Abstract
The species is one of the basic units of biological classification. Both species concepts and recognition are essential topics in taxonomic studies and other biological research. In the first part of this review, we briefly discuss the taxonomic history of the class Dothideomycetes. In the second part of the paper, we review four commonly used species concepts, focusing on morphological, ecological, biological and phylogenetic criteria and their applicability in the taxonomy of Dothideomycetes. The application and utility of the four criteria is discussed with examples in the genera Ascochyta, Cercospora and Neofusicoccum. Some problems and challenges of studying Dothideomycetes are analyzed and basic guidelines for classifying species under the above criteria are provided.
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Abdollahzadeh J, Zare R, Phillips A (2013) Phylogeny and taxonomy of Botryosphaeria and Neofusicoccum species in Iran, with description of Botryosphaeria scharifii sp. Nov Mycol 105:210–220
Abdollahzadeh J, Groenewald JZ, Coetzee M, Wingfield MJ, Crous P (2020) Evolution of lifestyles in Capnodiales. Stud Mycol 95:381–414
Aime MC, Miller AN, Aoki T, Bensch K, Cai L, Crous PW et al (2021) How to publish a new fungal species, or name, version 3.0. IMA Fungus 12:11
Ainsworth GC (1966) A general purpose classification of fungi. In: Bibliography of systematic mycology. Commonwealth Mycological Institute, Kew, pp 1–4
Ainsworth GC, James PW, Hawksworth DL (1971) Ainsworth and Bisby’s dictionary of the fungi, 6th edn. Commonwealth Mycological Institute, Kew
Ainsworth GC, Sparrow FK, Sussman AS (1973) The fungi: an advanced treatise, vol IV (B). Academic Press, New York
Albu S, Schneider RW, Price PP, Doyle VP (2016) Cercospora cf. flagellaris and Cercospora cf. sigesbeckiae are associated with Cercospora leaf blight and purple seed stain on soybean in North America. Phytopathology 106:1376–1385
Ali A, Gyulai M, Hidvégi G, Kerti B, Al Hemaid FMA, Pandey AK, Lee J (2014) The changing epitome of species identification—DNA barcoding. Saudi J Biol Sci 21:204–231
Ametrano CG, Grewe F, Crous PW, Goodwin SB, Liang C, Selbmann L et al (2019) Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota). IMA Fungus 10:19
Aptroot A, Lücking R, Sipman H, Umaña L, Chaves JL (2008) Pyrenocarpous lichens with bitunicate asci: a first assessment of the lichen biodiversity inventory in Costa Rica. Bibl Lichenol 97:1–162
Araújo JPM, Evans HC, Kepler R, Hughes DP (2018) Zombie-ant fungi across continents: 15 new species and new combinations within Ophiocordyceps I Myrmecophilous Hirsutelloid Species. Stud Mycol 90:119–160
Ariyawansa H, Phukhamsakda C, Thambugala K, Bulgakov T, Wanasinghe D, Perera R et al (2015a) Revision and phylogeny of Leptosphaeriaceae. Fungal Divers 74:19–51
Ariyawansa HA, Tanaka K, Thambugala KM, Phookamsak R, Tian Q, Camporesi E et al (2014) A molecular phylogenetic reappraisal of the Didymosphaeriaceae (= Montagnulaceae). Fungal Divers 68:69–104
Ariyawansa HA, Thambugala KM, Manamgoda DS, Jayawardena R, Camporesi E, Boonmee S et al (2015b) Towards a natural classification and backbone tree for Pleosporaceae. Fungal Divers 71:85–139
Ariyawansa HA, Tsai I, Thambugala KM, Chuang WY, Lin SR, Hozzein WN, Cheewangkoon R (2020) Species diversity of Pleosporalean taxa associated with Camellia sinensis (L.) Kuntze in Taiwan. Sci Rep 10:12762
Arnaud G (1925) Les asterinées. IV partie. Études sur la systématique des champignons pyrénomycètes. Ann Sci Nat Bot Sér 10(7): 643–723
Aveskamp MM, De Gruyter J, Crous PW (2008) Biology and recent developments in the systematics of Phoma, a complex genus of major quarantine significance. Fungal Divers 31:1–18
Aveskamp MM, de Gruyter J, Woudenberg JHC, Verkley GJM, Crous PW (2010) Highlights of the Didymellaceae: a polyphasic approach to characterize Phoma and related pleosporalean genera. Stud Mycol 65:1–60
Badotti F, Silva de Oliveira F, Fernando C, Vaz A, Fonseca PL, Fonseca C et al (2017) Effectiveness of ITS and sub-regions as DNA barcode markers for the identification of Basidiomycota (Fungi). BMC Microbiol 17:42
Bakhshi M, Arzanlou M, Babay ahari A, Groenewald JZ, Crous P (2015) Is morphology in Cercospora reliable reflection of generic affinity? Phytotaxa 213:22–34
Bakhshi M, Arzanlou M, Babay ahari A, Groenewald JZ, Crous P (2018) Novel primers improve species delimitation in Cercospora. IMA Fungus 9:299–332
Bandarupalli D, Calabon MS, Abeywickrama PD, Hyde KD, Jones EBG (2019) Molecular data reveals a new holomorphic marine fungus, Halobyssothecium estuariae, and the asexual morph of Keissleriella phragmiticola. Mycology 11:167–183
Barr ME (1976) Hypoxylon grandineum: a Loculoascomycete. Mycotaxon 3:325–329
Barr ME (1979) A classification of Loculoascomycetes. Mycologia 71:935–957
Barr ME (1983) The ascomycete connection. Mycologia 75:1–13
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 161–177
Batista AC (1959) Monografia dos fungos Micropeltaceae. Publicações Do Instituto De Micologia Da Universidade Do Recife 56:1–519
Bellemere A (1994) Asci and ascospores in ascomycete systematics. In: Hawksworth DL (ed) Ascomycete systematics: problems and perspectives in the nineties. Plenum, New York, pp 111–126
Bensch K, Braun U, Groenewald JZ, Crous PW (2012) The genus Cladosporium. Stud Mycol 72:1–401
Bensch K, Groenewald JZ, Meijer M, Dijksterhuis J, Jurjević Ž, Houbraken J et al (2018) Cladosporium species in indoor environments. Stud Mycol 89:177–301
Berbee ML (1996) Loculoascomycete origins and evolution of filamentous ascomycete morphology based on 18s rRNA gene sequence data. Mol Biol Evol 13:462–470
Berbee M, Taylor JW (1992a) Convergence in ascospore discharge mechanism among Pyrenomycete fungi based on 18s ribosomal RNA gene sequences. Mol Phylogen Evol 1:59–79
Berbee ML, Taylor JW (1992b) Detecting morphological convergence in true fungi, using 18S rRNA gene sequence data. Biosystems 28:117–125
Berbee ML, Pirseyedi M, Hubbard S (1999) Cochliobolus phylogenetics and the origin of known, highly virulent pathogens, inferred from ITS and glyceraldehyde-3-phosphate dehydrogenase gene sequences. Mycologia 91:964–977
Bessey EA (1935) A text-book of mycology. Blakiston’s, Philadelphia
Bessey EA (1950) Morphology and taxonomy of fungi. McGraw-Hill (Blakiston), New York, p xii
Bezerra J, Oliveira R, Paiva L, Silva G, Groenewald J, Crous P et al (2016) Bezerromycetales and Wiesneriomycetales ord. nov. (class Dothideomycetes), with two novel genera to accommodate endophytic fungi from Brazilian cactus. Mycol Prog 16
Bezerra JD, Oliveira RJ, Paiva LM, Silva GA, Groenewald JZ, Crous PW, Souza-Motta CM (2017) Bezerromycetales and Wiesneriomycetales ord. nov. (class Dothideomycetes), with two novel genera to accommodate endophytic fungi from Brazilian cactus. Mycol Prog 16:297–309
Bhunjun C, Phukhamsakda C, Jeewon R, Promputtha I, Hyde KD (2021) Integrating different lines of evidence to establish a novel ascomycete genus and family (Anastomitrabeculia, Anastomitrabeculiaceae) in Pleosporales. J Fungi 7:94
Bisby GR (1923) The literature on the classification of the Hysteriales. Trans Br Mycol Soc 8:176–189
Blackwell M (2011) The Fungi: 1, 2, 3 … 5.1 million species? Am J Bot 98:426–438
Blackwell M, Hibbett D, Taylor J, Spatafora J (2006) Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha). Mycologia 98:829–837
Boerema GH, Bollen GJ (1975) Conidiogenesis and conidial septation as differentiating criteria between Phoma and Ascochyta. Persoonia 8:111–144
Boerema GH, Loerakker WM, Hamers MEC (1996) Contributions towards a monograph of Phoma (Coelomycetes)—III. 2. Misapplications of the type species name and the generic synonyms of the section Plenodomus. Persoonia 16:141–190
Boise JR (1985) An amended description of Trematosphaeria. Mycologia 77:230–237
Boonmee S, Zhang Y, Chomnunti P, Chukeatirote E, Tsui C, Bahkali A, Hyde K (2011) Revision of lignicolous Tubeufiaceae based on morphological reexamination and phylogenetic analysis. Fungal Divers 51:63–102
Boonmee S, Rossman A, Liu JK, Li W, Dai DQ, Bhat DJ et al (2014) Tubeufiales, ord. nov., integrating sexual and asexual generic names. Fungal Divers 68:239–298
Boonmee S, Ekanayaka AH, Hyde KD, Hüseyin E, Ekici K, Selçuk F (2016) Phylogenetic placement of Neorhamphoria garethjonesii gen. et sp. nov (Tubeufiales, genus incertae sedis). Mycosphere 7:1447–1457
Boonmee S, Phookamsak R, Hongsanan S, Doilom M, Mapook A, McKenzie EHC et al (2017) Mycosphere notes 51–101. Revision of genera in Perisporiopsidaceae and Pseudoperisporiaceae and other Ascomycota genera incertae sedis. Mycosphere 8:1695–1801
