Skip to main content
Log in

Species concepts of Dothideomycetes: classification, phylogenetic inconsistencies and taxonomic standardization

  • Review
  • Published:
Fungal Diversity Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12

Similar content being viewed by others

References

  • 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

    Article  CAS  Google Scholar 

  • Abdollahzadeh J, Groenewald JZ, Coetzee M, Wingfield MJ, Crous P (2020) Evolution of lifestyles in Capnodiales. Stud Mycol 95:381–414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • Bakhshi M, Arzanlou M, Babay ahari A, Groenewald JZ, Crous P (2018) Novel primers improve species delimitation in Cercospora. IMA Fungus 9:299–332

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Google Scholar 

  • Barr ME (1976) Hypoxylon grandineum: a Loculoascomycete. Mycotaxon 3:325–329

    Google Scholar 

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

    Article  Google Scholar 

  • Barr ME (1983) The ascomycete connection. Mycologia 75:1–13

    Article  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Chapter  Google Scholar 

  • Bensch K, Braun U, Groenewald JZ, Crous PW (2012) The genus Cladosporium. Stud Mycol 72:1–401

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berbee ML (1996) Loculoascomycete origins and evolution of filamentous ascomycete morphology based on 18s rRNA gene sequence data. Mol Biol Evol 13:462–470

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Berbee ML, Taylor JW (1992b) Detecting morphological convergence in true fungi, using 18S rRNA gene sequence data. Biosystems 28:117–125

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Bessey EA (1935) A text-book of mycology. Blakiston’s, Philadelphia

    Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Bisby GR (1923) The literature on the classification of the Hysteriales. Trans Br Mycol Soc 8:176–189

    Article  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Blackwell M, Hibbett D, Taylor J, Spatafora J (2006) Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha). Mycologia 98:829–837

    Article  PubMed  Google Scholar 

  • Boerema GH, Bollen GJ (1975) Conidiogenesis and conidial septation as differentiating criteria between Phoma and Ascochyta. Persoonia 8:111–144

    Google Scholar 

  • 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

    Google Scholar 

  • Boise JR (1985) An amended description of Trematosphaeria. Mycologia 77:230–237

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Cabañes FJ, Bragulat MR, Castellá G (2012) Hortaea werneckii isolated from silicone scuba diving equipment in Spain. Med Mycol 50:852–857

    Article  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • Carbone I, Kohn LM (1999) A Method for Designing primer sets for speciation studies in filamentous ascomycetes. Mycologia 91:553–556

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Chadefaud M (1973) Les asques et la syst des Ascomycetes. Bull Soc Mycot Fr 89:127–170

    Google Scholar 

  • Chadefaud M (1982) Les principaux types d’ascocarpes: leur organization et leur evolution; Deuxieme partie: Les discocarpes. Cryptog Mycol 3:103–144

    Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen Q, Hou LW, Duan WJ, Crous PW, Cai L (2017) Didymellaceae revisited. Stud Mycol 87:105–159

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Chitaley SD, Patil GV (1972) Ebenaceous fossil wood infected with deuteromycetaceous fungus from the Deccan Intertrappean Beds of India. Botanique 3:99e106

    Google Scholar 

  • Chomnunti P, Hongsanan S, Aguirre-Hudson B, Tian Q, Peršoh D, Dhami MK et al (2014) The sooty moulds. Fungal Divers 66:1–36

    Article  Google Scholar 

  • Christias C, Hatzipapas P, Dara A, Kaliafas A, Chrysanthis G (2001) Alternaria alternata, a new pathotype pathogenic to aphids. Biocontrol 46:105–124

    Article  Google Scholar 

  • 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

    Google Scholar 

  • Coleman C, Radulovici A (2020) Challenges for the future of taxonomy: talents, databases and knowledge growth. Megataxa 1:28–34

    Article  Google Scholar 

  • Collins RA, Cruickshank R (2012) The seven deadly sins of DNA barcoding. Mol Ecol Res 13(6):969–975

    Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cracraft J (1982) Geographic differentiation, cladistics and vicariance biogeography: re constructing the tempo an dmode of evolution. Am Zool 22:411–424

    Article  Google Scholar 

  • Cronquist A (1978) Once again, what is a species? In: Knutson LV (ed) Biosystematics in agriculture. Allenheld Osmin, Montclair, pp 3–20

