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      Phylogeny of saprobic microfungi from Southern Europe

      research-article
      1 , 2 , , 3 , 4 , 5 , 1 , 2 , 6 , 3
      Studies in Mycology
      CBS Fungal Biodiversity Centre
      Biodiversity, Dothideomycetes, Eurotiomycetes, Leotiomycetes, Sordariomycetes, Systematics, Kirschsteiniotheliales Hern.-Restr., Gené, R.F. Castañeda & Crous, Lauriomycetales Hern.-Restr., R.F. Castañeda & Guarro, Parasympodiellales Hern.-Restr., Gené, R.F. Castañeda & Crous, Vermiculariopsiellales Hern.-Restr., J. Mena, Gené & Crous, Xenospadicoidales Hern.-Restr., J. Mena & Gené, Castanediellaceae Hern.-Restr., Guarro & Crous, Lauriomycetaceae Hern.-Restr., R.F. Castañeda & Guarro, Leptodontidiaceae Hern.-Restr., Crous & Gené, Parasympodiellaceae Hern.-Restr., Gené, Guarro & Crous, Pleomonodictydaceae Hern.-Restr., J. Mena & Gené, Vermiculariopsiellaceae Hern.-Restr., J. Mena, Gené & Crous, Xenospadicoidaceae Hern.-Restr., J. Mena & Gené, Anapleurothecium Hern.-Restr., R.F. Castañeda & Gené, Fuscosclera Hern.-Restr., J. Mena & Gené, Neoascotaiwania Hern.-Restr., R.F. Castañeda & Guarro, Paradiplococcium Hern.-Restr., J. Mena & Gené, Pleomonodictys Hern.-Restr., J. Mena & Gené, Pleotrichocladium Hern.-Restr., R.F. Castañeda & Gené, Pseudodiplococcium Hern.-Restr., J. Mena & Gené, Xenospadicoides Hern.-Restr., J. Mena & Gené, Xyladictyochaeta Hern.-Restr., R.F. Castañeda & Gené, Anapleurothecium botulisporum Hern.-Restr., R.F. Castañeda & Gené, Brachysporiella navarrica Hern.-Restr., R.F. Castañeda & Gené, Catenulostroma lignicola Hern.-Restr., J. Mena & Gené, Cirrenalia iberica Hern.-Restr. & Gené, Conioscypha pleiomorpha Hern.-Restr., R.F. Castañeda & Gené, Fuscosclera lignicola Hern.-Restr., J. Mena & Gené, Leptodontidium aureum Hern.-Restr., Guarro & Gené, Parasympodiella lauri Hern.-Restr., Gene & Guarro, Parasympodiella lauri Hern.-Restr., Gene & Guarro, Pirozynskiella laurisilvatica Hern.-Restr., R.F. Castañeda & Gené, Pleomonodictys descalsii Hern.-Restr., J. Mena & Gené, Pseudodiplococcium ibericum Hern.-Restr., J. Mena & Gené, Xyladictyochaeta lusitanica Hern.-Restr., R.F. Castañeda & Gené, Zanclospora iberica Hern.-Restr., J. Mena & Gené, Magnohelicospora fuscospora (Linder) R.F. Castañeda, Hern.-Restr. & Gené, Neoascotaiwania limnetica (H.S. Chang & S.Y. Hsieh) Hern.-Restr., R.F. Castañeda & Gené , Paradiplococcium singulare (Hern.-Restr., J. Mena, Gené & Guarro) Hern.-Restr., J. Mena & Gené , Pleomonodictys capensis (R.C. Sinclair, Boshoff & Eicker) Hern.-Restr., J. Mena & Gené , Pleotrichocladium opacum (Corda) Hern.-Restr., R.F. Castañeda & Gené, Xenospadicoides atra (Corda) Hern.-Restr., J. Mena & Gené, Camposporium aquaticum Dudka, Psilonia atra Corda, Sporidesmium asperum Corda, Sporidesmium opacum Corda, Magnohelicospora iberica R.F. Castañeda, Hern.-Restr., Gené & Guarro, Sporidesmium trigonellum Sacc., Sporidesmium opacum Corda, Sporidesmium asperum Corda, Camposporium aquatium Dudka, Psilonia atra Corda