Bretag T, Keane P, Price T (2006) The epidemiology and control of Ascochyta blight in field peas: a review. Aust J Agric Res 57:883–902
Cabañes FJ, Bragulat MR, Castellá G (2012) Hortaea werneckii isolated from silicone scuba diving equipment in Spain. Med Mycol 50:852–857
Caetano-Anollés G, Nasir A, Kim KM, Caetano-Anollés D (2018) Rooting phylogenies and the tree of life while minimizing ad hoc and auxiliary assumptions. Evol Bioinform Online 14
Cai L, Giraud T, Zhang N, Begerow D, Cai G, Shivas RG (2011) The evolution of species concepts and species recognition criteria in plant pathogenic fungi. Fungal Divers 50:121–133
Carbone I, Kohn LM (1999) A Method for Designing primer sets for speciation studies in filamentous ascomycetes. Mycologia 91:553–556
Castlebury LA, Rossman AY, Sung GH, Hyten AS, Spatafora JW (2004) Multigene phylogeny reveals new lineage for Stachybotrys chartarum, the indoor air fungus. Mycol Res 108:864–872
Chadefaud M (1973) Les asques et la syst des Ascomycetes. Bull Soc Mycot Fr 89:127–170
Chadefaud M (1982) Les principaux types d’ascocarpes: leur organization et leur evolution; Deuxieme partie: Les discocarpes. Cryptog Mycol 3:103–144
Chadefaud M (1960) Les Végétaux non Vasculaires (Cryptogamie). In: Chadefaud M, Emberger L (eds) Traité de Botanique Systématique 1. Masson, Paris
Chen Q, Jiang JR, Zhang GZ, Cai L, Crous PW (2015) Resolving the Phoma enigma. Stud Mycol 82:137–217
Chen Q, Hou LW, Duan WJ, Crous PW, Cai L (2017) Didymellaceae revisited. Stud Mycol 87:105–159
Chethana KWT, Manawasinghe IS, Hurdeal VG, Bhunjun CSB, Appadoo MA, Gentekaki E et al (2021) What are fungal species and how to delineate them? Fungal Divers (in press)
Chilvers M, Rogers J, Dugan F, Stewart J, Chen W, Peever T (2009) Didymella pisi sp. nov., the teleomorph of Ascochyta pisi. Mycol Res 113:391–400
Chitaley SD, Patil GV (1972) Ebenaceous fossil wood infected with deuteromycetaceous fungus from the Deccan Intertrappean Beds of India. Botanique 3:99e106
Chomnunti P, Hongsanan S, Aguirre-Hudson B, Tian Q, Peršoh D, Dhami MK et al (2014) The sooty moulds. Fungal Divers 66:1–36
Christias C, Hatzipapas P, Dara A, Kaliafas A, Chrysanthis G (2001) Alternaria alternata, a new pathotype pathogenic to aphids. Biocontrol 46:105–124
Chupp C (1954) A monograph of the fungus genus Cercospora. Published by author, Ithaca
Clements FE, Shear CL (1931) The genera of Fungi. The H.W. Wilson Company, New York
Coleman C, Radulovici A (2020) Challenges for the future of taxonomy: talents, databases and knowledge growth. Megataxa 1:28–34
Collins RA, Cruickshank R (2012) The seven deadly sins of DNA barcoding. Mol Ecol Res 13(6):969–975
Cornell MJ, Alam I, Soanes DM, Wong HM, Hedeler C, Paton NW et al (2007) Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi. Genome Res 17:1809–1822
Cracraft J (1982) Geographic differentiation, cladistics and vicariance biogeography: re constructing the tempo an dmode of evolution. Am Zool 22:411–424
Cronquist A (1978) Once again, what is a species? In: Knutson LV (ed) Biosystematics in agriculture. Allenheld Osmin, Montclair, pp 3–20
Crous P, Braun U (2003) Mycosphaerella and allied anamorphs: 1. Names published in Cercospora and Passalora. CBS Biodiversity Series 1. CBS, Fungal Biodiversity Centre, Utrecht
Crous PW, Aptroot A, Kang JC, Braun U, Wingfield MJ (2000) The genus Mycosphaerella and its anamorphs. Stud Mycol 45:107–121
Crous PW, Groenewald JZ, Mansilla JP, Hunter GC, Wingfield MJ (2004) Phylogenetic reassessment of Mycosphaerella species. and their anamorphs occurring on Eucalyptus. Stud Mycol 50:195–214
Crous PW, Slippers B, Wingfield MJ, Rheeder J, Marasas WFO, Philips AJL et al (2006) Phylogenetic lineages in the Botryosphaeriaceae. Stud Mycol 55:235–253
Crous PW, Summerell BA, Carnegie AJ, Mohammed C, Himaman W, Groenewald JZ (2007) Foliicolous Mycosphaerella species. and their anamorphs on Corymbia and Eucalyptus. Fungal Divers 26:143–185
Crous PW, Schoch CL, Hyde KD, Wood AR, Gueidan C et al (2009a) Phylogenetic lineages in the Capnodiales. Stud Mycol 64:17–47
Crous PW, Summerell BA, Carnegie AJ, Wingfield MJ, Hunter GC, Burgess TI, Andjic V, Barber PA, Groenewald JZ (2009b) Unraveling Mycosphaerella: do you believe in genera? Persoonia 23:99–118
Crous PW, Braun U, Hunter GC, Wingfield MJ, Verkley GJM, Shin HD et al (2013) Phylogenetic lineages in Pseudocercospora. Stud Mycol 75:37–114
Crous P, Wingfield MJ, Burgess T, Hardy G, Barber P, Alvarado P et al (2017a) Fungal Planet description sheets: 558–624. Persoonia Mol Phyl Evol Fungi 38:240–384
Crous PW, Wingield MJ, Burgess TI, Carnegie AJ, St J Hardy GE, Smith D et al (2017b) Fungal Planet description sheets: 625–715. Persoonia 39:270–467
Crous P, Schumacher RK, Akulov A, Thangavel R, Hernández-Restrepo M, Carnegie A et al. (2019) New and Interesting Fungi. 2. Fungal Syst Evol 3:420–436
Cruywagen E, Slippers B, Roux J, Wingfield M (2017) Phylogenetic species recognition and hybridisation in Lasiodiplodia: a case study on species from baobabs. Fungal Biol 121(4):420–436
Cummings MP, Meyer A (2005) Magic bullets and golden rules: data sampling in molecular phylogenetics. Zoology 108:329–336
Currey F (1856) On the reproductive organs of certain fungi, with some remarks on germination. Q J Microsc Sci 4:192–200
Damm U, Crous P, Fourie P (2008) A fissitunicate ascus mechanism in the Calosphaeriaceae, and novel species of Jattaea and Calosphaeria on Prunus wood. Persoonia 20:39–52
Damm U, Baroncelli R, Cai L, Kubo Y, O’Connell R, Weir B et al (2010) Colletotrichum: Species, ecology and interactions. IMA Fungus 1:161–165
Dao HT, Beattie GAC, Rossman AY, Burgess LW, Holford P (2016) Four putative entomopathogenic fungi of armoured scale insects on Citrus in Australia. Mycol Progress 15:47
Das D, Dwivedi BS, Datta SP, Datta SC, Meena MC, Agarwal BK et al (2019) Potassium supplying capacity of a red soil from eastern India after forty-two years of continuous cropping and fertilization. Geoderma 341:76–92
Dayarathne MC, Jones EBG, Maharachchikumbura SSN, Devadatha B, Sarma VV, Khongphinitbunjong K et al (2020) Morpho-molecular characterization of microfungi associated with marine based habitats. Mycosphere 11:1–188
De Bary A (1887) Comparative morphology and biology of the fungi, mycetozoa, and bacteria. Clarendon Press, Oxford
De Freitas Pereira MC, Veneault-Fourrey P, Vion F, Guinet E, Morin KW, Barry A (2018) Secretome analysis from the ectomycorrhizal ascomycete Cenococcum geophilum. Front Microbiol 9:141
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 113:508–519
De Gruyter J, Woudenberg JHC, Aveskamp MM, Verkley GJM, Groenewald JZ, Crous PW et al (2013) Redisposition of Phoma-like anamorphs in Pleosporales. Stud Mycol 75:1–36
Deacon JW (1997) Modern mycology, 3rd edn. Blackwell, London
Deighton FC (1967) Studies on Cercospora and allied genera. II. Passalora, Cercosporidium and some species of Fusicladium on Euphorbia. Mycol Pap 112:1–80
Deighton FC (1973) Studies on Cercospora and allied genera. IV. Cercosporella Sacc. Pseudocercosporella gen. nov. and Pseudocercosporidium gen. nov. Mycol Pap 133:1–62
Deighton FC (1974) Studies on Cercospora and allied genera. V. Mycovellosiella Rangel, and a new species of Ramulariopsis. Mycol Pap 137:1–76
Deighton FC (1976) Studies on Cercospora and allied genera. VI. Pseudocercospora Speg., Pantospora Cif. and Cercoseptoria Petr. Mycol Pap 140:1–168
Deighton FC (1979) Studies on Cercospora and allied genera. VII. New species and redispositions. Mycol Pap 144:1–56
Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nat Rev Gen 6:361–375
Desmazieres JBHJ (1843) Dixieme notice sur quelques plantes cryptogames. Ann Sci Nat Bot Ser 2(19):335–373
Diallo A, Lapointe FJ, Makarenkov V (2006) A new effective method for estimating missing values in the sequence data prior to phylogenetic analysis. Evol Bioinform Online 2:237–246
Diederich P, Christianse M (1994) Biatoropsis usnearum Räsänen, and Other Heterobasidiomycetes on Usnea. Lichenol 26:47–66
Diederich P, Zimmermann E, Sikaroodi M, Ghobad-Nejhad M, Lawrey J (2018) A first lichenicolous Corticium species (Corticiaceae, Corticiales), described from Thamnolia in Switzerland. Bull Soc Nat Luxemb 120:49–56
Dissanayake AJ, Bhunjun CS, Maharachchikumbura SSN, Liu JK (2020) Applied aspects of methods to infer phylogenetic relationships amongst fungi. Mycosphere 11:2652–2676
Doilom M, Dissanayake AJ, Wanasinghe DN, Boonmee S, Liu JK, Bhat DJ et al (2017) Microfungi on Tectona grandis (teak) in Northern Thailand. Fungal Divers 82:107–182