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Google Scholar 

  • Crous PW, Schoch CL, Hyde KD, Wood AR, Gueidan C et al (2009a) Phylogenetic lineages in the Capnodiales. Stud Mycol 64:17–47

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Crous PW, Braun U, Hunter GC, Wingfield MJ, Verkley GJM, Shin HD et al (2013) Phylogenetic lineages in Pseudocercospora. Stud Mycol 75:37–114

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Cummings MP, Meyer A (2005) Magic bullets and golden rules: data sampling in molecular phylogenetics. Zoology 108:329–336

    Article  PubMed  Google Scholar 

  • Currey F (1856) On the reproductive organs of certain fungi, with some remarks on germination. Q J Microsc Sci 4:192–200

    Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • De Bary A (1887) Comparative morphology and biology of the fungi, mycetozoa, and bacteria. Clarendon Press, Oxford

    Book  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Deacon JW (1997) Modern mycology, 3rd edn. Blackwell, London

    Google Scholar 

  • Deighton FC (1967) Studies on Cercospora and allied genera. II. Passalora, Cercosporidium and some species of Fusicladium on Euphorbia. Mycol Pap 112:1–80

    Google Scholar 

  • Deighton FC (1973) Studies on Cercospora and allied genera. IV. Cercosporella Sacc. Pseudocercosporella gen. nov. and Pseudocercosporidium gen. nov. Mycol Pap 133:1–62

    Google Scholar 

  • Deighton FC (1974) Studies on Cercospora and allied genera. V. Mycovellosiella Rangel, and a new species of Ramulariopsis. Mycol Pap 137:1–76

    Google Scholar 

  • Deighton FC (1976) Studies on Cercospora and allied genera. VI. Pseudocercospora Speg., Pantospora Cif. and Cercoseptoria Petr. Mycol Pap 140:1–168

    Google Scholar 

  • Deighton FC (1979) Studies on Cercospora and allied genera. VII. New species and redispositions. Mycol Pap 144:1–56

    Google Scholar 

  • Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nat Rev Gen 6:361–375

    Article  CAS  Google Scholar 

  • Desmazieres JBHJ (1843) Dixieme notice sur quelques plantes cryptogames. Ann Sci Nat Bot Ser 2(19):335–373

    Google Scholar 

  • 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

    Article  Google Scholar 

  • Diederich P, Christianse M (1994) Biatoropsis usnearum Räsänen, and Other Heterobasidiomycetes on Usnea. Lichenol 26:47–66

    Article  Google Scholar 

  • 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

    Google Scholar 

  • Dissanayake AJ, Bhunjun CS, Maharachchikumbura SSN, Liu JK (2020) Applied aspects of methods to infer phylogenetic relationships amongst fungi. Mycosphere 11:2652–2676

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Doppelbaur H (1960) Ein Beitrag zur Anatomie und Entwichlungsgeschichte von Dermatocarpon miniatum (L.) Mann. Nova Hedwig 2:279–286

    Google Scholar 

  • 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ellis MB (1971) Dematiaceous Hyphomycetes X. Mycol Pap 125:1–30

    Google Scholar 

  • Eriksson OE (1981) The families of bitunicate ascomycetes. Opera Bot 60:1–220

    Google Scholar 

  • Eriksson OE (1982) Outline of the Ascomycetes—1982. Mycotaxon 15:203–248

    Google Scholar 

  • Eriksson O (1983) Outline of the ascomycetes—1983. Systema Ascom 2:1–37

    Google Scholar 

  • Eriksson OE, Winka K (1997) Supraordinal taxa of Ascomycota. Myconet 1:1–16

    Google Scholar 

  • Ewaze J, Summerbell R, Scott J (2008) Ethanol physiology in the warehouse-staining fungus, Baudoinia compniacensis. Mycol Res 112:1373–1380

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Fresenius G (1863) Beitrage zur Mykologie 3. Heinrich Ludwig Brommer Verlag, Frankfurt

  • Fries EM (1818a) Observationes Mycologiae, vol 2. Hafniae, Bonnier

    Google Scholar 

  • Fries EM (1818b) Observationes Mycologicae. Gerh Bonnier Copenhagen 2:1–372

    Google Scholar 

  • Fuckel L (1870) Symbolae Mycologicae. Beitrage Zur Kenntniss Der Rheinischen Pilze, Wiesbaden 1870:329–330

