxonomical studies on genus Rhizopus. J Gen Appl Microbiol 11:1–121CrossRefGoogle 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 78:336–350Google 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 443:818–822PubMedCrossRefGoogle 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 25:378–392PubMedCrossRefGoogle 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 24:325–334PubMedCrossRefGoogle 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 474:200–203PubMedCrossRefGoogle 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):991–998Google Scholar
  75. Judd WS, Campbell CS, Kellogg, Stevens PF, Donoghue MJ (2002) Plant systematics: a phylogenetic approach, vol 2. Sinauer Associates, Sunderland, pp 1–39Google Scholar
  76. Kendrick B (ed) (1979) The whole fungus: the sexual-asexual synthesis, vol 1–2. National Museums of Canada, OttawaGoogle Scholar
  77. Kendrick B (1985) The fifth kingdom. Mycologue Publications, Canada p vii + p 363Google Scholar
  78. Kirk PM, Cannon PF, David JC, Stalpers JA (2001) Ainsworth & Bisby’s dictionary of the fungi, 9th edn. CAB International, WallingfordGoogle Scholar
  79. Knorr D (1998) Technology aspects related to microorganisms in functional foods. Trends Food Sci Technol p 295–306Google Scholar
  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):5271–5277PubMedCrossRefGoogle 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):259–263CrossRefGoogle 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 93:566–576PubMedCrossRefGoogle Scholar
  83. Lange L (2010) The importance of fungi for a more sustainable future on our planet. Fungal Biol Rev 24:90–92CrossRefGoogle Scholar
  84. Lange L (2014) The importance of fungi and mycology for addressing major global challenges. IMA Fungus 5:463–471PubMedCentralPubMedCrossRefGoogle 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 3:87–92PubMedCentralPubMedCrossRefGoogle 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 CrossRefGoogle 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 PubMedCrossRefGoogle 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 11–44CrossRefGoogle Scholar
  89. Liew EC, Aptroot A, Hyde KD (2000) Phylogenetic significance of the pseudoparaphyses in Loculoascomycete taxonomy. Mol Phylogenet Evol 16:392–402PubMedCrossRefGoogle 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):1288–1299Google Scholar
  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 1:1–64CrossRefGoogle 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 91:1446–1480PubMedCrossRefGoogle Scholar
  94. Maharachchikumbura SSN, Guo LD, Chukeatirote E, Bahkali AH, Hyde KD (2011) Pestalotiopsis–morphology, phylogeny, biochemistry and diversity. Fungal Divers 50:167–187CrossRefGoogle 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 56:95–129CrossRefGoogle 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 38:227–235CrossRefGoogle Scholar
  98. Maharachchikumbura SSN, Chukeatirote E, Guo LD, Crous PW, Mckenzie EHC, Hyde KD (2013c) Pestalotiopsis species associated with Camellia sinensis (tea). Mycotaxon 123:47–61CrossRefGoogle 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 72:199–301CrossRefGoogle 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 61:107–115CrossRefGoogle Scholar
  101. Martins CVB, da Silva DL, Neres ATM et al (2009) Curcumin as a promising antifungal of clinical interest. J Antimicrob Chemother 63:337–339PubMedCrossRefGoogle 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):688–698CrossRefGoogle 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):430–451PubMedCrossRefGoogle Scholar
  104. McLaughlin DJ, Frieders EM, Haisheng L (1995) A microscopist’s view of heterobasidiomycete phylogeny. Stud Mycol 38:91–109Google Scholar
  105. McLaughlin, David, Spatafora, Joseph W (2015) Systematics and evolution (Eds.) The Mycota, Springer-Verlag Berlin Heidelberg 7B:1–311Google Scholar
  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 60:243–286Google 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, KönigstenGoogle Scholar
  108. Mesirov JP (2010) Accessible reproducible research. Science 327(5964):415–416PubMedCrossRefGoogle 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 112:425–436PubMedCrossRefGoogle 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 49:278–305PubMedCrossRefGoogle 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 23:357–400PubMedCrossRefGoogle 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 92:74–93CrossRefGoogle 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 87:995–1012CrossRefGoogle Scholar