Domsch K, Gams W, Anderson TH (2007) Compendium of soil fungi, 2 677 edn. IHW-Verlag, Eching
Dong W, Wang B, Hyde KD, McKenzie EHC, Raja HA, Tanaka K et al (2020) Freshwater Dothideomycetes. Fungal Divers 105:319–575
Doppelbaur H (1960) Ein Beitrag zur Anatomie und Entwichlungsgeschichte von Dermatocarpon miniatum (L.) Mann. Nova Hedwig 2:279–286
Ebersberger I, de Matos SR, Kupczok A, Gube M, Kothe E, Voigt K, von Haeseler A (2011) A consistent phylogenetic backbone for the fungi. Mol Biol Evol 29:1319–1334
Egidi E, Hoog S, Isola D, Onofri S, Quaedvlieg W, de Vries M et al (2014) Phylogeny and taxonomy of meristematic rock-inhabiting black fungi in the Dothideomycetes based on multi-locus phylogenies. Fungal Divers 65:127–165
Egidi E, Delgado-Baquerizo M, Plett JM, Wang J, Eldridge DJ, Bardgett RD et al (2019) A few Ascomycota taxa dominate soil fungal communities worldwide. Nat Commun 10:2369
Ellis MB (1971) Dematiaceous Hyphomycetes X. Mycol Pap 125:1–30
Eriksson OE (1981) The families of bitunicate ascomycetes. Opera Bot 60:1–220
Eriksson OE (1982) Outline of the Ascomycetes—1982. Mycotaxon 15:203–248
Eriksson O (1983) Outline of the ascomycetes—1983. Systema Ascom 2:1–37
Eriksson OE, Winka K (1997) Supraordinal taxa of Ascomycota. Myconet 1:1–16
Ewaze J, Summerbell R, Scott J (2008) Ethanol physiology in the warehouse-staining fungus, Baudoinia compniacensis. Mycol Res 112:1373–1380
Eydoux L, Farrer E (2020) Does salinity affect lifestyle switching in the plant pathogen Fusarium solani? Access Microbiol. https://doi.org/10.1099/acmi.0.000114
Faris-Mokaiesh S, Boccara M, Denis JB, Derrien A, Spire D (1996) Differentiation of the ‘Ascochyta complex’ fungi of pea by biochemical and molecular markers. Curr Genet 29:182–190
Flavell RB, O’Dell M, Thompson WF, Vincentz M, Sardana R, Barker RF (1986) The differential expression of ribosomal RNA genes. Philos Trans R Soc Lond Ser B Biol Sci 314(1166):385–397
Fresenius G (1863) Beitrage zur Mykologie 3. Heinrich Ludwig Brommer Verlag, Frankfurt
Fries EM (1818a) Observationes Mycologiae, vol 2. Hafniae, Bonnier
Fries EM (1818b) Observationes Mycologicae. Gerh Bonnier Copenhagen 2:1–372
Fuckel L (1870) Symbolae Mycologicae. Beitrage Zur Kenntniss Der Rheinischen Pilze, Wiesbaden 1870:329–330
Fuckel L (1872) Symbolae mycologicae. Beiträge zur Kenntniss der rheinischen Pilze. Erster Nachtrag Jahrb Nassau Ver Naturkd 25–26:287–346
Gabriel M, Postigo I, Tomaz C, Martinez J (2016) Alternaria alternata allergens: Markers of exposure, phylogeny and risk of fungi-induced respiratory allergy. Environ Int 89–90:71–80
Gao R, Zhang G (2013) Potential of DNA barcoding for detecting quarantine fungi. Phytopathology 103(11):1103–1107
Gäumann E (1949) Die Pilze. Grundzüge ihrer Entwicklungsgeschichte und Morphologie, 1st edn. Birkhäuser Verlag, Basel (1964 end edition, 541 pp)
Gäumann E (1964) Die Pilze. Grundzüge ihrer Entwicklungsgechichte und Morphologie, 2nd edn, 541 pp., 610 figs. Birkhauser Verlag, Switzerland
Glass NL, Donaldson GC (1995) Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Appl Environ Microbiol 61:1323–1330
Goodwin SB, Dunkley LD, Zismann VL (2001) Phylogenetic analysis of Cercospora and Mycosphaerella based on the internal transcribed spacer region of ribosomal DNA. Phytopathology 91:648–658
Gordon T, Pfender W (2012) Effects of the mycoparasite Sphaerellopsis filum on overwintering survival of stem rust in perennial ryegrass. Plant Dis 96:1471–1481
Gossen BD, Hwang SF, Conner RL, Chang KF (2011) Managing the Ascochyta blight complex on field pea in western Canada. Pra Soils Crop J 4:135–141
Groenewald M, Groenewald JZ, Crous PW (2005) Distinct species exist within the Cercospora apii morphotype. Phytopathology 95:951–959
Groenewald M, Groenewald JZ, Braun U, Crous PW (2006) Host range of Cercospora apii and C. beticola, and description of C. apiicola, a novel species from celery. Mycologia 98:275–285
Groenewald M, Groenewald JZ, Braun U, Crous P (2010) Cercospora speciation and host range. In: Lartey RT et al (eds) Cercospora leaf spot of sugar beet and related species. APS Press, St Paul
Groenewald JZ, Nakashima C, Nishikawa J, Shin HD, Park JH, Jama AN et al (2013) Species concepts in Cercospora: spotting the weeds among the roses. Stud Mycol 75:115–170
Gross M (2012) Barcoding biodiversity. Current Biol 22:R73–R76
Guarro J, GenéJ SAM (1999) Developments in fungal taxonomy. Clin Microbiol Rev 12:454–500
Hale ME (1967) The biology of lichens. Arnold, London
Haridas S, Albert R, Binder M, Bloem J, LaButti K, Salamov A et al (2020) 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens. Stud Mycol 96:141–153
Harrington T, Rizzo D (1999) Defining species in the fungi. In: Worrall JJ (ed) Structure and dynamics of fungal populations. Kluwer, Dordrecht, pp 43–71
Hashimoto A, Matsumura M, Hirayama K, Tanaka K (2017) Revision of Lophiotremataceae (Pleosporales, Dothideomycetes): Aquasubmersaceae, Cryptocoryneaceae, and Hermatomycetaceae fam. nov. Persoonia 39:51–73
Hawksworth DL (1985) Problems and prospects in the systematics of the Ascomycotina. Proc Indian Acad Sci 94:319–339
Hawksworth DL (1991) The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycol Res 95:641–655
Hawksworth DL, Sutton BC, Ainsworth GC (1983) Ainsworth & Bisby’s dictionary of the fungi, 7th edn. Commonwealth Agricultural Bureaux, Slough
Heath TA, Hedtke SM, Hillis DM (2008) Taxon sampling and the accuracy of phylogenetic analyses. J Syst Evol 46:239–257
Hebert P, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Syst Biol 54:852–859
Hebert P, Penton E, Burns J, Janzen D, Hallwachs W (2004a) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci USA 101:14812–14817
Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004b) Identification of birds through DNA barcodes. PLoS Biol 2:e312
Hessen A, Jahns HM (1973) ‘1974’ lichens. Eine Einführung in die Flechtenkunde. Thiene, Stuttgart
Hey J, Pinho C (2012) Population genetics and objectivity in species diagnosis. Evolution 66:1313–1429
Hibbett DS (1992) Ribosomal RNA and fungal systematics. Trans Mycol Soc Jpn 33:533–556
Hibbett D, Abarenkov K, Kõljalg U, Opik M, Chai B, Cole J et al (2016) Sequence-based classification and identification of Fungi. Mycologia 108:1049–1068
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
Hofmann TA, Piepenbring M (2014) New records of plant parasitic Asterinaceae (Dothideomycetes, Ascomycota) with intercalary appressoria from Central America and Panama. Trop Plant Pathol 39:419–427
Hofstetter V, Buyck B, Eyssartier G, Schnee S, Gindro K (2019) The unbearable lightness of sequenced-based identification. Fungal Divers 96:243–284
Hongsanan S, Chomnunti P, Crous P, Chukeatirote E, Hyde K (2014a) Introducing Chaetothyriothecium, a new genus of Microthyriales. Phytotaxa 161:157–164
Hongsanan S, Li YM, Liu JK, Hofmann TA, Piepenbring M, Bhat DJ et al (2014b) Revision of genera in Asterinales. Fungal Divers 68:1–68
Hongsanan S, Hyde KD, Phookamsak R, Wanasinghe DN, McKenzie EHC et al (2020a) Refined families of Dothideomycetes: Dothideomycetidae and Pleosporomycetidae. Mycosphere 11:1553–2107
Hongsanan S, Hyde KD, Phookamsak R, Wanasinghe DN, McKenzie EHC, Sarma VV et al (2020b) Refined families of Dothideomycetes: orders and families incertae sedis in Dothideomycetes. Fungal Divers 105:17–318
Hongsanan S, Jeewon R, Purahong W, Xie N, Liu JK et al (2018) Can we use environmental DNA as holotypes? Fungal Divers 92:1–32
Hou LW, Groenewald JZ, Pfenning LH, Yarden O, Crous PW, Cai L (2020) The phoma-like dilemma. Stud Mycol 96:309–396
Hsieh WH, Goh TK (1990) Cercospora and similar fungi from Taiwan. Maw Chang Book Company, Taiwan
Huang S, Maharachchikumbura SSN, Jeewon R, Bhat DJ, Chomnunti P, Hyde KD et al (2018) Morphological and molecular taxonomy of Jahnula dianchia sp. nov. (Jahnulales) from submerged wood in Dianchi Lake, Yunnan China. Mycol Prog 17:547–555
Huanraluek N, Jayawardena RS, Thambugala KM, Tian Q (2020) New host records for three saprobic Dothideomycetes in Thailand. Asian J Mycol 3:345–361
Hyde KD, Jones EBG, Leaño E, Pointing SB, Poonyth AD, Vrijmoed LLP (1998) Role of fungi in marine ecosystems. Biodivers Conserv 7:1147–1161
Hyde KD, Jones E, Liu JK, Ariyawansa H, Boehm E, Boonmee S et al (2013) Families of Dothideomycetes. Fungal Divers 63:1–313
Hyde KD, Hongsanan S, Jeewon R, Bhat DJ, McKenzie EHC, Jones EBG et al (2016) Fungal diversity notes 367–490: taxonomic and phylogenetic contributions to fungal taxa. Fungal Divers 80:1–270
Hyde K, Norphanphoun C, Chen J, Dissanayake A, Doilom M, Hongsanan S et al (2018) Thailand’s amazing diversity: up to 96% of fungi in northern Thailand may be novel. Fungal Divers 93:215–239
