6 Pezizomycotina: Dothideomycetes and Arthoniomycetes

  • Conrad SchochEmail author
  • Martin Grube
Part of the The Mycota book series (MYCOTA, volume 7B)


The modern concepts of Dothideomycetes and Arthoniomycetes can be traced back to Luttrell (Mycologia 47:511–532, 1955) who, relying on data from a number of previous publications, combined lichenized and nonlichenized fungi in a single class, Loculoascomycetes. A current concept of two separate classes, as well-defined sister taxa, is still new, but it is closely tied to the use of DNA-sequence-based phylogenies to define fungal taxa. DNA sequence comparisons, which have now been in use in mycology since the early 1990s, confirmed that important morphological and developmental characters traditionally used in the taxonomy of loculoascomycetes are homoplasious. What was earlier referred to as the bitunicate ascomycetes contains multiple diverse lineages, which have now been placed in three different classes within Ascomycota. The class Eurotiomycetes contains Pyrenulales, Verrucariales, and Chaetothyriales within subclass Chaeothyriomycetidae (Geiser et al. Mycologia 98:1053–1064, 2006) and the remaining (and majority of) bitunicate species reside within two sister classes, Arthoniomycetes and Dothideomycetes. This review describes the latest taxonomic classifications substantiated with DNA and protein sequence comparisons and discusses morphology, biology, and ecology within this context.


Lichenized Species Sooty Mold Asexual Morph Asexual State 0Cenococcum Geophilum 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We appreciate the photos provided by Sabine Huhndorf (Field Museum) and Walter Obermayer (Karl-Franzens-University). We thank the Centraalbureau voor Schimmelcultures (CBS) and Studies in Mycology for allowing us to use illustrations from the 1975 publication by J. von Arx and E. Müller. Permission to use an adaptation from an illustration presented in the Ph.D. thesis of Tina Hoffman (Johann Wolfgang Goethe-University) is also appreciated. CLS acknowledges the Intramural Research Program of the National Institutes of Health, National Library of Medicine. We would like to thank Göran Thor (Swedish University of Agricultural Sciences) and Barbara Robbertse (NCBI) for critical readings of the manuscript.


  1. Aptroot A, Lücking R, Sipman HJM, Umaña L, Chaves JL (2008) Pyrenocarpous lichens with bitunicate asci: a first assessment of the lichen biodiversity inventory of Costa Rica. Biblioth Lichenol 97:1–162Google Scholar
  2. Arnaud G (1918) Lés Asterinées. Annals d’École National d’Agriculture de Montpellier série 2 16:1–288Google Scholar
  3. Arnold AE, Miadlikowska J, Higgins KL, Sarvate SD, Gugger P, Way A, Hofstetter V, Kauff F, Lutzoni F (2009) A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification? Syst Biol 58:283–297PubMedGoogle Scholar
  4. Arzanlou M, Groenewald JZ, Fullerton RA, Abeln ECA, Carlier J, Zapater MF, Buddenhagen IW, Viljoen A, Crous PW (2008) Multiple gene genealogies and phenotypic characters differentiate several novel species of Mycosphaerella and related anamorphs on banana. Persoonia 20:19–37PubMedCentralPubMedGoogle Scholar
  5. Aveskamp MM, de Gruyter J, Woudenberg JH, Verkley GJ, Crous PW (2010) Highlights of the Didymellaceae: a polyphasic approach to characterise Phoma and related pleosporalean genera. Stud Mycol 65:1–60PubMedCentralPubMedGoogle Scholar
  6. Barr ME (1979) A classification of Loculoascomycetes. Mycologia 71:935–957Google Scholar
  7. Barr ME (1987) Prodromus to class Loculoascomycetes. The Author, Amherst, MAGoogle Scholar
  8. Barr ME (1990) Melanommatales (Loculoascomycetes). North American Flora Series II 13:1–129Google Scholar
  9. Barr ME, Huhndorf SM (2001) Loculoascomycetes. In: McLaughlin DJ, McLaughlin EG, Lemke PA (eds) The Mycota, vol VII, Part A: systematics and evolution. Springer, Berlin, pp 161–177Google Scholar
  10. Batzer JC, Gleason ML, Harrington TC, Tiffany LH (2005) Expansion of the sooty blotch and flyspeck complex on apples based on analysis of ribosomal DNA gene sequences and morphology. Mycologia 97:1268–1286PubMedGoogle Scholar
  11. Batzer JC, Arias MM, Harrington TC, Gleason ML, Groenewald JZ, Crous PW (2008) Four species of Zygophiala (Schizothyriaceae, Capnodiales) are associated with the sooty blotch and flyspeck complex on apple. Mycologia 100:246–258PubMedGoogle Scholar
  12. Bellemère A (1994) Asci and ascospores in ascomycete systematics. In: Hawksworth DL (ed) Ascomycete systematics: Problems and Perspectives in the nineties. Plenum, New York, NY, pp 111–126Google Scholar
  13. Begerow D, Nilsson H, Unterseher M, Maier W (2010) Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Appl Microbiol Biotechnol 87:99–108PubMedGoogle Scholar
  14. Berbee ML (1996) Loculoascomycete origins and evolution of filamentous ascomycete morphology based on 18S rRNA gene sequence data. Mol Biol Evol 13:462–470PubMedGoogle Scholar
  15. Berbee ML, Taylor JW (1992) Two Ascomycete classes based on fruiting-body characters and ribosomal DNA sequence. Mol Biol Evol 9:278–284PubMedGoogle Scholar
  16. Boehm EW, Mugambi GK, Miller AN, Huhndorf SM, Marincowitz S, Spatafora JW, Schoch CL (2009a) A molecular phylogenetic reappraisal of the Hysteriaceae, Mytilinidiaceae and Gloniaceae (Pleosporomycetidae, Dothideomycetes) with keys to world species. Stud Mycol 64:49–83PubMedCentralPubMedGoogle Scholar
  17. Boehm EWA, Schoch CL, Spatafora JW (2009b) On the evolution of the Hysteriaceae and Mytilinidiaceae (Pleosporomycetidae, Dothideomycetes, Ascomycota) using four nuclear genes. Mycol Res 113:461–479PubMedGoogle Scholar
  18. Boustie J, Grube M (2005) Lichens, a promising source of bioactive secondary metabolites. Plant Genet Resour 3:273–287Google Scholar