  114. Nakamura Y, Cochrane G, Karsch-Mizrachi I (2013) The international nucleotide sequence database collaboration. Nucleic Acids Res 41:D21–D24PubMedCentralPubMedCrossRefGoogle 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)Google Scholar
  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 4:193–201Google 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):11–19CrossRefGoogle 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):140–150CrossRefGoogle Scholar
  119. O’Donnell K (1979) Zygomycetes in culture, vol 2, Palfrey contributions in botany. Department of Botany, University of Georgia, Athens, p 257Google Scholar
  120. Oberwinkler F (1987) Heterobasidiomycetes with ontogenetic yeast-stages—systematic and phylogenetic aspects. Stud Mycol 30:61–74Google 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 357–372Google 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 PubMedCentralPubMedCrossRefGoogle Scholar
  123. Petrini LE, Petrini O (2013) Identifying moulds a practical guide. J. Cramer: VII (191):37Google Scholar
  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 76:51–167PubMedCentralPubMedCrossRefGoogle 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 18:117–133Google 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 46:635–644PubMedCrossRefGoogle 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 56:251–278Google 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 43:170–218Google 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 20:167–186Google 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 53:579–590PubMedCrossRefGoogle Scholar
  131. Rehner SA, Uecker FA (1994) Nuclear ribosomal internal transcribed spacer phylogeny and host diversity in the coelomycete Phomopsis. Can J Bot 72:166–167CrossRefGoogle Scholar
  132. Reynolds DR, Taylor JW (eds) (1993) The fungal holomorph: mitotic, meiotic and pleomorphic speciation in fungal systematics. CAB International, OxonGoogle Scholar
  133. Roderic DM (2005) A taxonomic search engine: federating taxonomic databases using web services. BMC Bioinfomatics 6:48CrossRefGoogle Scholar
  134. Rossman AY, Farr DF, Castlebury LA (2007) A review of the phylogeny and biology of the Diaporthales. Mycoscience 48:135–144CrossRefGoogle 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 PubMedCentralPubMedCrossRefGoogle 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 CrossRefGoogle Scholar
  137. Santos JM, Phillips AJL (2009) Resolving the complex of Diaporthe (Phomopsis) species occurring on Foeniculum vulgare in Portugal. Fungal Divers 34:111–125Google Scholar
  138. Santos JM, Vrandečić K, Ćosić J, Duvnjak T, Phillips AJL (2011) Resolving the Diaporthe species occurring on soybean in Croatia. Persoonia 27:9–19PubMedCentralPubMedCrossRefGoogle Scholar
  139. Schadt CW, Martin AP, Lipson DA, Schmidt SK (2003) Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science 301:1359–1361PubMedCrossRefGoogle 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):553–556PubMedCentralPubMedGoogle 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 98:1041–1052PubMedCrossRefGoogle 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 PubMedCentralPubMedGoogle 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 33:734–744PubMedCentralPubMedCrossRefGoogle Scholar
  144. Seifert KA, Gams W, Crous PW, Samuels GJ (2000) Molecules, morphology and classification: towards monophyletic genera in the Ascomycetes. Stud Mycol 45:1–231Google Scholar
  145. Seifert K, Morgan-Jones G, Gams W, Kendrick B (2011) The genera of Hyphomycetes. CBS-KNAW Fungal Biodiversity Centre, UtrechtGoogle 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 CrossRefGoogle Scholar
  147. Shenoy BD, Jeewon R, Hyde KD (2007) Impact of DNA sequence-data on the taxonomy of anamorphic fungi. Fungal Divers 26:1–54Google Scholar
  148. Smil V (2003) The earth’s biosphere: evolution, dynamics, and change. Massachusetts Institute of Technology, 1st edn. MIT press, p 181Google Scholar
  149. Steenkamp ET, Wright J, Baldauf SL (2006) The protistan origins of animals and fungi. Mol Biol Evol 23:93–106PubMedCrossRefGoogle Scholar
  150. Stephenson SL (2011) From morphological to molecular: studies of myxomycetes since the publication of the Martin and Alexopoulos monograph. Fungal Divers 50:21–34CrossRefGoogle Scholar