Hyde KD, Tennakoon DS, Jeewon R, Bhat DJ, Maharachchikumbura SSN, Rossi W et al (2019a) Fungal diversity notes 1036–1150: taxonomic and phylogenetic contributions on genera and species of fungal taxa. Fungal Divers 96:1–242
Hyde KD, Xu J, Rapior S, Jeewon R, Lumyong S, Niego AGT et al (2019b) The amazing potential of fungi: 50 ways we can exploit fungi industrially. Fungal Divers 97:1–136
Hyde KD, Dong Y, Phookamsak R, Jeewon R, Bhat DJ, Jones EBG et al (2020) Fungal diversity notes 1151–1276: taxonomic and phylogenetic contributions on genera and species of fungal taxa. Fungal Divers 100:5–277
Index Fungorum 2021 http://www.indexfungorum.org/
James T, Kauff F, Schoch C, Matheny P, Valerie H, Cox CJ et al (2006) Reconstructing the early evolution of the fungi using a six gene phylogeny. Nature 443:818–822
Jantzen F, Lynch JH, Kappel C, Höfflin J, Skaliter O, Wozniak N et al (2019) Retracing the molecular basis and evolutionary history of the loss of benzaldehyde emission in the genus Capsella. New Phytol 224:1349–1360
Jayasiri SC, Hyde KD, Jones EBG, Peršoh D, Camporesi E, Kang JC (2018) Taxonomic novelties of Hysteriform Dothideomycetes. Mycosphere 9:803–837
Jayasiri S, Hyde K, Jones E, McKenzie E, Jeewon R, Phillips A et al (2019) Diversity morphology and molecular phylogeny of Dothideomycetes on decaying wild seed pods and fruits. Mycosphere 10:1–186
Jayawardena RS, McKenzie EHC, Chen YJ, Phillips AJL, Hongsanan S, Norphanphoun C et al (2019) https://onestopshopfungi.org/, a database to enhance identification of phytopathogenic genera. Asian J Mycol 2:281–286
Jeewon R, Hyde K (2016) Establishing species boundaries and new taxa among fungi: recommendations to resolve taxonomic ambiguities. Mycosphere 7:1669–1677
Jiang SH, Lücking R, Xavier-Leite AB, Cáceres MES, Aptroot A, Viñas Portilla C et al (2020) Reallocation of foliicolous species of the genus Strigula into six genera (lichenized Ascomycota, Dothideomycetes, Strigulaceae). Fungal Divers 102:257–291
Jiang W, Chen SY, Wang H, Li DZ, Wiens JJ (2014) Should genes with missing data be excluded from phylogenetic analyses? Mol Phyl Evol 80:308–318
Jones E, Devadatha B, Abdel-Wahab M, Dayarathne M, Zhang S, Hyde K et al (2019a) Phylogeny of new marine Dothideomycetes and Sordariomycetes from mangroves and deep-sea sediments. Bot Mar. https://doi.org/10.1515/bot-2019-0014
Jones E, Pang KL, Abdel-Wahab M, Scholz B, Hyde K, Boekhout T et al (2019b) An online resource for marine fungi. Fungal Divers 96:347–433
Kahvejian A, Quackenbush J, Thompson JF (2008) What would you do if you could sequence everything? Nat Biotechnol 26:1125–1133
Kamilar JM, Cooper N (2013) Phylogenetic signal in primate behaviour, ecology and life history. Philos Trans R Soc Lond B Biol Sci 368
Kim W, Chen W (2019) Phytotoxic metabolites produced by legume-associated Ascochyta and its related genera in the Dothideomycetes. Toxins 11:627
Kirk PM, Cannon PF, David JC, Stalpers JA (2001) Ainsworth & Bisby’s dictionary of the fungi, 9th edn. CABI, Wallingford
Kirk PM, Cannon PF, Minter DW, Stalpers JA (2008) Ainsworth & Bisby’s dictionary of the fungi, 10th edn. CABI, Wallingford
Kirschner R (2009) Cercosporella and Ramularia. Mycologia 101:110–119
Kitching IJ, Culverwell CL, Harbach RE (2014) Data from: the phylogenetic conundrum of Lutzia (Diptera: Culicidae: Culicini): a cautionary account of conflict and support. Dryad Digit Repository. https://doi.org/10.5061/dryad.5s790
Knudsen H, Rosendahl S (2002) DJ McLaughlin EG Mclaughlin & P.A. Lemke (vol.eds.): Systematics and Evolution, Part B. In: K. Esser & P.A. Lemke (eds.): The Mycota VII. Springer Verlag Berlin Heidelberg New York 2001, 259 pp. Mycorrhiza 12:223
Kodsueb R, Dhanasekaran V, Aptroot A, Lumyong S, McKenzie EHC, Hyde KD, Jeewon R (2006a) The family Pleosporaceae: intergeneric relationships and phylogenetic perspectives based on sequence analyses of partial 28S rDNA. Mycologia 98:571–583
Kodsueb R, Jeewon R, Dhanasekaran V, McKenzie E, Lumyong P, Lumyong S et al (2006b) Systematic revision of Tubeufiaceae based on morphological and molecular data. Fungal Divers 21:105–130
Kohlmeyer J (1969) Marine fungi of Hawaii including the new genus Heliascus. Can J Bot 47:1469–1487
Kong W, Wei R, Logrieco A, Wei J, Wen J, Xiao X, Yang M (2014) Occurrence of toxigenic fungi and determination of mycotoxins by HPLC-FLD in functional foods and spices in China markets. Food Chem 146:320–326
Kreisel H (1969) Grundzüge eines natürlichen Systems der Pilze. Gustav Fischer, Jena
Kress W, García-Robledo C, Uriarte M, Erickson D (2014) DNA barcodes for ecology evolution and conservation. Trends Ecol Evol 30:25–35
Kress WJ, Erickson DL (2008) DNA barcodes: genes, genomics, and bioinformatics. Proc Natl Acad Sci USA 105:2761–2762
Kruys A, Wedin M (2009) Phylogenetic relationships and an assessment of traditionally used taxonomic characters in the Sporormiaceae (Pleosporales, Dothideomycetes, Ascomycota), utilising multi-gene phylogenies. Sys Biodivers 7:465–478
Kulski J (2016) Next-generation sequencing—an overview of the history tools and “omic”applications. In: Next generation sequencing—advances applications and challenges. InTech, Croatia, pp 3–60
Lawrey J, Diederich P (2003) Lichenicolous fungi: interactions, evolution, and biodiversity. Bryologist 106:80–120
Lawrey J, Diederich P, Nelsen M, Freebury C, Van den Broeck D, Sikaroodi M, Ertz D (2012) Phylogenetic placement of lichenicolous Phoma species in the Phaeosphaeriaceae (Pleosporales, Dothideomycetes). Fungal Divers 55:195–213
Le Renard L, Stockey R, Upchurch G, Berbee M (2020) A new epiphyllous fly-speck fungus from the Early Cretaceous Potomac Group of Virginia (125–112 Ma): Protographum luttrellii, gen. et sp. nov. Mycologia 112:1–15
Leitch I, Kooij P, Coker T, Grigoriev IG, Nagy L, Martin F et al (2018) State of the World's Fungi 2018 6. Fungal genomes: exploring understanding and utilizing their diversity. In: Willis KJ (ed) State of the World's Fungi Report. Royal Botanic Gardens, Kew, pp 40–47
Letrouit-Galinou MA (1973) Les asques des lichens et le type archaeasce. Bryologist 76:30–47
Levetin E, Horner W, Scott J (2015) Taxonomy of Allergenic Fungi. J Allergy Clin Immunol Pract 4:375–385
Li WJ, Bhat J, Hyde KD, Wang Y (2014) Towards a natural classification of Dothideomycetes 4: The genera Bryopelta, Bryorella, Bryosphaeria, Lophiosphaerella and Maireella (Dothideomycetes incertae sedis). Phytotaxa 176:28–41
Li J, Bhat D, Phookamsak R, Mapook A, Lumyong S, Hyde K (2016) Sporidesmioides thailandica gen. et sp. nov. (Dothideomycetes) from northern Thailand. Mycol Prog 15(10–11):1169–1178
Libert MA (1830) Mémoire concernant les plantes cryptogames qui peuent être réunies sous le nom d’ Ascoxytacei. Mem Soc Sci Agr Lille 1829–1830(1831):174–176
Lindau G (1897) Pyrenomycetineae. In: Engler A, Prantl K (eds) Die natürlichen Pflanzenfamilien. Wilhelm Engelmann, Leipzig
Lindemuth R, Wirtz N, Lumbsch HT (2001) Phylogenetic analysis of nuclear and mitochondrial rDNA sequences supports the view that loculoascomycetes (Ascomycota) are not monophyletic. Mycol Res 105:1176–1181
Linnaeus C (1758) Systema naturae per regina tria naturae secundum Classes Ordines Genera Species. Tomus I. Regnum Animale. Holmiae Editio Decima Reformata
Liu D, Ma J (2011) The information systems for DNA barcode data. In: Systems and computational biology bioinformatics and computational modeling. InTechOpen, London
Liu YJ, Whelen S, Hall BD (1999) Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit. Mol Biol Evol 16:1799–1808
Liu AR, Chen SC, Wu SY, Xu T, Guo LD, Jeewon R, Wei JG (2010) Cultural studies coupled with DNA based sequence analyses and its implication on pigmentation as a phylogenetic marker in Pestalotiopsis taxonomy. Mol Phy Evol 57:528–535
Liu JK, Phookamsak R, Jones E, Zhang Y, Ko Ko T, Hu H et al (2011) Astrosphaeriella is polyphyletic, with species in Fissuroma gen. nov., and Neoastrosphaeriella gen. nov. Fungal Divers 51:135–154
Liu JK, Phookamsak R, Doilom M, Wikee S, Li YM, Ariyawansa H et al (2012) Towards a natural classification of Botryosphaeriales. Fungal Divers 57:149–210
Liu D, Liu L, Guo G, Wang W, Sun Q, Parani M, Ma J (2013) BOLDMirror: a global mirror system of DNA barcode data. Mol Ecol Res 13:991–995
Liu NG, Ariyawansa HA, Hyde KD, Maharachchikumbura SSN, Zhao RL, Phillips AJL et al (2016) Perspectives into the value of genera families and orders in classification. Mycosphere 7:1649–1668