  19. Bowen JK, Mesarich CH, Bus VGM, Beresford RM, Plummer KM, Templeton MD (2011) Venturia inaequalis: the causal agent of apple scab. Mol Plant Pathol 12:105–122PubMedGoogle Scholar
  20. Braun U, Crous PW, Dugan F, Groenewald JZ, de Hoog GS (2003) Phylogeny and taxonomy of Cladosporium-like hyphomycetes, including Davidiella gen. nov., the teleomorph of Cladosporium s. str. Mycol Prog 2:3–18Google Scholar
  21. Campbell J, Ferrer A, Raja HA, Sivichai S, Shearer C (2007) Phylogenetic relationships among taxa in the Jahnulales inferred from 18S and 28S nuclear ribosomal DNA sequences. Can J Bot 85:873–882Google Scholar
  22. Chomnunti P, Schoch C, Aguirre-Hudson B, Ko-Ko T, Hongsanan S, Jones E, Kodsueb R, Phookamsak R, Chukeatirote E, Bahkali A, Hyde K (2011) Capnodiaceae. Fung Divers 51:1–32Google Scholar
  23. Chomnunti P, Ko TWK, Chukeatirote E, Hyde KD, Cai L, Jones EBG, Kodsueb R, Hassan BA, Chen H (2012) Phylogeny of Chaetothyriaceae in northern Thailand including three new species. Mycologia 104:382–395PubMedGoogle Scholar
  24. Chung KR (2011) Elsinoё fawcettii and Elsinoё australis: the fungal pathogens causing citrus scab. Mol Plant Pathol 12:123–135PubMedGoogle Scholar
  25. Cole GT, Sampson RA (1979) Patterns of development in conidial fungi, 2 vols. Academic, New YorkGoogle Scholar
  26. Corlett M (1967) The developmental morphology of Clathrospora heterospora var. simmonsii. Can J Bot 45:221–227Google Scholar
  27. Coppins B, Aptroot A (2009) Arthonia. In: Aptroot A, Coppins BJ, Fletcher A, Gilbert OL, James PW, Wolseley PA, Smith CW (eds) The lichens of Great Britain and Ireland. British Lichen Society, UK, pp 1–47Google Scholar
  28. Coppins BJ, James PW (1979) New or interesting British lichens III. Lichenologist 11:27–45Google Scholar
  29. Crous PW, Slippers B, Wingfield MJ, Rheeder J, Marasas WFO, Philips AJL, Alves A, Burgess T, Barber P, Groenewald JZ (2006) Phylogenetic lineages in the Botryosphaeriaceae. Stud Mycol 55:235–253PubMedCentralPubMedGoogle Scholar
  30. Crous PW, Braun U, Groenewald JZ (2007a) Mycosphaerella is polyphyletic. Stud Mycol 58:1–32PubMedCentralPubMedGoogle Scholar
  31. Crous PW, Schubert K, Braun U, de Hoog GS, Hocking AD, Shin H-D, Groenewald JZ (2007b) Opportunistic, human-pathogenic species in the Herpotrichiellaceae are phenotypically similar to saprobic or phytopathogenic species in the Venturiaceae. Stud Mycol 58:185–217PubMedCentralPubMedGoogle Scholar
  32. Crous PW, Schoch CL, Hyde KD, Wood AR, Gueidan C, de Hoog GS, Groenewald JZ (2009a) Phylogenetic lineages in the Capnodiales. Stud Mycol 64:17–47PubMedCentralPubMedGoogle Scholar
  33. Crous PW, Summerbell RC, Carnegie AJ, Wingfield MJ, Hunter GC, Burgess TI, Andjic V, Barber PA, Groenewald JZ (2009b) Unravelling Mycosphaerella: do you believe in genera? Persoonia 23:99–118PubMedCentralPubMedGoogle Scholar
  34. Currey F (1856) Original communications: on the reproductive organs of certain fungi, with some remarks on germination. Q J Microsc Sci s1–4:192–200Google Scholar
  35. De Bary A (1887) Comparative morphology and biology of the fungi, mycetozoa, and bacteria. Clarendon Press, OxfordGoogle Scholar
  36. de Gruyter J, Aveskamp MM, Woudenberg JHC, Verkley GJM, Groenewald JZ, Crous PW (2009) Molecular phylogeny of Phoma and allied anamorph genera: towards a reclassification of the Phoma complex. Mycol Res 113:508–519PubMedGoogle Scholar
  37. de Gruyter J, Woudenberg JHC, Aveskamp MM, Verkley GJM, Groenewald JZ, Crous PW (2012) Redisposition of Phoma-like anamorphs in Pleosporales. Stud Mycol 75:1–36PubMedCentralGoogle Scholar
  38. de Wit PJGM, Mehrabi R, van den Burg HA, Stergiopoulos I (2009) Fungal effector proteins: past, present and future. Mol Plant Pathol 10:735–747PubMedGoogle Scholar
  39. Del Prado R, Schmitt I, Kautz S, Palice Z, Lücking R, Lumbsch HT (2006) Molecular data place Trypetheliaceae in Dothideomycetes. Mycol Res 110:511–520PubMedGoogle Scholar
  40. De los Ríos A, Grube M (2000) Host-parasite interfaces of some lichenicolous fungi in the Dacampiaceae (Dothideales, Ascomycota). Mycol Res 104:1348–1353Google Scholar
  41. Desmazières JBHJ (1843) Dixième notice sur quelques plantes cryptogames. Ann Sci Nat Bot Sér 2 19:335–373Google Scholar
  42. Diederich P, Lawrey JD, Sikaroodi M, van den Boom PPG, Ertz D (2011) Briancoppinsia, a new coelomycetous genus of Arthoniaceae (Arthoniales) for the lichenicolous Phoma cytospora, with a key to this and similar taxa. Fung Divers 52:1–12Google Scholar
  43. Eriksson OE (1981) The families of bitunicate ascomycetes. Opera Bot 60:1–220Google Scholar
  44. Eriksson OE, Winka K (1997) Supraordinal taxa of Ascomycota. Myconet 1:1–16Google Scholar
  45. Ertz D, Tehler A (2011) The phylogeny of Arthoniales (Pezizomycotina) inferred from nucLSU and RPB2 sequences. Fung Divers 49:47–71Google Scholar
  46. Ertz D, Elix J, Grube M (2010) Arthonia borbonica (Ascomycota, Arthoniales), a new species from La Réunion. Plant Ecol Evol 143:222–224Google Scholar
  47. Ertz D, Bungartz F, Diederich P, Tibell L (2011) Molecular and morphological data place Blarneya in Tylophoron (Arthoniaceae). Lichenologist 43:345–356Google Scholar
  48. Ertz D, Lawrey JD, Common RS, Diederich P (2013) Arthoniomycetes sister to the primarily lichenized Arthoniales and composed of black yeasts, lichenicolous and rock-inhabiting species. Fung Divers 66:113–137Google Scholar
  49. Ertz D, Miadlikowska J, Lutzoni F, Dessein S, Raspé O, Vigneron N, Hofstetter V, Diederich P (2009) Towards a new classification of the Arthoniales (Ascomycota) based on a three-gene phylogeny focusing on the genus Opegrapha. Mycol Res 113:141–152PubMedGoogle Scholar
  50. Fries EM (1818) Observationes mycologicae. Gerhard Bonnier, CopenhagenGoogle Scholar