  151. Sugiyama J (ed) (1987) Pleomorphic fungi: the diversity and its taxonomic implications. Kodansha, Tokyo, pp 1–325Google Scholar
  152. Sugiyama J (1998) Relatedness, phylogeny, and evolution of the fungi. Mycoscience 39:487–511CrossRefGoogle Scholar
  153. Swann EC, Taylor JW (1993) Higher taxa of basidiomycetes: an 18S rRNA gene perspective. Mycologia 85:923–936CrossRefGoogle Scholar
  154. Swann EC, Taylor JW (1995) Phylogenetic perspectives on basidiomycete systematics: evidence from the 18S rRNA gene. Can J Bot 73:S862–S868CrossRefGoogle Scholar
  155. Swann EC, Frieders EM, McLaughlin DJ (1999) Microbotryum, Kriegeria and the changing paradigm in basidiomycete classification. Mycologia 91:51–66CrossRefGoogle Scholar
  156. Talbot PHB (1971) Principles of fungal taxonomy, Macmillan, London, p 274Google Scholar
  157. Tan YP, Edwards J, Grice KRE, Shivas RG (2013) Molecular phylogenetic analysis reveals six new Diaporthe species from Australia. Fungal Divers 61:251–260CrossRefGoogle 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 16:253–262PubMedCrossRefGoogle 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 30:438–449PubMedCrossRefGoogle 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 51:267–276PubMedCrossRefGoogle 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 31:21–32PubMedCrossRefGoogle 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 4:34PubMedCentralPubMedCrossRefGoogle 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):105–158CrossRefGoogle 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 106:22157–22162PubMedCentralPubMedCrossRefGoogle 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 50:189–225CrossRefGoogle 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 33:295–309CrossRefGoogle 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 56:157–171CrossRefGoogle 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):203–229CrossRefGoogle 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 40:1–11PubMedCentralPubMedCrossRefGoogle 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 396:69–72CrossRefGoogle Scholar
  172. Wehmeyer LE (1933) The genus Diaporthe Nitschke and its segregates. University of Michigan Press, Ann ArborGoogle 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 331–356Google Scholar
  174. Weresub LK, Hennebert GL (1979) Anamorph and teleomorph: terms for organs of reproduction rather than karyological phases. Mycotaxon 8:181–186Google 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 172Google Scholar
  176. White MM (2006) Evolutionary implications of a rRNA based phylogeny of Harpellales. Mycol Res 110:1011–1024PubMedCrossRefGoogle 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 27–37Google 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):1–55CrossRefGoogle Scholar
  179. Woudenberg JHC, Groenewald JZ, Binder M, Crous PW (2013) Alternaria redefined. Stud Mycol 75:171–212PubMedCentralPubMedCrossRefGoogle Scholar
  180. Zhang N, Blackwell M (2001) Molecular phylogeny of dogwood anthracnose fungus (Discula destructiva) and the Diaporthales. Mycologia 93:355–365CrossRefGoogle 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):1076–1087PubMedCrossRefGoogle 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 75:5863–5870PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© School of Science 2015

Authors and Affiliations

  • Subashini C. Jayasiri
    • 1
  • Kevin D. Hyde
    • 1
    • 2
    • 3
  • Hiran A. Ariyawansa
    • 1
    • 4
  • Jayarama Bhat
    • 5
    • 6
  • Bart Buyck
    • 7
  • Lei Cai
    • 8
  • Yu-Cheng Dai
    • 9
  • Kamel A. Abd-Elsalam
    • 1
    • 10
  • Damien Ertz
    • 11
    • 12
  • Iman Hidayat
    • 13
  • Rajesh Jeewon
    • 14
  • E. B. Gareth Jones
    • 3
  • Ali H. Bahkali
    • 3
  • Samantha C. Karunarathna
    • 1
    • 2
  • Jian-Kui Liu
    • 1
    • 4
  • J. Jennifer Luangsa-ard
    • 15
  • H. Thorsten Lumbsch
    • 16
  • Sajeewa S. N. Maharachchikumbura
    • 1
    • 4
  • Eric H. C. McKenzie
    • 17
  • Jean-Marc Moncalvo
    • 18
  • Masoomeh Ghobad-Nejhad
    • 19
  • Henrik Nilsson
    • 20
  • Ka-Lai Pang
    • 21
  • Olinto L. Pereira
    • 22
  • Alan J. L. Phillips
    • 23
  • Olivier Raspé
    • 11
    • 12
  • Adam W. Rollins
    • 24
  • Andrea I. Romero
    • 25
  • Javier Etayo
    • 26
  • Faruk Selçuk
    • 27
  • Steven L. Stephenson
    • 28
  • Satinee Suetrong
    • 29
  • Joanne E. Taylor
    • 30
  • Clement K. M. Tsui