Liu JK, Hyde K, Jeewon R, Phillips A, Maharachchikumbura S, Ryberg M et al (2017) Ranking higher taxa using divergence times: a case study in Dothideomycetes. Fungal Divers 84:75–99
Liu NG, Lin CG, Liu JK, Samarakoon MC, Hongsanan S, Bhat D et al (2018) Lentimurisporaceae, a New Pleosporalean Family with divergence times estimates. Cryptogam Mycol 39:259–282
Locquin MV (1984) Mycologie generale et structural. Masson, Paris
Lopes A, Barradas C, Phillips AJL, Alves A (2016) Diversity and phylogeny of Neofusicoccum species occurring in forest and urban environments in Portugal. Mycosphere 7:906–920
Lopes A, Phillips AJL, Alves A (2017) Mating type genes in the genus Neofusicoccum: Mating strategies and usefulness in species delimitation. Fungal Biol 121:394–404
Lu YZ, Liu JK, Hyde KD, Jeewon R, Kang JC, Fan C et al (2018) A taxonomic reassessment of Tubeufiales based on multi-locus phylogeny and morphology. Fungal Divers 92:131–344
Lücking R, Aptroot A, Thor G (1997) New species or interesting records of foliicolous lichens. II. Flavobathelium Epiphyllum (Lichenized Ascomycetes: Melanommatales). Lichenologist 29:221–228
Lücking R, Hodkinson BP, Leavitt SD (2017) The 2016 classification of lichenized fungi in the Ascomycota and Basidiomycota-approaching one thousand genera. Bryologist 119:361–416
Lücking R, Lumbsch HT, Di Stefano JF, Lizano D, Carranza J, Bernecker A et al (2008) Eremithallus costaricensis (Ascomycota: Lichinomycetes: Eremothallales), a new fungal lineage with a novel lichen symbiotic lifestyle discovered in an urban relict forest in Costa Rica. Symbiosis 46:161–170
Lücking R, Nelsen MP, Aptroot A, Barillas de Klee R, Bawingan PA, Benatti MN et al (2016) A phylogenetic framework for reassessing generic concepts and species delimitation in the lichenized family Trypetheliaceae (Ascomycota: Dothideomycetes). Lichenologist 48:739–762
Lücking R, Aime M, Robbertse B, Miller A, Ariyawansa H, Aoki T et al (2020) Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 11:14
Lücking R, Aime MC, Robbertse B, Miller AN, Aoki T, Ariyawansa HA et al (2021) Fungal taxonomy and sequence-based nomenclature. Nat Microbiol 6:540–548
Lumbsch HT (2000) Phylogeny of filamentous ascomycetes. Naturwissenschaften 87:335–342
Lumbsch HT, Huhndorf SM (2007) Whatever happened to the pyrenomycetes and loculoascomycetes? Mycol Res 111:1064–1074
Lumbsch HT, Wirtz N, Lindemuth R, Schmitt I (2002) Higher level phylogenetic relationships of euascomycetes (Pezizomycotina) inferred from a combined analysis of nuclear and mitochondrial sequence data. Mycol Prog 1:57–70
Lumbsch HT, Schmitt I, Palice Z, Wiklund E, Ekman S, Wedin M (2004) Supraordinal phylogenetic relationships of Lecanoromycetes based on a Bayesian analysis of combined nuclear and mitochondrial sequences. Mol Phyl Evol 31:822–832
Luo ZL, Bhat D, Jeewon R, Boonmee S, Bao DF, Zhao YC et al (2017a) Molecular phylogeny and morphological characterization of asexual fungi (Tubeufiaceae) from freshwater habitats in Yunnan, China. Cryptogam Mycol 38:27–53
Luttrell ES (1951) Taxonomy of Pyrenomycetes. Univ Missouri Stud 24:1–120
Luttrell ES (1955) The ascostromatic ascomycetes. Mycologia 47:511–532
Lutzoni F, Pagel M, Reeb V (2001) Major fungal lineages are derived from lichen symbiotic ancestors. Nature 411:937–940
Lutzoni F, Kauff F, Cox C, McLaughlin D, Celio G, Dentinger B et al (2004) Assembling the fungal tree of life: progress classification and evolution of subcellular traits. Am J Bot 91:1446–1480
Ma LJ, Fedorova ND (2010) A practical guide to fungal genome projects: strategy technology cost and completion. Mycology 1:9–24
Manamgoda D, Cai L, Crous P, Madrid H, Chukeatirote E, Shivas R (2012a) A phylogenetic and taxonomic re-evaluation of the Bipolaris-Cochliobolus-Curvularia Complex. Fungal Divers 56:131–144
Manamgoda DS, Cai L, McKenzie EHC, Chukeatirote E, Hyde KD (2012b) Two new Curvularia species from northern Thailand. Sydowia 64:255–266
Mapook A, Hyde KD, Li J, Hongsanan S, Phukhamsakda C, Boonmee S (2016) Palawaniaceae fam. nov., a new family (Dothideomycetes, Ascomycota) to accommodate Palawania species and their evolutionary time estimates. Mycosphere 7:1732–1745
Marthinsen G, Rui S, Timdal E (2019) OLICH: a reference library of DNA barcodes for Nordic lichens. Biodivers Data J 7:e36252
Martin GW (1945) The classification of the Tremellales. Mycologia 37:527–554
Matheny P, Liu Y, Ammirati J, Hall B (2002) Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales). Am J Bot 89:688–698
Mayr (1957) Species concepts and definitions. In: Mayr E (ed) The species problem. American Association for the. Advancement of Science Publication No. 50, Washington
McLaughlin DJ, McLaughlin EG, Lemke PA (eds) (2001) The Mycota, vol VII. Part A. Systematics and evolution. Springer, Berlin
McLaughlin D, Hibbett D, Lutzoni F, Spatafora J, Vilgalys R (2009) The search for the fungal tree of life. Trends Microbiol 17:488–497
Meghvansi M, Khan M, Gupta R, Veer V (2013) Identification of new species of Cercospora causing leaf spot disease in Capsicum assamicum in northeastern India. Res Microbial 164(9):894–902
Meyer C, Paulay G (2006) DNA barcoding: error rates based on comprehensive sampling. PLoS Biol 3:e422
Meyer W, Irinyi L, Hoang M, Robert V, Garcia-Hermoso D, Desnos-Ollivier M et al (2018) Database establishment for the secondary fungal DNA barcode Translational Elongation Factor 1α (TEF1α). Genome 62
Miadlikowska J, Kauff F, Hofstetter V, Fraker E, Grube M, Hafellner J et al (2006) New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia 98:1088–1103
Miller JH (1928) Biologic studies in the Sphaeriales-I. Mycologia 20:187–213
Miller JH (1941) Georgia Pyrenomycetes. II. Mycologia 33:74–81
Miller JH (1949) A revision of the classification of the Ascomycetes with special emphasis on the Pyrenomycetes. Mycologia 41:99–127
Milne RI (2009) Effects of taxon sampling on molecular dating for within-genus divergence events when deep fossils are used for calibration. J Syst Evol 47:383–401
Min XJ, Hickey DA (2007) Assessing the effect of varying sequence length on DNA barcoding of fungi. Mol Ecol Notes 7:365–373
Mindell R, Stockey R, Beard G, Currah R (2007) Margaretbarromyces dictyosporus gen. sp nov.: a permineralized corticolous ascomycete from the Eocene of Vancouver Island, British Columbia. Mycol Res 111:680–684
Montenegro-Calderón JG, Martínez-Álvarez JA, Vieyra-Hernández MT, Rangel Macías LI, Razzo-Soria T, Chávez-Herrera R et al (2011) Molecular identification of two strains of Cercospora rodmanii isolated from water hyacinth present in Yuriria lagoon, Guanajuato, Mexico and identification of new hosts for several other strains. Fungal Biol 115:1151–1162
Moritz C, Cicero C (2004) DNA barcoding: promise and pitfalls. PLOS Biol 2:e354
Muggia L, Fleischhacker A, Kopun T, Grube M (2016) Extremotolerant fungi from alpine rock lichens and their phylogenetic relationships. Fungal Divers 76:119–142
Muller E, Arx V (1950) Einige Aspekte zur Systematik pseudosphaerialer Ascomyceten. Ber Schioeic Bot Ges 60:329–397
Nabhan AR, Sarkar IN (2012) The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy. Brief Bioinform 13:122–134
Nair D, Padmavathy S (2014) Impact of endophytic microorganisms on plants, environment and humans. Sci World J 2014:250693
Nanney DL (1982) Genes and phenes in Tetrahymena. Bioscience 32:783–788
Nannfeldt JA (1932) Studien uber die Morphologie und Systematik der nicht–lichenisierten inoperkulaten Discomyceten. Nova Acta Regiae Soc Sci Upsal IV 8:1–368
Nater A, Burri R, Kawakami T, Smeds L, Ellegren H (2015) Resolving evolutionary relationships in closely related species with whole-genome sequencing data. Syst Biol 64:1000–1017
Nelsen MP, Lücking R, Grube M, Mbatchou JS, Muggia L, Rivas Plata E, Lumbsch HT (2009) Unravelling the phylogenetic relationships of lichenized fungi in Dothideomyceta. Stud Mycol 64:135–144
Obase K, Douhan G, Matsuda Y, Smith M (2016) Revisiting phylogenetic diversity and cryptic species of Cenococcum geophilum sensu lato. Mycorrhiza 26:529–540
Onfroy C, Tivoli B, Corbiere R, Bouznad Z (1999) Cultural, molecular and pathogenic variability of Mycosphaerella pinodes and Phoma medicaginis var. pinodella isolates from dried pea in France. Plant Pathol 48:218–229
Onofri S, Noetzel R, de Vera JP, Ott S, Zucconi L, Selbmann L et al (2012) Survival of rock-colonizing organisms after 1.5 years in outer space. Astrobiology 12:508–516
Onofri S, Zucconi L, Isola D, Selbmann L (2014) Rock-inhabiting fungi and their role in deterioration of stone in the Mediterranean area. Plant Biosyst 148:384–391