  51. Frisch A, Thor G, Ertz D, Grube M (2014) The Arthonialean challenge: restructuring Arthoniaceae. Taxon 63:727–744Google Scholar
  52. Frisch A, Thor G (2010) Crypthonia, a new genus of byssoid Arthoniaceae (lichenised Ascomycota). Mycol Prog 9:281–303Google Scholar
  53. Fuckel L (1870) Symbolae Mycologicae. Beitrage zur Kenntniss der rheinischen Pilze, Wiesbaden 1870:329–330Google Scholar
  54. Funk A, Shoemaker RA (1967) Layered structure in the bitunicate ascus. Can J Bot 45:1265–1266Google Scholar
  55. Furtado JS, Olive LS (1971) Ascospore discharge and ultrastructure of the ascus in Leptospharulina australis. Nova Hedw 19:799–824Google Scholar
  56. Gargas A, DePriest PT, Grube M, Tehler A (1995) Multiple origins of lichen symbioses in Fungi suggested by SSU rDNA phylogeny. Science 268:1492–1495PubMedGoogle Scholar
  57. Greif MD, Gibas CFC, Tsuneda A, Currah RS (2007) Ascoma development and phylogeny of an apothecioid dothideomycete, Catinella olivacea. Am J Bot 94:1890–1899PubMedGoogle Scholar
  58. Grube M (1998) Classification and phylogeny in the Arthoniales. Bryologist 101:377–391Google Scholar
  59. Grube M (2001a) Sporostigma gen. nov., another calicioid genus in Arthoniales. Lichenologist 33:78–391Google Scholar
  60. Grube M (2001b) Coniarthonia gen. a new genus of arthonioid lichens. Lichenologist 33:491–502Google Scholar
  61. Grube M (2007) Arthonia. In: Nash TH III, Gries C, Bungartz F (eds) Lichen flora of the Greater Sonoran Desert region, vol 3, Lichens Unlimited. Arizona State University, Tempe, AZ, pp 39–61Google Scholar
  62. Grube M, Giralt M (1996) Studies on some species of Arthothelium occurring in the western Mediterranean. Lichenologist 28:15–36Google Scholar
  63. Grube M, Hafellner J (1990) Studien an flechtenbewohnenden Pilzen der Sammelgattung Didymella (Ascomycetes, Dothideales). Nova Hedw 51:283–360Google Scholar
  64. Grube M, Lendemer JC (2009) Arthonia rubrocincta: belated validation of a name for a common species endemic to Sabal palmetto in the southeastern United States. Opusc Philolich 7:7–12Google Scholar
  65. Grube M, Lücking R (2001) Ascogenous hyphae in foliicolous species of Arthonia and allied genera. Mycol Res 105:1007–1013Google Scholar
  66. Grube M, Matzer M (1997) Taxonomic concepts of lichenicolous Arthonia species. Biblioth Lichenol 68:1–17Google Scholar
  67. Grube M, Lücking R, Umana-Tenorio L (2004) A new, isidiate species of Arthonia (Ascomycota: Arthoniaceae) from Costa Rica. Mycologia 96:1159–1162PubMedGoogle Scholar
  68. Gueidan C, Ruibal C, de Hoog S, Schneider H (2011) Rock-inhabiting fungi originated during periods of dry climate in the late Devonian and middle Triassic. Fung Biol 115:987–996Google Scholar
  69. Hane J, Rouxel T, Howlett B, Kema G, Goodwin S, Oliver R (2011) A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi. Genome Biol 12:R45PubMedCentralPubMedGoogle Scholar
  70. Harris RC, Ladd D (2007) New taxa of lichens and lichenicolous fungi from the Ozark ecoregion. Opusc Philolich 4:57–68Google Scholar
  71. Hawksworth DL (1985) Problems and prospects in the systematics of the Ascomycotina. Proc Indian Acad Sci 94:319–339Google Scholar
  72. 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 1:7–20Google Scholar
  73. Hawksworth DL (2012) Managing and coping with names of pleomorphic fungi in a period of transition. IMA Fungus 3:15–24PubMedCentralPubMedGoogle Scholar
  74. Hawksworth DL, Eriksson OE (1986) The names of accepted orders of Ascomycetes. Systema Ascomycetum 5:175–184Google Scholar
  75. Henssen A, Jahns HM (1974) Lichenes. Eine Einführung in die Flechtenkunde. Georg Thieme, StuttgartGoogle Scholar
  76. Henssen A, Thor G (1994) Developmental morphology of the “Zwischengruppe” between Ascohymeniales and Ascoloculares. In: Hawksworth DL (ed) Ascomycete systematics. Problems and perspectives in the nineties. Plenum, New York, pp 43–61Google Scholar
  77. Henssen A, Thor G (1998) Studies in taxonomy and developmental morphology in Chiodecton, Dichosporidium, Erythrodecton and the new genus Pulvinodecton (Arthoniales, lichenized Ascomycetes). Nordic J Bot 18:95–120Google Scholar
  78. Higgins KL, Arnold AE, Miadlikowska J, Sarvate SD, Lutzoni F (2007) Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages. Mol Phylogenet Evol 42:543–555PubMedGoogle Scholar
  79. Hofmann TA (2009) Plant parasitic Asterinaceae and Microthyriaceae from the Neotropics (Panama). PhD thesis, Faculty of Biological Sciences, Johann Wolfgang Goethe-University, Frankfurt am Main, GermanyGoogle Scholar
  80. Hofmann TA, Piepenbring M (2006) New records and host plants of fly-speck fungi from Panama. Fung Divers 22:55–70Google Scholar
  81. Hofmann TA, Kirschner R, Piepenbring M (2010) Phylogenetic relationships and new records of Asterinaceae (Dothideomycetes) from Panama. Fung Divers 43:39–53Google Scholar
  82. Hofstetter V, Miadlikowska J, Kauff F, Lutzoni F (2007) Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota). Mol Phylogenet Evol 44:412–426PubMedGoogle Scholar
  83. von Höhnel F (1909) Fragmente zur Mykologie IV No. 244. Revision der Myriangiaceen und der Gattung Saccardia. Sitz-berr Kaiserl Akad Wiss Wien 118:349–376Google Scholar
  84. de Hoog GS, Hermanides-Nijhof EJ (1977) The black yeasts and allied Hyphomycetes. Stud Mycol 15:1–222Google Scholar
  85. Hughes SJ (1976) Sooty molds. Mycologia 48:693–820Google Scholar
  86. Hyde KD, Wong SW (1999) Tropical Australian freshwater fungi. XV The ascomycete genus Jahnula, with five new species and one new combination. Nova Hedw 68:489–509Google Scholar
  87. Hyde KD, Zhang Y (2008) Epitypification: should we epitypify? J Zhejiang Univ Sci B 9:842–846PubMedCentralPubMedGoogle Scholar