    • 31
  • Alfredo Vizzini
    • 32
  • Mohamed A. Abdel-Wahab
    • 33
  • Ting-Chi Wen
    • 34
  • Saranyaphat Boonmee
    • 1
  • Dong Qin Dai
    • 1
    • 2
  • Dinushani A. Daranagama
    • 1
    • 8
  • Asha J. Dissanayake
    • 1
    • 35
  • Anusha H. Ekanayaka
    • 1
  • S. C. Fryar
    • 36
  • Sinang Hongsanan
    • 1
  • Ruvishika S. Jayawardena
    • 1
    • 35
  • Wen-Jing Li
    • 1
    • 2
  • Rekhani H. Perera
    • 1
  • R. Phookamsak
    • 1
  • Nimali I. de Silva
    • 37
  • Kasun M. Thambugala
    • 1
    • 4
  • Qing Tian
    • 1
    • 2
  • Nalin N. Wijayawardene
    • 1
    • 34
  • Rui-Lin Zhao
    • 8
  • Qi Zhao
    • 2
    • 38
  • Ji-Chuan Kang
    • 34
  • Itthayakorn Promputtha
    • 37
    Email author
  1. 1.Center of Excellence in Fungal ResearchMae Fah Luang UniversityChiang RaiThailand
  2. 2.World Agro forestry Centre East and Central Asia OfficeKunmingChina
  3. 3.Botany and Microbiology Department, College of ScienceKing Saud UniversityRiyadhSaudi Arabia
  4. 4.Guizhou Key Laboratory of Agricultural BiotechnologyGuizhou Academy of Agricultural SciencesGuiyangChina
  5. 5.GoaIndia
  6. 6.Department of BotanyGoa UniversityGoaIndia
  7. 7.Muséum National d’Histoire Naturelle, Département Systématique et Evolution, CP 39ISYEB, UMR 7205 CNRS MNHN UPMC EPHEParisFrance
  8. 8.State Key Laboratory of Mycology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
  9. 9.Institute of MicrobiologyBeijing Forestry UniversityBeijingChina
  10. 10.Plant Pathology Research InstituteAgricultural Research Center (ARC)GizaEgypt
  11. 11.Botanic Garden Meise, Department Bryophytes-Thallophytes (BT)MeiseBelgium
  12. 12.Fédération Wallonie-Bruxelles, Direction Générale de l’Enseignement non obligatoire et de la Recherche scientifiqueBruxellesBelgium
  13. 13.Microbiology DivisionResearch Center for Biology, Indonesian Institute of Sciences (LIPI)CibinongIndonesia
  14. 14.Department of Health Sciences, Faculty of ScienceUniversity of MauritiusReduitMauritius
  15. 15.Microbe Interaction Laboratory (BMIT), BIOTECNational Science and Technology Development Agency (NSTDA)Amphoe Khlong LuangThailand
  16. 16.Science & Education, The Field MuseumChicagoUSA
  17. 17.Manaaki Whenua Landcare ResearchAucklandNew Zealand
  18. 18.Department of Natural History, Royal Ontario Museum, and Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoCanada
  19. 19.Department of BiotechnologyIranian Research Organization for Science and Technology (IROST)TehranIran
  20. 20.Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
  21. 21.Institute of Marine Biology and Centre of Excellence for the OceansNational Taiwan Ocean UniversityKeelungRepublic of China
  22. 22.Departamento de FitopatologiaUniversidade Federal de ViçosaViçosaBrazil
  23. 23.UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e TecnologiaUniversidade Nova de LisboaCaparicaPortugal
  24. 24.Department of Biology & The Cumberland Mountain Research CenterLincoln Memorial UniversityHarrogateUSA
  25. 25.PROPLAME-PRHIDEB, Consejo Nacional de Investigaciones Científicas y Técnicas, Dep. de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales (UBA)Ciudad UniversitariaBuenos AiresArgentina
  26. 26.Department of Biology and Geology (English)Instituto ES ZizurZizur MayorSpain
  27. 27.Department of Biology, Sciences and Arts FacultyAhi Evran UniversityKırsehirTurkey
  28. 28.Department of Biological SciencesUniversity of ArkansasFayettevilleUSA
  29. 29.Fungal Biodiversity Laboratory (BFBD)BIOTEC, National Science and Technology Development Agency (NSTDA)Amphoe Khlong Luang12120 Thailand
  30. 30.Royal Botanic Garden EdinburghEdinburghUK
  31. 31.Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverCanada
  32. 32.Department of Life Sciences and Systems BiologyUniversity of TurinTurinItaly
  33. 33.Department of Botany and Microbiology, Faculty of ScienceSohag UniversitySohagEgypt
  34. 34.Engineering Research Center of Southwest Bio-Pharmaceutical Resources, Ministry of EducationGuizhou UniversityGuiyangChina
  35. 35.Institute of Plant and Environment ProtectionBeijing Academy of Agriculture and Forestry SciencesBeijingChina
  36. 36.School of BiologyFlinders UniversityAdelaideAustralia
  37. 37.Department of Biology, Faculty of ScienceChiang Mai University Chiang MaiThailand
  38. 38.Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural ScienceKunmingChina

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