Padder BA, Kapoor V, Kaushal R (2012) Identification and genetic diversity analysis of Ascochyta species associated with blight complex of pea in a northwestern hill state of India. Agric Res 1:325–337
Park SH, Choi IY, Lee W, Lee KJ, Galea V, Shin HD (2017) Identification and characterization of Cercospora malayensis causing leaf spot on kenaf. Mycobiology 45(2):114–118
Pavlic D, Slippers B, Coutinho TA, Wingfield MJ (2009) Molecular and phenotypic characterization of three phylogenetic species discovered within the Neofusicoccum parvum/N. ribis complex. Mycologia 101:636–664
Pavlic-Zupanc D, Wingfield M, Barber P, Slippers B, Hardy G, Burgess T (2008) Seven new species of the Botryosphaeriaceae discovered on baobabs and other native trees in Western Australia. Mycologia 100:851–866
Peever T, Barve MP, Stone LJ (2007) Evolutionary relationships among Ascochyta species infecting wild and cultivated hosts in the legume tribes Cicereae and Vicieae. Mycologia 99:59–77
Peintner U, Kuhnert-Finkernagel R, Wille V, Biasioli F, Shiryaev A, Perini C (2019) How to resolve cryptic species of polypores: an example in Fomes. IMA Fungus 10:17
Pem D, Gaforov Y, Jeewon R, Hongsanan S, Promputtha I, Doilom M, Hyde KD (2018) Multigene phylogeny coupled with morphological characterization reveal two new species of Holmiella and taxonomic insights within Patellariaceae. Cryptogam Mycol 39:193–210
Pem D, Hongsanan S, Doilom M, Tibpromma S, Wanasinghe DN, Dong W et al (2019a) https://www.dothideomycetes.org: an online taxonomic resource for the classification identification and nomenclature of Dothideomycetes. Asian J Mycol 2:287–297
Pem D, Hyde KD, Doilom M, Camporesi E, Hongsanan S, Rampadarath S et al (2019b) Multigene phylogenetic analyses to establish new Valsaria species and taxonomic significance of spore ornamentation. PLoS ONE 14:e0217982
Pem D, Jeewon R, Bhat DJ, Doilom M, Boonmee S, Hongsanan S et al (2019c) Mycosphere Notes 275–324: A morphotaxonomic revision and typification of obscure Dothideomycetes genera (incertae sedis). Mycosphere 10:1115–1246
Pem D, Jeewon R, Bulgakov T, Gafforov Y, Hongsanan S, Phookamsak R et al (2019d) Taxonomy and molecular phylogeny of Thyrostroma ephedricola sp. nov. (Dothidotthiaceae) and proposal for Thyrostroma jaczewskii comb. nov. Phytotaxa 416:243–256
Pem D, Jeewon R, Gafforov Y, Hongsanan S, Phukhamsakda C, Promputtha I et al (2019e) Melanocamarosporioides ugamica gen. et sp. nov. a novel member of the family Melanommataceae from Uzbekistan. Mycol Prog 18:471–481
Pem D, Jeewon R, Selcuk F, Ulukapi M, Bhat J, Doilom M et al (2020) Ribosomal and Protein Gene Phylogeny Reveals Novel Saprobic Fungal Species from Juglans regia and Urtica dioica. Front Microbiol 11:1303
Pem D, Jeewon R, Bulgakov TS, Bondarenko-Borisova I, Doilom M, Elborban A et al (2021) New host and distributional records for Camarosporidiella in Italy, Russia, and Ukraine. Mycotaxon 39:451–489
Philippe H, Delsuc F, Brinkmann H, Lartillot N (2005) Phylogenomics. Annu Rev Ecol Evol Syst 36:541–562
Philippe H, Brinkmann H, Lavrov D, Littlewood DTJ, Manuel M, Wörheide G, Baurain D (2011) Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol 9:e1000602
Phillips AJL, Alves A, Abdollahzadeh J, Slippers B, Wingfield MJ, Groenewald JZ, Crous PW (2013) The Botryosphaeriaceae: genera and species known from culture. Stud Mycol 76:51–167
Phookamsak R, Liu JK, McKenzie E, Manamgoda D, Ariyawansa H, Thambugala K et al (2014) Revision of Phaeosphaeriaceae. Fungal Divers 68:159–238
Phookamsak R, Manamgoda D, Li W, Dai DQ, Singtripop C, Hyde K (2015a) Poaceascoma helicoides gen et sp. nov., a New Genus with Scolecospores in Lentitheciaceae. Cryptogam Mycol 36:225–236
Phookamsak R, Norphanphoun C, Tanaka K, Dai DQ, Luo ZL, Liu JK et al (2015b) Towards a natural classification of Astrosphaeriella-like species; introducing Astrosphaeriellaceae and Pseudoastrosphaeriellaceae fam. nov. and Astrosphaeriellopsis, gen. nov. Fungal Divers 74:161
Phookamsak R, Boonmee S, Norphanphoun C, Wanasinghe DN, de Silva NI, Dayarathne MC et al (2016) Schizothyriaceae. Mycosphere 7:154–189
Phookamsak R, Hyde KD, Jeewon R, Bhat DJ, Jones GB, Maharachchikumbura SSN et al (2019) Fungal diversity notes 929–1035: taxonomic and phylogenetic contributions on genera and species of fungi. Fungal Divers 95:1–273
Planet P (2006) Tree disagreement: measuring and testing incongruence in phylogenies. J Biomed Inf 39:86–102
Poelt J (1974) ‘1973’ Classification. In: Ahmadjian V, Hale ME (eds) The lichens. Academic Press, New York, pp 599–632
Pollack FG (1987) An annotated compilation of Cercospora names. Mycol Mem 12:1–212
Pratibha J, Prabhugaonkar A, Hyde KD, Bhat DJ (2014) Phylogenetic placement of Bahusandhika, Cancellidium and Pseudoepicoccum (asexual Ascomycota). Phytotaxa 176:68–80
Prieto M, Wedin M (2013) Dating the diversification of the major lineages of Ascomycota (Fungi). PLoS ONE 8:e65576
Purty RS, Chatterjee S (2016) DNA barcoding: an effective technique in molecular taxonomy. Austin J Biotech Bioeng 3:1059
Qiao M, Zheng H, Lv R, Yu Z (2020) Neodactylariales (Dothideomycetes, Ascomycota) Neodactylariales, Neodactylariaceae (Dothideomycetes, Ascomycota): new order and family, with a new species from China. MycoKeys 73:69–85
Quaedvlieg W, Binder M, Groenewald JZ, Summerell BA, Carnegie AJ, Burgess TI, Crous PW (2014) Introducing the consolidated species concept to resolve species in the Teratosphaeriaceae. Persoonia 33:1–40
Radulovici A, Archambault P, Dufresne F (2010) DNA barcodes for marine biodiversity: moving fast forward? Fungal Divers 2:450–472
Rai MK (2000) The genus Phoma (identity and taxonomy). International Book Distributors, Dehra Dun, p 159
Raja HA, Miller AN, Pearce CJ, Oberlies NH (2017) Fungal identification using molecular tools: a primer for the natural products research community. J Nat Prod 80:756–770
Rannala B (1998) Taxon Sampling and the Accuracy of Large Phylogenies. Syst Biol 47:702–710
Rehner SA, Buckley E (2005) A Beauveria phylogeny inferred from nuclear ITS and EF1-alpha sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs. Mycologia 97:84–98
Rehner SA, Samuels GJ (1994) Taxonomy and phylogeny of Gliocladium analyzed from nuclear large subunit ribosomal DNA sequences. Mycol Res 98:625–634
Rehner S, Minnis A, Sung GH, Luangsa-Ard J, Devotto L (2011) Phylogeny and systematics of the anamorphic, entomopathogenic genus Beauveria. Mycologia 103:1055–1073
Reynolds DR (1991) A phylogeny of fissitunicate ascostromatic fungi. Mycotaxon 42:99–123
Rosenberg M, Kumar S (2001) Incomplete taxon sampling is not a problem for phylogenetic inference. Proc Natl Acad Sci USA 98:10751–10756
Ruibal C, Gueidan C, Selbmann L, Gorbushina A, Crous P, Groenewald JZ et al (2009) Phylogeny of rock-inhabiting fungi related to Dothideomycetes. Stud Mycol 64:123–133S127
Saccardo PA (1883) Sylloge Fungorum 2: i 1–815 ii-lxix 1–77. P.A. Saccardo, Italy
Sakai H, Ito Y, Shedko SV, Safronov SN, Frolov SV, Chereshnev IA et al (2006) Phylogenetic and taxonomic relationships of Northern Far Eastern Phoxinin Minnows Phoxinus and Rhynchocypris (Pisces Cyprinidae) as inferred from allozyme and mitochondrial 16S rRNA sequence analyses. Zool Soc Jpn Zool Sci 23:323–331
Sakalidis M, Slippers B, Wingfield B, Hardy G, Burgess T (2013) The challenge of understanding the origin, pathways and extent of fungal invasions: global populations of the Neofusicoccum parvum–. ribis species complex. Divers Distrib 19:873–883
Santesson R (1952) Foliicolous lichens I. A revision of the taxonomy of the obligately foliicolous, lichenized fungi. Symb Bot Upsal 12:1–590
Schoch C, Grube M (2015) 6 Pezizomycotina: Dothideomycetes and Arthoniomycetes. In: McLaughlin D, Spatafora J (eds) Systematics and evolution. The Mycota (a comprehensive treatise on fungi as experimental systems for basic and applied research), vol 7B. Springer, Berlin
Schoch CL, Shoemaker RA, Seifert KA, Hambleton S, Spatafora JW, Crous PW (2006) A multigene phylogeny of the Dothideomycetes using four nuclear loci. Mycologia 98:1041–1052
Schoch C, Sung GH, Lopez-Giraldez F, Townsend J, Miadlikowska J, Valerie H et al (2009a) The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Syst Biol 58:224–239
Schoch CL, Crous PW, Groenewald JZ, Boehm EWA, Burgess TI, de Gruyter J et al (2009b) A class-wide phylogenetic assessment of Dothideomycetes. Stud Mycol 64:1–15S10
Selbmann L, Egidi E, Isola D, Onofri S, Zucconi L, Hoog S et al (2013) Biodiversity, evolution and adaptation of fungi in extreme environments. Plant Biosyst 147(1):237–246
Senwanna C, Wanasinghe DN, Bulgakov TS, Wang Y, Bhat DJ, Tang AMC et al (2019) Towards a natural classification of Dothidotthia and Thyrostroma in Dothidotthiaceae (Pleosporineae, Pleosporales). Mycosphere 10:701–738