    Google Scholar 

  • Fuckel L (1872) Symbolae mycologicae. Beiträge zur Kenntniss der rheinischen Pilze. Erster Nachtrag Jahrb Nassau Ver Naturkd 25–26:287–346

    Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Gao R, Zhang G (2013) Potential of DNA barcoding for detecting quarantine fungi. Phytopathology 103(11):1103–1107

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • Groenewald M, Groenewald JZ, Crous PW (2005) Distinct species exist within the Cercospora apii morphotype. Phytopathology 95:951–959

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Gross M (2012) Barcoding biodiversity. Current Biol 22:R73–R76

    Article  CAS  Google Scholar 

  • Guarro J, GenéJ SAM (1999) Developments in fungal taxonomy. Clin Microbiol Rev 12:454–500

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hale ME (1967) The biology of lichens. Arnold, London

    Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Chapter  Google Scholar 

  • Hashimoto A, Matsumura M, Hirayama K, Tanaka K (2017) Revision of Lophiotremataceae (Pleosporales, Dothideomycetes): Aquasubmersaceae, Cryptocoryneaceae, and Hermatomycetaceae fam. nov. Persoonia 39:51–73

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hawksworth DL (1985) Problems and prospects in the systematics of the Ascomycotina. Proc Indian Acad Sci 94:319–339

    Article  Google Scholar 

  • Hawksworth DL (1991) The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycol Res 95:641–655

    Article  Google Scholar 

  • Hawksworth DL, Sutton BC, Ainsworth GC (1983) Ainsworth & Bisby’s dictionary of the fungi, 7th edn. Commonwealth Agricultural Bureaux, Slough

    Google Scholar 

  • Heath TA, Hedtke SM, Hillis DM (2008) Taxon sampling and the accuracy of phylogenetic analyses. J Syst Evol 46:239–257

    Google Scholar 

  • Hebert P, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Syst Biol 54:852–859

    Article  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004b) Identification of birds through DNA barcodes. PLoS Biol 2:e312

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hessen A, Jahns HM (1973) ‘1974’ lichens. Eine Einführung in die Flechtenkunde. Thiene, Stuttgart

    Google Scholar 

  • Hey J, Pinho C (2012) Population genetics and objectivity in species diagnosis. Evolution 66:1313–1429

    Article  Google Scholar 

  • Hibbett DS (1992) Ribosomal RNA and fungal systematics. Trans Mycol Soc Jpn 33:533–556

    CAS  Google Scholar 

  • 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

    PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • Hofstetter V, Buyck B, Eyssartier G, Schnee S, Gindro K (2019) The unbearable lightness of sequenced-based identification. Fungal Divers 96:243–284

    Article  Google Scholar 

  • Hongsanan S, Chomnunti P, Crous P, Chukeatirote E, Hyde K (2014a) Introducing Chaetothyriothecium, a new genus of Microthyriales. Phytotaxa 161:157–164

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Hongsanan S, Hyde KD, Phookamsak R, Wanasinghe DN, McKenzie EHC et al (2020a) Refined families of Dothideomycetes: Dothideomycetidae and Pleosporomycetidae. Mycosphere 11:1553–2107

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Hou LW, Groenewald JZ, Pfenning LH, Yarden O, Crous PW, Cai L (2020) The phoma-like dilemma. Stud Mycol 96:309–396

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • Huanraluek N, Jayawardena RS, Thambugala KM, Tian Q (2020) New host records for three saprobic Dothideomycetes in Thailand. Asian J Mycol 3:345–361

    Article  Google Scholar 

  • Hyde KD, Jones EBG, Leaño E, Pointing SB, Poonyth AD, Vrijmoed LLP (1998) Role of fungi in marine ecosystems. Biodivers Conserv 7:1147–1161

    Article  Google Scholar 

  • Hyde KD, Jones E, Liu JK, Ariyawansa H, Boehm E, Boonmee S et al (2013) Families of Dothideomycetes. Fungal Divers 63:1–313

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Jayasiri SC, Hyde KD, Jones EBG, Peršoh D, Camporesi E, Kang JC (2018) Taxonomic novelties of Hysteriform Dothideomycetes. Mycosphere 9:803–837