  88. 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 IC, 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, De Hoog S, 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, Yacharoen S, Yan JY, Zhang M (2013) Families of Dothideomycetes. Fung Divers 63:1–313Google Scholar
  89. Inderbitzin P, Bostock RM, Trouillas FP, Michailides TJ (2010) A six locus phylogeny reveals high species diversity in Botryosphaeriaceae from California almond. Mycologia 102:1350–1368PubMedGoogle Scholar
  90. Ingold CT (1933) Spore discharge in the Ascomycetes. New Phytol 32:175–196Google Scholar
  91. James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung GH, Johnson D, O’Rourke B, Crockett M, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schussler A, Longcore JE, O’Donnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Humber RA, Morton JB, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lucking R, Budel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, Vilgalys R (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818–822PubMedGoogle Scholar
  92. Jones EBG, Sakayaroj J, Suetrong S, Somrithipol S, Pang KL (2009) Classification of marine Ascomycota, anamorphic taxa and Basidiomycota. Fung Divers 35:1–187Google Scholar
  93. Jong S-C, Birmingham JM (2001) Cultivation and preservation of fungi in culture. In: McLaughlin DJ, McLaughlin EG, Lemke PA (eds) The Mycota, vol VII, Part B: Systematics and evolution. Springer, Berlin, pp 193–202Google Scholar
  94. Kirk P, Cannon P, David J, Stalpers J (2001) Ainsworth and Bisby’s dictionary of the fungi, 9th edn. CAB International, Wallingford, UKGoogle Scholar
  95. Kirk PM, Cannon PF, Minter DW, Stalpers JA (2008) Ainsworth and Bisby’s dictionary of the fungi, 10th edn. CAB International, Wallingford, UKGoogle Scholar
  96. Kirschstein V (1936) Beiträge zur Kenntnis der Ascomyceten und ihrer Nebenformen besonders aus der Mark Brandenburg und dem Bayerischen Walde. Ann Mycol 34:180–210Google Scholar
  97. Kodsueb R, Dhanasekaran V, Aptroot A, Lumyong P, McKenzie EHC, Hyde KD, Jeewon R (2006a) The family Pleosporaceae: intergeneric relationships and phylogenetic perspectives based on sequence analyses of partial 28S rDNA. Mycologia 98:571–583PubMedGoogle Scholar
  98. Kodsueb R, Jeewon R, Vijaykrishna D, McKenzie EHC, Lumyong P, Lumyong S, Hyde KD (2006b) Systematic revision of Tubeufiaceae based on morphological and molecular data. Fung Divers 21:105–130Google Scholar
  99. Kruys Å, Wedin M (2009) Phylogenetic relationships and an assessment of traditionally used taxonomic characters in the Sporormiaceae (Pleosporales, Dothideomycetes, Ascomycota), utilizing multi-gene phylogenies. Syst Biodiver 7:465–478Google Scholar
  100. Kruys Å, Eriksson OE, Wedin M (2006) Phylogenetic relationships of coprophilous Pleosporales (Dothideomycetes, Ascomycota), and the classification of some bitunicate taxa of unknown position. Mycol Res 110:527–536PubMedGoogle Scholar
  101. Kohlmeyer J, Kohlmeyer E (1979) Marine mycology: the higher fungi. Academic, New YorkGoogle Scholar
  102. Lawrey J, Diederich P (2003) Lichenicolous fungi: interactions, evolution, and biodiversity. Bryologist 106:81–120Google Scholar
  103. Lawrey JD, Diederich P, Nelsen MP, Sikaroodi M, Gillevet PM, Brand AM, Van den Boom P (2011) The obligately lichenicolous genus Lichenoconium represents a novel lineage in the Dothideomycetes. Fung Biol 115:176–187Google Scholar
  104. Lawrey JD, Diederich P, Nelsen MP, Freeburg C, van den Broeck D, Sikaroodi M, Ertz D (2012) Phylogenetic placement of lichenicolous Phoma species in the Phaeosphaeriaceae (Pleosporales, Dothideomycetes). Fung Divers 55:195–213Google Scholar
  105. Liew EC, Aptroot A, Hyde KD (2000) Phylogenetic significance of the pseudoparaphyses in Loculoascomycete taxonomy. Mol Phylogenet Evol 16:392–402PubMedGoogle Scholar
  106. Lindau G (1897) Pyrenomycetineae. In: Engler A, Prantl K (eds) Die natürlichen Pflanzenfamilien. Wilhelm Engelmann, Leipzig, GermanyGoogle Scholar
  107. Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T (2009) Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 324:1561–1564PubMedGoogle Scholar
  108. Liu YJ, Hall BD (2004) Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny. Proc Natl Acad Sci U S A 101:4507–4512PubMedCentralPubMedGoogle Scholar
  109. Liu YJ, Whelen S, Hall BD (1999) Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Mol Biol Evol 16:1799–1808PubMedGoogle Scholar
  110. LoBuglio KF, Berbee ML, Taylor JW (1996) Phylogenetic origins of the asexual mycorrhizal symbiont Cenococcum geophilum Fr. and other mycorrhizal fungi among the ascomycetes. Mol Phylogenet Evol 6:287–294PubMedGoogle Scholar
  111. Lücking R (1995) Additions and corrections to the foliicolous lichen flora of Costa Rica (Central America). I. The family Arthoniaceae, with notes on the genus Stirtonia. Lichenologist 27:127–153Google Scholar
  112. Lücking R (2008) Foliicolous lichenized fungi. Flora Neotropica Monograph 103:1–873Google Scholar
  113. Lumbsch HT, Huhndorf S (2007) Whatever happened to the pyrenomycetes and loculoascomycetes? Mycol Res 111:1064–1074PubMedGoogle Scholar
  114. Lumbsch HT, Huhndorf S (2010) Myconet volume 14. Part one. Outline of Ascomycota 2009. Part two. notes on Ascomycete systematics 4751–5113. Fieldiana 1:1–64Google Scholar
  115. Lumbsch HT, Lindemuth R (2001) Major lineages of Dothideomycetes (Ascomycota) inferred from SSU and LSU rDNA sequences. Mycol Res 105:901–908Google Scholar
  116. Lumbsch HT, Lindemuth R, Schmitt I (2000) Evolution of filamentous ascomycetes inferred from LSU rDNA sequence data. Plant Biol 5:525–529Google Scholar
  117. Lumbsch HT, Schmitt I, Lindemuth R, Miller A, Mangold A, Fernandez F, Huhndorf S (2005) Performance of four ribosomal DNA regions to infer higher-level phylogenetic relationships of inoperculate euascomycetes (Leotiomyceta). Mol Phylogenet Evol 34:512–524PubMedGoogle Scholar