Sharma R, Polkade A, Shouche Y (2015) Species concept’ microbial taxonomy and systematics. Curr Sci 108:1804–1814
Sharma P, Nassereddin A, Sonthalia S (2021) Black Piedra. In: StatPearls. StatPearls Publishing, Treasure Island
Shearer CA, Raja HA, Miller AN, Nelson P, Tanaka K, Hirayama K et al (2009) The molecular phylogeny of freshwater Dothideomycetes. Stud Mycol 64:145–153
Silva-Hanlin DM, Hanlin R (1999) Small subunit ribosomal RNA gene phylogeny of several loculoascomycetes and its taxonomic implications. Fungal Biol 103:153–160
Singtripop C, Hongsanan S, Li J, de Silva N, Phillips A, Jones G et al (2016) Chaetothyrina mangiferae sp. nov., a new species of Chaetothyrina. Phytotaxa 255:21
Sivanesan A (1984) The bitunicate ascomycetes and their anamorphs. Cramer, Vaduz
Slippers B, Johnson GI, Crous PW, Coutinho TA, Wingfield BD, Wingfield MJ (2005) Phylogenetic and morphological reevaluation of the Botryosphaeria species causing diseases of Mangifera indica. Mycologia 97:99–110
Slippers B, Crous P, Jami F, Groenewald J, Wingfield M (2017) Diversity in the Botryosphaeriales: looking back, looking forward. Fungal Biol 121:322–346
Som A (2015) Causes, consequences and solutions of phylogenetic incongruence. Brief Bioinform 16:536–548
Song N, Geng Y, Li X (2020) The mitochondrial genome of the phytopathogenic fungus Bipolaris sorokiniana and the utility of mitochondrial genome to infer phylogeny of Dothideomycetes. Front Microbiol 11:863–863
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 33:1322–1326
Spatafora J, Sung GH, Johnson D, Hesse C, O’Rourke B, Serdani M et al (2006) A five-gene phylogeny of Pezizomycotina. Mycologia 98:1018–1028
Spatafora J, Aime M, Grigoriev I, Martin F, Stajich J, Blackwell M (2017) The fungal tree of life: from molecular systematics to genome-scale phylogenies. Microbiol Spec. https://doi.org/10.1128/microbiolspec.FUNK-0053-2016
Species Fungorum (2021) http://www.speciesfungorum.org/
Spegazzini C (1881) Fungi argentini additis nonnullis brasiliensibus montevideensibusque. Pugillus quartus (Continuacion). Anales De La Sociedad Científica Argentina 12:193–227
Stajich J (2017) Fungal genomes and insights into the evolution of the kingdom. Microbiol Spec. https://doi.org/10.1128/microbiolspec.FUNK-0055-2016
Sterflinger K (2010) Fungi: their role in deterioration of cultural heritage. Fungal Biol Rev 24:47–55
Sterflinger K, de Hoog GS, Haase G (1999) Phylogeny and ecology of meristematic ascomycetes. Stud Mycol 43:5–22
Stewart EL, Liu Z, Crous PW, Szabo LJ (1999) Phylogenetic relationships among some cercosporoid anamorphs of Mycosphaerella based on rDNA sequence analysis. Mycol Res 103:1491–1499
Stewart J, Thomas K, Lawrence C, Dang H, Pryor B, Timmer P, Peever T (2013) Signatures of recombination in clonal lineages of the citrus brown spot pathogen, Alternaria alternata sensu lato. Phytopathology 103(7):741–749
Stielow JB, Lévesque CA, Seifert KA, Meyer W, Iriny L, Smits D et al (2015) One fungus which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes. Persoonia 35:242–263
Suetrong S, Schoch CL, Spatafora JW, Kohlmeyer J, Volkmann-Kohlmeyer B, Sakayaroj J et al (2009) Molecular systematics of the marine Dothideomycetes. Stud Mycol 64:155–173
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 102:83–92
Suetrong S, Boonyuen N, Pang KL, Ueapattanakit J, Klaysuban A, Sri-indrasutdhi V et al (2011) A taxonomic revision and phylogenetic reconstruction of the Jahnulales (Dothideomycetes), and the new family Manglicolaceae. Fungal Divers 51:163–188
Summerell B, Laurence M, Liew ECY, Leslie J (2010) Biogeography and phylogeography of Fusarium: a review. Fungal Divers 44:3–13
Sun H, Buhler JD (2012) PhyLAT: a phylogenetic local alignment tool. Bioinformatics 28(10):1336–1344
Sun ZB, Sun MH, Li SD (2015) Identification of mycoparasitism-related genes in Clonostachys rosea 67–1 active against Sclerotinia sclerotiorum. Sci Rep 5(1):18169
Sutton B (1996) A century of mycology. Cambridge University Press, Cambridge
Suwannarach N, Kumla J, Lumyong S (2018) Spissiomyces endophytica (Dothideomycetes, Ascomycota), a new endophytic fungus from Thailand. Phytotaxa 333:219
Tanaka K, Hirayama K, Yonezawa H, Sato G, Toriyabe A, Kudo H et al (2015) Revision of the Massarineae (Pleosporales, Dothideomycetes). Stud Mycol 82:75–136
Taylor DL, Sinsabaugh R (2015a) The soil fungi, occurrence, phylogeny and ecology. In: Soil biology and biochemistry. University of New Mexico, Albuquerque, pp 77–110
Tehler A, Farris JS, Lipscomb DL, Källersjö M (2000) Phylogenetic analyses of the fungi based on large rDNA data sets. Mycologia 92:459–474
Tehler A, Little D, Farris JS (2003) The full-length phylogenetic tree from 1551 ribosomal sequences of chitinous fungi, Fungi. Mycol Res 107:901–916
Tessmann DJ, Charudatton R, Kistler HC, Rosskopf EN (2001) A molecular characterization of Cercospora species pathogenic to water hyacinth and emendation of C. piaropi. Mycologia 93:323–334
Thambugala KM, Hyde KD, Tanaka K, Tian Q, Wanasinghe DN, Ariyawansa HA et al (2015) Towards a natural classification and backbone tree for Lophiostomataceae Floricolaceae and Amorosiaceae fam. nov. Fungal Divers 74:199–266
Thambugala KM, Wanasinghe DN, Phillips AJL, Camporesi E, Bulgakov TS, Phukhamsakda C et al (2017) Mycosphere notes 1–50: Grass (Poaceae) inhabiting Dothideomycetes. Mycosphere 8:697–796
Theissen F (1913) Hemisphaeriales. Ann Mycol 11:425–467
Theissen F (1916, publ. 1917) Beiträge zur Systematic der Ascomyzeten. Ann Mycol 14:401–439
Theissen F (1916b) Mykologische Abhandlungen. Verhandlungen Der Zoologisch-Botanischen Gesellschaft in Wien 66:296–400
Theissen F (1919) Neue Original-Untersuchungen von Ascomyzeten. Verhandlungen Der Kaiserlich-Köninglichen Zoologisch-Botanischen Gesellschaft 69:1–24
Theissen F, Sydow H (1915) Die Dothideales. Ann Mycol 13:149–746
Theissen F, Sydow H (1918) Vorentwürfe zu den Pseudosphaeriales. Ann Mycol 16:1–34
Tian Q, Liu JK, Hyde KD, Wanasinghe DN, Boonmee S, Jayasiri SC et al (2015) Phylogenetic relationships and morphological reappraisal of Melanommataceae (Pleosporales). Fungal Divers 74:267–324
To-anun C, Hidayat I, Meeboon J (2011) Genus Cercospora in Thailand: taxonomy and phylogeny (with a dichotomous key to species). Plant Pathol Q 1:11–87
Trakunyingcharoen T, Lombard L, Groenewald J, Cheewangkoon R, To-anun C, Alfenas A, Crous P (2014) Mycoparasitic species of Sphaerellopsis, and allied lichenicolous and other genera. IMA Fungus 5:391–414
Trillas MI, Segarra G (2009) Interactions between nonpathogenic fungi and plants. Adv Bot Res 51:321–359
Tripathi M, Joshi Y (2019) Endolichenic fungi: present and future trends. Springer, Singapore
Tsuneda A, Davey M, Hambleton S, Currah R (2008) Endosporium, a new endoconidial genus allied to the Myriangiales. Botany 86:1020–1033
Tuimala J (2004) A primer to phylogenetic analysis using Phylip Package, 2nd edn. Center for Scientific Computing, Espoo
Untereiner WA (1995) Fruiting studies in species of Capronia (Herpotrichiellaceae). Antonie Van Leeuwenhoek Int J Gen Molec Microbiol 68:3–17
Vaghefi N, Kikkert J, Hay F, Carver G, Koenick L, Bolton M et al (2018) Cryptic diversity, pathogenicity, and evolutionary species boundaries in Cercospora populations associated with Cercospora leaf spot of Beta vulgaris. Fungal Biol 122(4):264–282
Valenzuela-Lopez N, Magaña-Dueñas V, Cano-Lira JF, Wiederhold N, Guarro J, Stchigel AM (2019) Two new species of Gloniopsis (Hysteriales, Ascomycota) from clinical specimens: morphological and molecular characterization. Mycoses 62:1164–1173
van Nieuwenhuijzen EJ, Miadlikowska JM, Houbraken JAMP, Adan OCG, Lutzoni FM, Samson RA (2016) Wood staining fungi revealed taxonomic novelties in Pezizomycotina: new order Superstratomycetales and new species Cyanodermella oleoligni. Stud Mycol 85:107–124
Van Valen L (1976) Ecological species, multispecies, and oaks. Taxon 25:233–239
Venditti C, Pagel M (2008) Speciation and bursts of evolution. Evol Educ Outreach 1:274–280
Verkley G, Silva M, Wicklow D, Crous P (2004) Paraconiothyrium, a new genus to accommodate the mycoparasite Coniothyrium minitans, anamorphs of Paraphaeosphaeria, and four new species. Stud Mycol 50:50
Videira SIR, Groenewald JZ, Nakashima C, Braun U, Barreto RW, de Wit PJG, Crous PW (2017) Mycosphaerellaceae—chaos or clarity? Stud Mycol 87:257–421
Vilgalys R, Hester M (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol 172:4238–4246