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Kahvejian A, Quackenbush J, Thompson JF (2008) What would you do if you could sequence everything? Nat Biotechnol 26:1125–1133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed Central  Google Scholar 

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

    Google Scholar 

  • Kirk PM, Cannon PF, Minter DW, Stalpers JA (2008) Ainsworth & Bisby’s dictionary of the fungi, 10th edn. CABI, Wallingford

    Book  Google Scholar 

  • Kirschner R (2009) Cercosporella and Ramularia. Mycologia 101:110–119

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • Kohlmeyer J (1969) Marine fungi of Hawaii including the new genus Heliascus. Can J Bot 47:1469–1487

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Kreisel H (1969) Grundzüge eines natürlichen Systems der Pilze. Gustav Fischer, Jena

    Google Scholar 

  • Kress W, García-Robledo C, Uriarte M, Erickson D (2014) DNA barcodes for ecology evolution and conservation. Trends Ecol Evol 30:25–35

    Article  PubMed  Google Scholar 

  • Kress WJ, Erickson DL (2008) DNA barcodes: genes, genomics, and bioinformatics. Proc Natl Acad Sci USA 105:2761–2762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • Levetin E, Horner W, Scott J (2015) Taxonomy of Allergenic Fungi. J Allergy Clin Immunol Pract 4:375–385

    Article  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Google Scholar 

  • Lindau G (1897) Pyrenomycetineae. In: Engler A, Prantl K (eds) Die natürlichen Pflanzenfamilien. Wilhelm Engelmann, Leipzig

    Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Locquin MV (1984) Mycologie generale et structural. Masson, Paris

    Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Lumbsch HT (2000) Phylogeny of filamentous ascomycetes. Naturwissenschaften 87:335–342

    Article  CAS  PubMed  Google Scholar 

  • Lumbsch HT, Huhndorf SM (2007) Whatever happened to the pyrenomycetes and loculoascomycetes? Mycol Res 111:1064–1074

    Article  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Luttrell ES (1951) Taxonomy of Pyrenomycetes. Univ Missouri Stud 24:1–120

    Google Scholar 

  • Luttrell ES (1955) The ascostromatic ascomycetes. Mycologia 47:511–532

    Article  Google Scholar 

  • Lutzoni F, Pagel M, Reeb V (2001) Major fungal lineages are derived from lichen symbiotic ancestors. Nature 411:937–940

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Ma LJ, Fedorova ND (2010) A practical guide to fungal genome projects: strategy technology cost and completion. Mycology 1:9–24

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • Manamgoda DS, Cai L, McKenzie EHC, Chukeatirote E, Hyde KD (2012b) Two new Curvularia species from northern Thailand. Sydowia 64:255–266

    Google Scholar 

  • 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

    Article  Google Scholar 

  • Marthinsen G, Rui S, Timdal E (2019) OLICH: a reference library of DNA barcodes for Nordic lichens. Biodivers Data J 7:e36252

    Article  PubMed  PubMed Central  Google Scholar 

  • Martin GW (1945) The classification of the Tremellales. Mycologia 37:527–554

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • Meyer C, Paulay G (2006) DNA barcoding: error rates based on comprehensive sampling. PLoS Biol 3:e422

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Miller JH (1928) Biologic studies in the Sphaeriales-I. Mycologia 20:187–213

    Article  Google Scholar 

  • Miller JH (1941) Georgia Pyrenomycetes. II. Mycologia 33:74–81

    Article  Google Scholar 

  • Miller JH (1949) A revision of the classification of the Ascomycetes with special emphasis on the Pyrenomycetes. Mycologia 41:99–127

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Min XJ, Hickey DA (2007) Assessing the effect of varying sequence length on DNA barcoding of fungi. Mol Ecol Notes 7:365–373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Moritz C, Cicero C (2004) DNA barcoding: promise and pitfalls. PLOS Biol 2:e354

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Muggia L, Fleischhacker A, Kopun T, Grube M (2016) Extremotolerant fungi from alpine rock lichens and their phylogenetic relationships. Fungal Divers 76:119–142