  118. Lumbsch HT, Lücking R, Tibell L (2009) Molecular data place Tylophoron as an additional calicioid genus in the Arthoniales (Ascomycota). Biblioth Lichenol 99:285–296Google Scholar
  119. Luttrell ES (1951) Taxonomy of Pyrenomycetes. Univ Missouri Stud 24:1–120Google Scholar
  120. Luttrell ES (1955) The ascostromatic Ascomycetes. Mycologia 47:511–532Google Scholar
  121. Luttrell ES (1965) Paraphysoids, pseudoparaphyses, and apical paraphyses. Trans Br Mycol Soc 48:135–144Google Scholar
  122. Luttrell ES (1973) Loculoascomycetes. Academic, New YorkGoogle Scholar
  123. Lutzoni F, Pagel M, Reeb V (2001) Major fungal lineages are derived from lichen symbiotic ancestors. Nature 411:937–940PubMedGoogle Scholar
  124. Lutzoni F, Kauff F, Cox CJ, McLaughlin D, Celio G, Dentinger B, Padamsee M, Hibbett D, 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, Lucking 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 91:1446–1480PubMedGoogle Scholar
  125. Manamgoda DS, Cai L, McKenzie EHC, Crous PW, Madrid H, Chukeatirote E, Shivas RG, Tan YP, Hyde KD (2012) A phylogenetic and taxonomic re-evaluation of the BipolarisCochliobolusCurvularia Complex. Fung Divers 56:131–144Google Scholar
  126. Mangenot F, Reisinger O (1976) Form and function of conidia as related to their development. In: Weber DJ, Hess WM (eds) The fungal spore: form and function. Wiley, New York, pp 789–846Google Scholar
  127. Manitchotpisit P, Leathers TD, Peterson SW, Kurtzman CP, Li XL, Eveleigh DE, Lotrakul P, Prasongsuk S, Dunlap CA, Vermillion KE, Punnapayak H (2009) Multilocus phylogenetic analyses, pullulan production and xylanase activity of tropical isolates of Aureobasidium pullulans. Mycol Res 113:1107–1120PubMedGoogle Scholar
  128. Mayer KM, Ford J, Macpherson GR, Padgett D, Volkmann-Kohlmeyer B, Kohlmeyer J, Murphy C, Douglas SE, Wright JM, Wright JL (2007) Exploring the diversity of marine-derived fungal polyketide synthases. Can J Microbiol 53:291–302PubMedGoogle Scholar
  129. Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE), 14 Nov 2010, New Orleans, pp 1–8Google Scholar
  130. Mindell RA, Stockey RA, Beard G, Currah RS (2007) Margaretbarromyces dictyosporus gen. sp nov.: a permineralized corticolous ascomycete from the Eocene of Vancouver Island, British Columbia. Mycol Res 111:680–684PubMedGoogle Scholar
  131. Minter D, Peredo H, Watson A (2007) Acrospermum chilense sp. nov. from Chile and Acrospermales ord. nov. Bol Soc Argent Bot 42:107–112Google Scholar
  132. Mugambi GK, Huhndorf SM (2009a) Molecular phylogenetics of Pleosporales: Melanommataceae and Lophiostomataceae re-circumscribed (Pleosporomycetidae, Dothideomycetes, Ascomycota). Stud Mycol 64:103–121PubMedCentralPubMedGoogle Scholar
  133. Mugambi GK, Huhndorf SM (2009b) Parallel evolution of hysterothecial ascomata in ascolocularous fungi (Ascomycota, Fungi). Syst Biodiver 7:453–464Google Scholar
  134. Muggia L, Hafellner J, Wirtz N, Hawksworth DL, Grube M (2008) The sterile microfilamentous lichenized fungi Cystocoleus ebeneus and Racodium rupestre are relatives of plant pathogens and clinically important dothidealean fungi. Mycol Res 112:50–56PubMedGoogle Scholar
  135. Muggia L, Gueidan C, Knudsen K, Perlmutter G, Grube M (2013) The lichen connections of black fungi. Mycopathologia 175:523–535PubMedGoogle Scholar
  136. Müller E (1981) The bitunicate ascus. In: Reynolds DR (ed) Ascomycete systematics: the Luttrellian concept. Springer, New York, pp 49–53Google Scholar
  137. Nannfeldt JA (1932) Studien über die Morphologie und Systematik der nicht-lichenisierten inoperculaten Discomyceten. . Nova Acta Regiae Soc Sci Upsal/Almqvist and Wiksells, Uppsala, SwedenGoogle Scholar
  138. Nelsen MP, Lücking R, Grube M, Mbatchou JS, Muggia L, Rivas Plata E, Lumbsch HT (2009) Unravelling the phylogenetic relationships of lichenised fungi in Dothideomyceta. Stud Mycol 64:135–144PubMedCentralPubMedGoogle Scholar
  139. Nelsen MP, Lücking R, Mbatchou JS, Andrew CJ, Spielmann AA, Lumbsch HT (2011) New insights into relationships of lichen-forming Dothideomycetes. Fung Divers 51:155–162Google Scholar
  140. Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, Barry KW, Condon BJ, Copeland AC, Dhillon B, Glaser F, Hesse CN, Kosti I, LaButti K, Lindquist EA, Lucas S, Salamov AA, Bradshaw RE, Ciuffetti L, Hamelin RC, Kema GHJ, Lawrence C, Scott JA, Spatafora JW, Turgeon BG, de Wit PJGM, Zhong S, Goodwin SB, Grigoriev IV (2012) Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes Fungi. PLoS Pathog 8:e1003037PubMedCentralPubMedGoogle Scholar
  141. Onofri S, Selbmann L, Zucconi L, de Hoog GS, de los Rios A, Ruisi S, Grube M (2007) Fungal associations at the cold edge of life. In: Seckbach J (ed) Algae and cyanobacteria in extreme environments. Springer, Dordrecht, pp 735–757Google Scholar
  142. Pang KL, Abdel-Wahab MA, Sivichai S, El-Sharouney HM, Jones EBG (2002) Jahnulales (Dothideomycetes, Ascomycota): a new order of lignicolous freshwater ascomycetes. Mycol Res 106:1031–1042Google Scholar
  143. Phillips AJL, Alves A, Pennycook SR, Johnston PR, Ramaley A, Akulov A, Crous PW (2008) Resolving the phylogenetic and taxonomic status of dark-spored teleomorph genera in the Botryosphaeriaceae. Persoonia 21:29–55PubMedCentralPubMedGoogle Scholar
  144. Pleijel F, Jondelius U, Norlinder E, Nygren A, Oxelman B, Schander C, Sundberg P, Thollesson M (2008) Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies. Mol Phylogenet Evol 48:369–371PubMedGoogle Scholar
  145. Poelt J (1970) Das Konzept der Artenpaare bei den Flechten. Vortrage aus dem Gesamtgebiet der Botanik. NF Dtsch Bot Ges 4:187–198Google Scholar