Vilgalys R, Sun BL (1994) Ancient and recent patterns of geographic speciation in the oyster mushroom Pleurotus revealed by phylogenetic analysis of ribosomal DNA sequences. Proc Natl Acad Sci USA 91:4599–4603
Vinayaka KS, Krishnamurthy YL, Banakar S, Kekuda TRP (2016) Association and variation of endophytic fungi among some macrolichens in central Western Ghats, Southern India. Int J Curr Microbiol Appl Sci 5:115–124
Vincent D, Rafiqi M, Job D (2020) The multiple facets of plant–fungal interactions revealed through plant and fungal secretomics. Front Plant Sci 10:1626
Voglmayr H, Gardiennet A, Jaklitsch WM (2016) Asterodiscus and Stigmatodiscus two new apothecial dothideomycete genera and the new order Stigmatodiscales. Fungal Divers 80:271–284
von Arx JA (1979) Ascomycetes as Fungi imperfecti. in The whole fungus (ed.) B Kendrick (Ottawa: National Museums of Canada) 201–213
von Arx JA (1981) The genera of fungi sporulating in pure culture. 3rd. Ed. J. Cramer, Vaduz, 424 pp
Von Arx JA, Müller E (1975) A re-evaluation of the bitunicate ascomycetes with keys to families and genera. Stud Mycol 9:1–159
von Höhnel FXR (1907) Eumycetes et Myxomycetes. In Schiffner, V. [ed.] Ergebnisse der Botanischen Expedition der Kaiserlichen Akademie der Wissenschaften nach Süd-Brasilien 1901. Denkschriften der Kaiserlichen Akademie der Wissenschaften. Mathematische-Naturwissenschaftliche Klasse 83: 1–45
von Höhnel F (1909) Fragmente zur Mykologie IV No. 244. Revision der Myriangiaceen und der Gattung Saccardia. Sitz-Berr Kaiserl Akad Wiss Wien 118:349–376
Wägele JW, Mayer C (2007) Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects. BMC Evol Biol 7:147
Wanasinghe D, Jones E, Erio C, Boonmee S, Ariyawansa H, Wijayawardene N et al (2014) An Exciting Novel Member of Lentitheciaceae in Italy from Clematis Vitalba. Cryptogam Mycol 35:323–337
Wanasinghe DN, Hyde KD, Jeewon R, Crous PW, Wijayawardene NN, Jones EBG et al (2017a) Phylogenetic revision of Camarosporium (Pleosporineae, Dothideomycetes) and allied genera. Stud Mycol 87:207–256
Wanasinghe D, Jeewon R, Tibpromma S, Jones EB, Hyde K (2017b) Saprobic Dothideomycetes in Thailand: Muritestudina gen. et sp. nov. (Testudinaceae) a new terrestrial pleosporalean ascomycete, with hyaline and muriform ascospores. Stud Fungi 2:219
Wanasinghe DN, Phukhamsakda C, Hyde KD, Jeewon R, Lee HB, Jones EBG (2018) Fungal diversity notes 709–839: taxonomic and phylogenetic contributions to fungal taxa with an emphasis on fungi on Rosaceae. Fungal Divers 89:1–236
Wang HK, Aproot A, Crous PW, Hyde KD, Jeewon R (2007) The polyphyletic nature of Pleosporales: An example from Massariosphaeria based on ribosomal DNA and RBP2 gene phylogenies. Fungal Biol 111:1268–1276
Ware SB (2006) Aspects of sexual reproduction in Mycosphaerella species on wheat and barley: genetic studies on specificity, mapping, and fungicide resistance. PhD Thesis, Wageningen University, The Netherlands with summaries in English and Dutch
Wehmeyer LE (1975) The pyrenomycetous fungi. Mycol Mem 6:1–250
White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols. Academic Press, San Diego, pp 315–322
Wiens JJ (2003a) Incomplete taxa incomplete characters and phylogenetic accuracy: is there a missing data problem? J Vertebr 23:297–310
Wiens JJ (2003b) Missing data incomplete taxa and phylogenetic accuracy. Syst Biol 52:528–538
Wiens JJ (2006) Missing data and the design of phylogenetic analyses. J Biomed Inform 39:34–42
Wiens JJ, Tiu J (2012) Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling. PLoS ONE 7:e42925
Wijayawardene N, Hyde KD, Bhat D, Goonasekara I, Wanasinghe D, Erio C et al (2015) Additions to brown spored coelomycetous taxa in Massarinae, Pleosporales: introducing Phragmocamarosporium gen. nov. and Suttonomyces gen. nov. Cryptogam Mycol 36(2):213–224
Wijayawardene NN, Hyde KD, Wanasinghe DN, Papizadeh M, Goonasekara ID, Camporesi E et al (2016) Taxonomy and phylogeny of dematiaceous coelomycetes. Fungal Divers 77:1–316
Wijayawardene NN, Papizadeh M, Phillips AJL, Wanasinghe DN, Bhat DJ, Weerahewa HLD et al (2017) Mycosphere essays 19: recent advances and future challenges in taxonomy of coelomycetous fungi. Mycosphere 8:934–950
Wikee S, Udayanga D, Crous PW, Chukeatirote E, McKenzie EHC et al (2011) Phyllosticta—an overview of current status of species recognition. Fungal Divers 51:43–61
Wikee S, Lombard L, Nakashima C, Motohashi K, Chukeatirote E, Cheewangkoon R et al (2013) A phylogenetic re-evaluation of Phyllosticta (Botryosphaeriales). Stud Mycol 76:1–29
Winka K (2000) Phylogenetic relationships within the Ascomycota based on 18S rDNA sequences. PhD study, University, Umea, Umea
Winka K, Eriksson OE, Bang A (1998) Molecular evidence for recognizing the Chaetothyriales. Mycologia 90:822–830
Wong M, Goh TK, Hodgkiss I, Hyde K, Ranghoo V, Tsui C et al (1998) Role of fungi in freshwater ecosystems. Biodivers Conserv 7:1187–1206
Woudenberg JHC, De Gruyter J, Crous PW, Zwiers LH (2012) Analysis of the mating-type loci of co-occurring and phylogenetically related species of Ascochyta and Phoma. Mol Plant Pathol 13:350–362
Woudenberg JHC, Seidl MF, Groenewald JZ, de Vries M, Stielow JB, Thomma B et al (2015) Alternaria section Alternaria: species formae speciales or pathotypes? Stud Mycol 82:1–21
Xu YJ, Luo F, Li B, Shang Y, Wang C (2016) Metabolic conservation and diversification of Metarhizium species correlate with fungal host-specificity. Front Microbiol 7
Yacharoen S, Tian Q, Chomnunti P, Boonmee S, Chukeatirote E, Bhat JD, Hyde KD (2015) Patellariaceae revisited. Mycosphere 6:290–326
Yahr R, Schoch CL, Dentinger BTM (2016) Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches. Philos Trans R Soc B Sci 371:20150336
Yao H, Sun X, He C, Maitra P, Li XC, Guo LD (2019) Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem. Microbiome 7:57
Young AD, Gillung JP (2020) Phylogenomics—principles opportunities and pitfalls of big-data phylogenetics. Syst Entomol 45:225–247
Yuan HS, Lu X, Dai YC, Hyde KD, Kan YH, Kušan I et al (2020) Fungal diversity notes 1277–1386: taxonomic and phylogenetic contributions to fungal taxa. Fungal Divers 104:1–266
Zalar P, Zupancic J, Gostinčar C, Zajc J, Hoog S, De Leo F et al (2019) The extremely halotolerant black yeast Hortaea werneckii—a model for intraspecific hybridization in clonal fungi. IMA Fungus. https://doi.org/10.1186/s43008-019-0007-5
Zamora JC, Svensson M, Kirschner R, Olariaga I, Ryman S, Parra L et al (2018) Considerations and consequences of allowing DNA sequence data as types of fungal taxa. IMA Fungus 9:167–175
Zhang Y, Jeewon R, Fournier J, Hyde KD (2008) Multi-gene phylogeny and morphotaxonomy of Amniculicola lignicola: novel freshwater fungus from France and its relationships to the Pleosporales. Fungal Biol 112:1186–1194
Zhang Y, Schoch CL, Fournier J, Crous PW, de Gruyter J, Woudenberg JHC et al (2009) Multi-locus phylogeny of Pleosporales: a taxonomic ecological and evolutionary re-evaluation. Stud Mycol 64:85–102S105
Zhang Y, Ko Ko T, Hyde K (2011) Towards a monograph of Dothideomycetes: studies on Diademaceae. Cryptogam Mycol 32:115–126
Zhang Y, Crous PW, Schoch CL, Hyde KD (2012) Pleosporales. Fungal Divers 53:1–221
Zhang S, Hyde K, Jones E, Cheewangkoon R, Liu JK (2018) Acuminatispora palmarum gen. et sp. nov. from mangrove habitats. Mycol Prog 17:1–16
Zhang S, Hyde K, Jones EB, Jeewon R, Cheewangkoon R, Liu JK (2019) Striatiguttulaceae, a new pleosporalean family to accommodate Longicorpus and Striatiguttula gen. Nov. from Palms. Mycokeys 49:99–129
Acknowledgements
We would like to thank the Thailand Research Fund, grant RDG6130001 entitled “Impact of climate change on fungal diversity and biogeography in the Greater Mekong Subregion”. K. D. Hyde thanks Chiang Mai University for the award of Visiting Professor. Rajesh Jeewon would like to acknowledge the support from University of Mauritius and the Mauritius Research and Innovative Council (MRC/RUN/1705). We thank Robert Lucking for providing pictures of Constrictolumina cinchonae, Eremithallus costaricensis, Flagellostrigula laureriformis, Flavobathelium epiphyllum and Nigrovothelium tropicum. D. Pem thanks Ishani Goonasekara for helping with dataset. Mae Fah Luang University is acknowledged for supporting studies in dothideomycete species.
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Pem, D., Jeewon, R., Chethana, K.W.T. et al. Species concepts of Dothideomycetes: classification, phylogenetic inconsistencies and taxonomic standardization. Fungal Diversity 109, 283–319 (2021). https://doi.org/10.1007/s13225-021-00485-7
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DOI: https://doi.org/10.1007/s13225-021-00485-7