    Article  PubMed  Google Scholar 

  • Muller E, Arx V (1950) Einige Aspekte zur Systematik pseudosphaerialer Ascomyceten. Ber Schioeic Bot Ges 60:329–397

    Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Nair D, Padmavathy S (2014) Impact of endophytic microorganisms on plants, environment and humans. Sci World J 2014:250693

    Article  Google Scholar 

  • Nanney DL (1982) Genes and phenes in Tetrahymena. Bioscience 32:783–788

    Article  Google Scholar 

  • Nannfeldt JA (1932) Studien uber die Morphologie und Systematik der nicht–lichenisierten inoperkulaten Discomyceten. Nova Acta Regiae Soc Sci Upsal IV 8:1–368

    Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Obase K, Douhan G, Matsuda Y, Smith M (2016) Revisiting phylogenetic diversity and cryptic species of Cenococcum geophilum sensu lato. Mycorrhiza 26:529–540

    Article  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • Philippe H, Delsuc F, Brinkmann H, Lartillot N (2005) Phylogenomics. Annu Rev Ecol Evol Syst 36:541–562

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Phookamsak R, Liu JK, McKenzie E, Manamgoda D, Ariyawansa H, Thambugala K et al (2014) Revision of Phaeosphaeriaceae. Fungal Divers 68:159–238

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Planet P (2006) Tree disagreement: measuring and testing incongruence in phylogenies. J Biomed Inf 39:86–102

    Article  CAS  Google Scholar 

  • Poelt J (1974) ‘1973’ Classification. In: Ahmadjian V, Hale ME (eds) The lichens. Academic Press, New York, pp 599–632

    Google Scholar 

  • Pollack FG (1987) An annotated compilation of Cercospora names. Mycol Mem 12:1–212

    Google Scholar 

  • Pratibha J, Prabhugaonkar A, Hyde KD, Bhat DJ (2014) Phylogenetic placement of Bahusandhika, Cancellidium and Pseudoepicoccum (asexual Ascomycota). Phytotaxa 176:68–80

    Article  Google Scholar 

  • Prieto M, Wedin M (2013) Dating the diversification of the major lineages of Ascomycota (Fungi). PLoS ONE 8:e65576

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Purty RS, Chatterjee S (2016) DNA barcoding: an effective technique in molecular taxonomy. Austin J Biotech Bioeng 3:1059

    Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Radulovici A, Archambault P, Dufresne F (2010) DNA barcodes for marine biodiversity: moving fast forward? Fungal Divers 2:450–472

    CAS  Google Scholar 

  • Rai MK (2000) The genus Phoma (identity and taxonomy). International Book Distributors, Dehra Dun, p 159

    Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rannala B (1998) Taxon Sampling and the Accuracy of Large Phylogenies. Syst Biol 47:702–710

    Article  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Rehner SA, Samuels GJ (1994) Taxonomy and phylogeny of Gliocladium analyzed from nuclear large subunit ribosomal DNA sequences. Mycol Res 98:625–634

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Reynolds DR (1991) A phylogeny of fissitunicate ascostromatic fungi. Mycotaxon 42:99–123

    Google Scholar 

  • Rosenberg M, Kumar S (2001) Incomplete taxon sampling is not a problem for phylogenetic inference. Proc Natl Acad Sci USA 98:10751–10756

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • Santesson R (1952) Foliicolous lichens I. A revision of the taxonomy of the obligately foliicolous, lichenized fungi. Symb Bot Upsal 12:1–590

    Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Sharma R, Polkade A, Shouche Y (2015) Species concept’ microbial taxonomy and systematics. Curr Sci 108:1804–1814

    CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Silva-Hanlin DM, Hanlin R (1999) Small subunit ribosomal RNA gene phylogeny of several loculoascomycetes and its taxonomic implications. Fungal Biol 103:153–160

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Slippers B, Crous P, Jami F, Groenewald J, Wingfield M (2017) Diversity in the Botryosphaeriales: looking back, looking forward. Fungal Biol 121:322–346

    Article  Google Scholar 

  • Som A (2015) Causes, consequences and solutions of phylogenetic incongruence. Brief Bioinform 16:536–548

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Google Scholar 

  • Stajich J (2017) Fungal genomes and insights into the evolution of the kingdom. Microbiol Spec. https://doi.org/10.1128/microbiolspec.FUNK-0055-2016