  146. Pringsheim N (1858) Über das Austreten der Sporen von Sphaeria scripi aus ihren Schläuchen. Jahrb Wiss Bot 1:189–921Google Scholar
  147. Promputtha I, Miller AN (2010) Three new species of Acanthostigma (Tubeufiaceae, Dothideomycetes) from Great Smoky Mountains National Park. Mycologia 102:574–587PubMedGoogle Scholar
  148. Quaedvlieg W, Kema GHJ, Groenewald JZ, Verkley GJM, Seifbarghi S, Razavi M, Gohari AM, Mehrabi R, Crous PW (2011) Zymoseptoria gen. nov.: a new genus to accommodate Septoria-like species occurring on graminicolous hosts. Persoonia 26:57–69PubMedCentralPubMedGoogle Scholar
  149. Rateb ME, Ebel R (2011) Secondary metabolites of fungi from marine habitats. Nat Prod Rep 28:290–344PubMedGoogle Scholar
  150. Reynolds DR (1971) Wall structure of a bitunicate ascus. Planta 98:244–257PubMedGoogle Scholar
  151. Reynolds DR (1989) The bitunicate ascus paradigm. Bot Rev 55:1–52Google Scholar
  152. Reynolds DR (1991) A phylogeny of fissitunicate ascostromatic fungi. Mycotaxon 42:99–123Google Scholar
  153. Reynolds DR (1998) Capnodiaceous sooty mold phylogeny. Can J Bot 76:2125–2130Google Scholar
  154. Richards TA (2011) Genome evolution: horizontal movements in the Fungi. Curr Biol 21:R166–R168PubMedGoogle Scholar
  155. Rossman AY, Schoch CL, Farr DF, Nishijima K, Keith L, Goenaga R (2010) Dolabra nepheliae on rambutan and lychee represents a novel lineage of phytopathogenic Eurotiomycetes. Mycoscience 51:300–309PubMedCentralPubMedGoogle Scholar
  156. Rouxel T, Balesdent M-H (2005) The stem canker (blackleg) fungus, Leptosphaeria maculans, enters the genomic era. Mol Plant Pathol 6:225–241PubMedGoogle Scholar
  157. Rouxel T, Grandaubert J, Hane JK, Hoede C, van de Wouw AP, Couloux A, Dominguez V, Anthouard V, Bally P, Bourras S, Cozijnsen AJ, Ciuffetti LM, Degrave A, Dilmaghani A, Duret L, Fudal I, Goodwin SB, Gout L, Glaser N, Linglin J, Kema GHJ, Lapalu N, Lawrence CB, May K, Meyer M, Ollivier B, Poulain J, Schoch CL, Simon A, Spatafora JW, Stachowiak A, Turgeon BG, Tyler BM, Vincent D, Weissenbach J, Amselem J, Quesneville H, Oliver RP, Wincker P, Balesdent MH, Howlett BJ (2011) Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeat-induced point mutations. Nat Commun 2:202PubMedCentralPubMedGoogle Scholar
  158. Ruibal C, Gueidan C, Selbmann L, Gorbushina AA, Crous PW, Groenewald JZ, Muggia L, Grube M, Isola D, Schoch CL, Staley JT, Lutzoni F, de Hoog GS (2009) Phylogeny of rock-inhabiting fungi related to Dothideomycetes. Stud Mycol 64:123–133PubMedCentralPubMedGoogle Scholar
  159. Saccardo PA (1882–1931) Sylloge Fungorum, 25 vols. The Author, PadovaGoogle Scholar
  160. Sáánchez RM, Miller AN, Bianchinotti MV (2012) A new species of Acanthostigma (Tubeufiaceae, Dothideomycetes) from the Southern Hemisphere. Mycologia 104:223–231Google Scholar
  161. Santesson R (1952) Foliicolous lichens I. A revision of the taxonomy of the obligately foliicolous, lichenized fungi. Symb Bot Upsal 12:1–590Google Scholar
  162. Schlick-Steiner BC, Steiner FM, Konrad H, Seifert B, Christian E, Moder K, Stauffer C, Crozier RH (2008) Specificity and transmission mosaic of ant nest-wall fungi. Proc Natl Acad Sci U S A 105:940–943PubMedCentralPubMedGoogle Scholar
  163. Schmidt AR, Beimforde C, Seyfullah LJ, Wege S-E, Dörfelt H, Girard V, Grabenhorst H, Gube M, Heinrichs J, Nel A, Nel P, Perrichot V, Reitner J, Rikkinen J (2014) Amber fossils of sooty moulds. Rev Palaeobot Palynol 200:53–64Google Scholar
  164. Schoch CL, Shoemaker RA, Seifert KA, Hambleton S, Spatafora JW, Crous PW (2006) A multigene phylogeny of the Dothideomycetes using four nuclear loci. Mycologia 98:1041–1052PubMedGoogle Scholar
  165. Schoch CL, Crous PW, Groenewald JZ, Boehm EW, Burgess TI, de Gruyter J, de Hoog GS, Dixon LJ, Grube M, Gueidan C, Harada Y, Hatakeyama S, Hirayama K, Hosoya T, Huhndorf SM, Hyde KD, Jones EB, Kohlmeyer J, Kruys A, Li YM, Lucking R, Lumbsch HT, Marvanova L, Mbatchou JS, McVay AH, Miller AN, Mugambi GK, Muggia L, Nelsen MP, Nelson P, Owensby CA, Phillips AJ, Phongpaichit S, Pointing SB, Pujade-Renaud V, Raja HA, Plata ER, Robbertse B, Ruibal C, Sakayaroj J, Sano T, Selbmann L, Shearer CA, Shirouzu T, Slippers B, Suetrong S, Tanaka K, Volkmann-Kohlmeyer B, Wingfield MJ, Wood AR, Woudenberg JH, Yonezawa H, Zhang Y, Spatafora JW (2009a) A class-wide phylogenetic assessment of Dothideomycetes. Stud Mycol 64:1–15PubMedCentralPubMedGoogle Scholar
  166. Schoch CL, Sung GH, Lopez-Giraldez F, Townsend JP, Miadlikowska J, Hofstetter V, Robbertse B, Matheny PB, Kauff F, Wang Z, Gueidan C, Andrie RM, Trippe K, Ciufetti LM, Wynns A, Fraker E, Hodkinson BP, Bonito G, Groenewald JZ, Arzanlou M, de Hoog GS, Crous PW, Hewitt D, Pfister DH, Peterson K, Gryzenhout M, Wingfield MJ, Aptroot A, Suh SO, Blackwell M, Hillis DM, Griffith GW, Castlebury LA, Rossman AY, Lumbsch HT, Lucking R, Budel B, Rauhut A, Diederich P, Ertz D, Geiser DM, Hosaka K, Inderbitzin P, Kohlmeyer J, Volkmann-Kohlmeyer B, Mostert L, O’Donnell K, Sipman H, Rogers JD, Shoemaker RA, Sugiyama J, Summerbell RC, Untereiner W, Johnston PR, Stenroos S, Zuccaro A, Dyer PS, Crittenden PD, Cole MS, Hansen K, Trappe JM, Yahr R, Lutzoni F, Spatafora JW (2009b) The Ascomycota Tree of Life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Syst Biol 58:224–239PubMedGoogle Scholar
  167. Schoch CL, Wang Z, Townsend JP, Spatafora JW (2009c) Geoglossomycetes cl. nov., Geoglossales ord. nov. and taxa above class rank in the Ascomycota Tree of Life. Persoonia 22:129–138PubMedCentralPubMedGoogle Scholar
  168. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Bolchacova E, Voigt K, Crous PW, Miller AN, Wingfield MJ, Aime MC, An KD, Bai FY, Barreto RW, Begerow D, Bergeron MJ, Blackwell M, Boekhout T, Bogale M, Boonyuen N, Burgaz AR, Buyck B, Cai L, Cai Q, Cardinali G, Chaverri P, Coppins BJ, Crespo A, Cubas P, Cummings C, Damm U, de Beer ZW, de Hoog GS, Del-Prado R, Dentinger B, Dieguez-Uribeondo J, Divakar PK, Douglas B, Duenas M, Duong TA, Eberhardt U, Edwards JE, Elshahed MS, Fliegerova K, Furtado M, Garcia MA, Ge ZW, Griffith GW, Griffiths K, Groenewald JZ, Groenewald M, Grube M, Gryzenhout M, Guo LD, Hagen F, Hambleton S, Hamelin RC, Hansen K, Harrold P, Heller G, Herrera G, Hirayama K, Hirooka Y, Ho HM, Hoffmann K, Hofstetter V, Hognabba F, Hollingsworth PM, Hong SB, Hosaka K, Houbraken J, Hughes K, Huhtinen S, Hyde KD, James T, Johnson EM, Johnson JE, Johnston PR, Jones EB, Kelly LJ, Kirk PM, Knapp DG, Koljalg U, Kovacs GM, Kurtzman CP, Landvik S, Leavitt SD, Liggenstoffer AS, Liimatainen K, Lombard L, Luangsa-Ard JJ, Lumbsch HT, Maganti H, Maharachchikumbura SS, Martin MP, May TW, McTaggart AR, Methven AS, Meyer W, Moncalvo JM, Mongkolsamrit S, Nagy LG, Nilsson RH, Niskanen T, Nyilasi I, Okada G, Okane I, Olariaga I, Otte J, Papp T, Park D, Petkovits T, Pino-Bodas R, Quaedvlieg W, Raja HA, Redecker D, Rintoul T, Ruibal C, Sarmiento-Ramirez JM, Schmitt I, Schussler A, Shearer C, Sotome K, Stefani FO, Stenroos S, Stielow B, Stockinger H, Suetrong S, Suh SO, Sung GH, Suzuki M, Tanaka K, Tedersoo L, Telleria MT, Tretter E, Untereiner WA, Urbina H, Vagvolgyi C, Vialle A, Vu TD, Walther G, Wang QM, Wang Y, Weir BS, Weiss M, White MM, Xu J, Yahr R, Yang ZL, Yurkov A, Zamora JC, Zhang N, Zhuang WY, Schindel D (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A 109:6241–6246Google Scholar
  169. Scott JA, Untereiner WA, Ewaze JO, Wong B, Doyle D (2007) Baudoinia, a new genus to accommodate Torula compniacensis. Mycologia 99:592–601PubMedGoogle Scholar
  170. Seifert K, Morgan-Jones G, Gams W, Kendrick B (2011) The genera of Hyphomycetes. CBS-KNAW, UtrechtGoogle Scholar
  171. Shearer CA, Raja HA, Miller AN, Nelson P, Tanaka K, Hirayama K, Marvanová L, Hyde KD, Zhang Z (2009) The molecular phylogeny of freshwater Dothideomycetes. Stud Mycol 64:145–153PubMedCentralPubMedGoogle Scholar
  172. Shoemaker RA (2003) Proposal to conserve the name Dothidea with a conserved type (Fungi: Dothideomycetes). Taxon 52:623–625Google Scholar
  173. Shoemaker RA, Hambleton S (2005) Dothidea sambuci and Diaporthe spiculosa. Can J Bot 83:484–490Google Scholar
  174. Silva-Hanlin DMW, Hanlin RT (1999) Small subunit ribosomal RNA gene phylogeny of several loculoascomycetes and its taxonomic implications. Mycol Res 103:153–160Google Scholar
  175. Simon UK, Bauer R, Rioux D, Simard M, Oberwinkler F (2005) The vegetative life-cycle of the clover pathogen Cymadothea trifolii as revealed by transmission electron microscopy. Mycol Res 109:764–778PubMedGoogle Scholar
  176. Singh RS, Saini GK, Kennedy JF (2008) Pullulan: microbial sources, production and applications. Carbohydr Polym 73:515–531Google Scholar
  177. Sivanesan A (1996) Corynesporasca caryotae gen. et sp. nov. with a Corynespora anamorph, and the family Corynesporascaceae. Mycol Res 100:783–788Google Scholar
  178. Slippers B, Wingfield MJ (2007) Botryosphaeriaceae as endophytes and latent pathogens of woody plants: diversity, ecology and impact. Fung Biol Rev 21:90–106Google Scholar
  179. Slippers B, Boissin E, Phillips AJ, Groenewald JZ, Lombard L, Wingfield MJ, Postma A, Burgess T, Crous PW (2013) Phylogenetic lineages in the Botryosphaeriales: a systematic and evolutionary framework. Stud Mycol 76:31–49PubMedCentralPubMedGoogle Scholar
  180. Spatafora JW, Mitchell TG, Vilgalys R (1995) Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens. J Clin Microbiol 33:1322–1326PubMedCentralPubMedGoogle Scholar
  181. Spatafora JW, Sung G-H, Johnson D, Hesse C, O’Rourke B, Serdani M, Spotts R, Lutzoni F, Hofstetter V, Miadlikowska J, Reeb V, Gueidan C, Fraker E, Lumbsch T, Lücking R, Schmitt I, Hosaka K, Aptroot A, Roux C, Miller AN, Geiser DM, Hafellner J, Hestmark G, Arnold AE, Büdel B, Rauhut A, Hewitt D, Untereiner WA, Cole MS, Scheidegger C, Schultz M, Sipman H, Schoch CL (2006) A five-gene phylogeny of Pezizomycotina. Mycologia 98:1018–1028PubMedGoogle Scholar
  182. Spatafora JW, Owensby CA, Douhan G, Boehm EWA, Schoch CL (2012) Phylogenetic placement of the ectomycorrhizal genus Cenococcum in Gloniaceae (Dothideomycetes). Mycologia 104:758–765PubMedGoogle Scholar
  183. Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57:758–771PubMedGoogle Scholar
  184. Stocker-Wörgötter E, Hager A (2008) Appendix: culture methods for lichens and lichen symbionts. In: Nash TH (ed) III: Lichen Biology, 2nd edn. Cambridge University Press, Cambridge, UK, pp 353–363Google Scholar
  185. Suetrong S, Schoch CL, Spatafora JW, Kohlmeyer J, Volkmann-Kohlmeyer B, Sakayaroj J, Phongpaichit S, Tanaka K, Hirayama K, Jones EB (2009) Molecular systematics of the marine Dothideomycetes. Stud Mycol 64:155–173PubMedCentralPubMedGoogle Scholar
  186. Suetrong S, Sakayaroj J, Phongpaichit S, Jones EBG (2010) Morphological and molecular characteristics of a poorly known marine ascomycete, Manglicola guatemalensis (Jahnulales: Pezizomycotina; Dothideomycetes, Incertae sedis): new lineage of marine ascomycetes. Mycologia 102:83–92PubMedGoogle Scholar
  187. Suetrong S, Boonyuen N, Pang K-L, Ueapattanakit J, Klaysuban A, Sri-indrasutdhi V, Sivichai S, Jones E (2011) A taxonomic revision and phylogenetic reconstruction of the Jahnulales (Dothideomycetes), and the new family Manglicolaceae. Fung Divers 51:163–188Google Scholar
  188. Sundin R, Tehler A (1998) Phylogenetic studies of the genus Arthonia. Lichenologist 30:381–413Google Scholar
  189. Sutton BC (1980) The Coelomycetes. Fungi imperfecti with pycnidial acervuli and stromata. Commonwealth Mycological Institute, KewGoogle Scholar