    Article  Google Scholar 

  • Sterflinger K (2010) Fungi: their role in deterioration of cultural heritage. Fungal Biol Rev 24:47–55

    Article  Google Scholar 

  • Sterflinger K, de Hoog GS, Haase G (1999) Phylogeny and ecology of meristematic ascomycetes. Stud Mycol 43:5–22

    Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • Summerell B, Laurence M, Liew ECY, Leslie J (2010) Biogeography and phylogeography of Fusarium: a review. Fungal Divers 44:3–13

    Article  Google Scholar 

  • Sun H, Buhler JD (2012) PhyLAT: a phylogenetic local alignment tool. Bioinformatics 28(10):1336–1344

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sutton B (1996) A century of mycology. Cambridge University Press, Cambridge

    Google Scholar 

  • Suwannarach N, Kumla J, Lumyong S (2018) Spissiomyces endophytica (Dothideomycetes, Ascomycota), a new endophytic fungus from Thailand. Phytotaxa 333:219

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Theissen F (1913) Hemisphaeriales. Ann Mycol 11:425–467

    Google Scholar 

  • 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

    Google Scholar 

  • Theissen F (1919) Neue Original-Untersuchungen von Ascomyzeten. Verhandlungen Der Kaiserlich-Köninglichen Zoologisch-Botanischen Gesellschaft 69:1–24

    Google Scholar 

  • Theissen F, Sydow H (1915) Die Dothideales. Ann Mycol 13:149–746

    Google Scholar 

  • Theissen F, Sydow H (1918) Vorentwürfe zu den Pseudosphaeriales. Ann Mycol 16:1–34

    Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • Trillas MI, Segarra G (2009) Interactions between nonpathogenic fungi and plants. Adv Bot Res 51:321–359

    Article  CAS  Google Scholar 

  • Tripathi M, Joshi Y (2019) Endolichenic fungi: present and future trends. Springer, Singapore

    Book  Google Scholar 

  • Tsuneda A, Davey M, Hambleton S, Currah R (2008) Endosporium, a new endoconidial genus allied to the Myriangiales. Botany 86:1020–1033

    Article  Google Scholar 

  • Tuimala J (2004) A primer to phylogenetic analysis using Phylip Package, 2nd edn. Center for Scientific Computing, Espoo

    Google Scholar 

  • Untereiner WA (1995) Fruiting studies in species of Capronia (Herpotrichiellaceae). Antonie Van Leeuwenhoek Int J Gen Molec Microbiol 68:3–17

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • Van Valen L (1976) Ecological species, multispecies, and oaks. Taxon 25:233–239

    Article  Google Scholar 

  • Venditti C, Pagel M (2008) Speciation and bursts of evolution. Evol Educ Outreach 1:274–280

    Article  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vilgalys R, Hester M (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol 172:4238–4246

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Google Scholar 

  • Wiens JJ (2003a) Incomplete taxa incomplete characters and phylogenetic accuracy: is there a missing data problem? J Vertebr 23:297–310

    Article  Google Scholar 

  • Wiens JJ (2003b) Missing data incomplete taxa and phylogenetic accuracy. Syst Biol 52:528–538

    Article  PubMed  Google Scholar 

  • Wiens JJ (2006) Missing data and the design of phylogenetic analyses. J Biomed Inform 39:34–42

    Article  CAS  PubMed  Google Scholar 

  • Wiens JJ, Tiu J (2012) Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling. PLoS ONE 7:e42925

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • Young AD, Gillung JP (2020) Phylogenomics—principles opportunities and pitfalls of big-data phylogenetics. Syst Entomol 45:225–247

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • Zhang Y, Crous PW, Schoch CL, Hyde KD (2012) Pleosporales. Fungal Divers 53:1–221

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

Download references

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.

Funding

The authors received no specific funding for this work.

Author information

Authors and Affiliations

Authors

Contributions

DP, RJ and KDH designed the study and are involved in writing up. All authors contributed to the manuscript preparation and submission.

Corresponding author

Correspondence to Kevin David Hyde.

Ethics declarations

Conflict of interest

There is no conflict of interest (financial or non-financial) and all authors have agreed to submission of paper.

Additional information

Handling Editor: Jian-Kui Liu.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13225-021-00485-7

Keywords

Navigation