  190. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739PubMedCentralPubMedGoogle Scholar
  191. Tanaka K, Hirayama K, Yonezawa H, Hatakeyama S, Harada Y, Sano T, Shirouzu T, Hosoya T (2009) Molecular taxonomy of bambusicolous fungi: Tetraplosphaeriaceae, a new pleosporalean family with Tetraploa-like anamorphs, and notes on the phylogeny of selected species from bamboo. Stud Mycol 64:175–209PubMedCentralPubMedGoogle Scholar
  192. Tanaka K, Mel’nik VA, Kamiyama M, Hirayama K, Shirouzu T (2010) Molecular phylogeny of two coelomycetous fungal genera with stellate conidia, Prosthemium and Asterosporium, on Fagales trees. Botany 88:1057–1071Google Scholar
  193. Tedersoo L, May TW, Smith ME (2010) Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages. Mycorrhiza 20:217–263PubMedGoogle Scholar
  194. Tehler A (1990) A new approach to the phylogeny of Euascomycetes with a cladistic outline of Arthoniales focusing on Roccellaceae. Can J Bot 68:2458–2492Google Scholar
  195. Tehler A, Irestedt M (2007) Parallel evolution of lichen growth forms in the family Roccellaceae (Arthoniales, Ascomycota). Cladistics 23:432–454Google Scholar
  196. Tehler A, Irestedt M, Bungartz F, Wedin M (2009) Evolution and reproduction modes in the Roccella galapagoensis aggregate (Roccellaceae, Arthoniales). Taxon 58:438–456Google Scholar
  197. Theissen F, Sydow H (1918) Vorentwürfe zu den Pseudosphaeriales. Ann Mycol 16:1–34Google Scholar
  198. Thomma BJ, van Esse HP, Crous PW, de Wit PJGM (2005) Cladosporium fulvum (syn. Passalora fulva), a highly specialized plant pathogen as a model for functional studies on plant pathogenic Mycosphaerellaceae. Mol Plant Pathol 6:379–393PubMedGoogle Scholar
  199. Thor G (1990) The lichen genus Chiodecton and five allied genera. Opera Bot 103:1–92Google Scholar
  200. Tsui CKM, Berbee ML (2006) Phylogenetic relationships and convergence of helicosporous fungi inferred from ribosomal DNA sequences. Mol Phylogenet Evol 39:587–597PubMedGoogle Scholar
  201. Tsui CK, Sivichai S, Berbee ML (2006) Molecular systematics of Helicoma, Helicomyces and Helicosporium and their teleomorphs inferred from rDNA sequences. Mycologia 98:94–104PubMedGoogle Scholar
  202. Tsui CKM, Sivichai S, Rossman AY, Berbee ML (2007) Tubeufia asiana, the teleomorph of Aquaphila albicans in the Tubeufiaceae, Pleosporales, based on cultural and molecular data. Mycologia 99:884–894PubMedGoogle Scholar
  203. Untereiner WA, Straus NA, Malloch D (1995) A molecular morphotaxonomic approach to the systematics of the Herpotrichiellaceae and allied black yeasts. Mycol Res 99:897–913Google Scholar
  204. U’Ren J, Lutzoni F, Miadlikowska J, Arnold A (2010) Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens. Microb Ecol 60:340–353PubMedGoogle Scholar
  205. van de Wouw AP, Howlett BJ (2011) Fungal pathogenicity genes in the age of ‘omics’. Mol Plant Pathol 12:507–514Google Scholar
  206. Voglmayr H, Jaklitsch W (2011) Molecular data reveal high host specificity in the phylogenetically isolated genus Massaria (Ascomycota, Massariaceae). Fung Divers 46:133–170Google Scholar
  207. von Arx J, Müller E (1975) A re-evaluation of the bitunicate ascomycetes with keys to families and genera. Stud Mycol 9:1–159Google Scholar
  208. Wingfield MJ, De Beer ZW, Slippers B, Wingfield BD, Groenewald JZ, Lombard L, Crous PW (2012) One fungus, one name promotes progressive plant pathology. Mol Plant Pathol 13:1–10Google Scholar
  209. Winka K, Eriksson OE, Bang A (1998) Molecular evidence for recognizing the Chaetothyriales. Mycologia 90:822–830Google Scholar
  210. Winton LM, Stone JK, Hansen EM (2007) The systematic position of Phaeocryptopus gaeumannii. Mycologia 99:240–252PubMedGoogle Scholar
  211. Woronichin NN (1925) Über die Capnodiales. Ann Mycol 23:174–178Google Scholar
  212. Wu H, Schoch C, Boonmee S, Bahkali A, Chomnunti P, Hyde K (2011) A reappraisal of Microthyriaceae. Fung Divers 51:189–248Google Scholar
  213. Yang HL, Sun GY, Batzer JC, Crous PW, Groenewald JZ, Gleason ML (2010) Novel fungal genera and species associated with the sooty blotch and flyspeck complex on apple in China and the USA. Persoonia 24:29–37PubMedCentralPubMedGoogle Scholar
  214. Zahlbruckner A (1907) Lichenes. B. Specieller Teil. In: Engler A, Prantl K (eds) Die natürlichen pflanzenfamilien 1. Leipzig, pp 49–249Google Scholar
  215. Zalar P, Gostincar C, de Hoog GS, Ursic V, Sudhadham M, Gunde-Cimerman N (2008) Redefinition of Aureobasidium pullulans and its varieties. Stud Mycol 61:21–38PubMedCentralPubMedGoogle Scholar
  216. Zhang Y, Schoch CL, Fournier J, Crous PW, de Gruyter J, Woudenberg JH, Hirayama K, Tanaka K, Pointing SB, Spatafora JW, Hyde KD (2009) Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation. Stud Mycol 64:85–102PubMedCentralPubMedGoogle Scholar
  217. Zhang Y, Crous PW, Schoch CL, Hyde KD (2012) Pleosporales. Fung Divers 53:1–221Google Scholar
  218. Zhdanova NN, Zakharchenko VA, Vember VV, Nakonechnaya LT (2000) Fungi from Chernobyl: mycobiota of the inner regions of the containment structures of the damaged nuclear reactor. Mycol Res 104:1421–1426Google Scholar
  219. Zogg H (1962) Die Hysteriaceae s. str. und Lophiaceae unter besonderer Berücksichtigung der mitteleuropäischen Formen. Beitr Kryptogamenfl Schweiz 11:1–190Google Scholar
  220. Zuccaro A, Schoch CL, Spatafora JW, Kohlmeyer J, Draeger S, Mitchell JI (2008) Detection and identification of fungi intimately associated with the brown seaweed Fucus serratus. Appl Environ Microbiol 74:931–941PubMedCentralPubMedGoogle Scholar

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© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.NCBI/NLM/NIHBethesdaUSA
  2. 2.Institute of Plant SciencesKarl-Franzens-UniversityGrazAustria

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