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          Abstract

          During a survey of saprophytic microfungi on decomposing woody, herbaceous debris and soil from different regions in Southern Europe, a wide range of interesting species of asexual ascomycetes were found. Phylogenetic analyses based on partial gene sequences of SSU, LSU and ITS proved that most of these fungi were related to Sordariomycetes and Dothideomycetes and to lesser extent to Leotiomycetes and Eurotiomycetes. Four new monotypic orders with their respective families are proposed here, i.e. Lauriomycetales, Lauriomycetaceae; Parasympodiellales, Parasympodiellaceae; Vermiculariopsiellales, Vermiculariopsiellaceae and Xenospadicoidales, Xenospadicoidaceae. One new order and three families are introduced here to accommodate orphan taxa, viz. Kirschsteiniotheliales, Castanediellaceae, Leptodontidiaceae and Pleomonodictydaceae. Furthermore, Bloxamiaceae is validated. Based on morphology and phylogenetic affinities Diplococcium singulare, Trichocladium opacum and Spadicoides atra are moved to the new genera Paradiplococcium, Pleotrichocladium and Xenospadicoides, respectively. Helicoon fuscosporum is accommodated in the genus Magnohelicospora. Other novel genera include Neoascotaiwania with the type species N. terrestris sp. nov., and N. limnetica comb. nov. previously accommodated in Ascotaiwania; Pleomonodictys with P. descalsii sp. nov. as type species, and P. capensis comb. nov. previously accommodated in Monodictys; Anapleurothecium typified by A. botulisporum sp. nov., a fungus morphologically similar to Pleurothecium but phylogenetically distant; Fuscosclera typified by F. lignicola sp. nov., a meristematic fungus related to Leotiomycetes; Pseudodiplococcium typified by P. ibericum sp. nov. to accommodate an isolate previously identified as Diplococcium pulneyense; Xyladictyochaeta typified with X. lusitanica sp. nov., a foliicolous fungus related to Xylariales and similar to Dictyochaeta, but distinguished by polyphialidic conidiogenous cells produced on setiform conidiophores. Other novel species proposed are Brachysporiella navarrica, Catenulostroma lignicola, Cirrenalia iberica, Conioscypha pleiomorpha, Leptodontidium aureum, Pirozynskiella laurisilvatica, Parasympodiella lauri and Zanclospora iberica. To fix the application of some fungal names, lectotypes and/or epitypes are designated for Magnohelicospora iberica, Sporidesmium trigonellum, Sporidesmium opacum, Sporidesmium asperum, Camposporium aquaticum and Psilonia atra.

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          One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes

          The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across > 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1–D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial β -tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5–6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1α. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections, a novel high fidelity primer pair for TEF1α, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.
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            Towards an integrated phylogenetic classification of the Tremellomycetes

            Families and genera assigned to Tremellomycetes have been mainly circumscribed by morphology and for the yeasts also by biochemical and physiological characteristics. This phenotype-based classification is largely in conflict with molecular phylogenetic analyses. Here a phylogenetic classification framework for the Tremellomycetes is proposed based on the results of phylogenetic analyses from a seven-genes dataset covering the majority of tremellomycetous yeasts and closely related filamentous taxa. Circumscriptions of the taxonomic units at the order, family and genus levels recognised were quantitatively assessed using the phylogenetic rank boundary optimisation (PRBO) and modified general mixed Yule coalescent (GMYC) tests. In addition, a comprehensive phylogenetic analysis on an expanded LSU rRNA (D1/D2 domains) gene sequence dataset covering as many as available teleomorphic and filamentous taxa within Tremellomycetes was performed to investigate the relationships between yeasts and filamentous taxa and to examine the stability of undersampled clades. Based on the results inferred from molecular data and morphological and physiochemical features, we propose an updated classification for the Tremellomycetes. We accept five orders, 17 families and 54 genera, including seven new families and 18 new genera. In addition, seven families and 17 genera are emended and one new species name and 185 new combinations are proposed. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the species names that are temporarily maintained.
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              Mycosphaerella is polyphyletic

              Mycosphaerella, one of the largest genera of ascomycetes, encompasses several thousand species and has anamorphs residing in more than 30 form genera. Although previous phylogenetic studies based on the ITS rDNA locus supported the monophyly of the genus, DNA sequence data derived from the LSU gene distinguish several clades and families in what has hitherto been considered to represent the Mycosphaerellaceae. Several important leaf spotting and extremotolerant species need to be disposed to the genus Teratosphaeria, for which a new family, the Teratosphaeriaceae, is introduced. Other distinct clades represent the Schizothyriaceae, Davidiellaceae, Capnodiaceae, and the Mycosphaerellaceae. Within the two major clades, namely Teratosphaeriaceae and Mycosphaerellaceae, most anamorph genera are polyphyletic, and new anamorph concepts need to be derived to cope with dual nomenclature within the Mycosphaerella complex.
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                Author and article information

                Contributors
                Journal
                Stud Mycol
                Stud. Mycol
                Studies in Mycology
                CBS Fungal Biodiversity Centre
                0166-0616
                1872-9797
                17 May 2017
                March 2017
                17 May 2017
                : 86
                : 53-97
                Affiliations
                [1 ]Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
                [2 ]Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
                [3 ]Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, 43201 Reus, Spain
                [4 ]Instituto de Investigaciones Fundamentales en Agricultura Tropical “Alejandro de Humboldt” (INIFAT), 17200, La Habana, Cuba
                [5 ]Instituto de Ecología y Sistemática, Carretera Varona 11835 e/Oriente y Lindero, Capdevila, Boyeros, 11900, La Habana 19, Cuba
                [6 ]Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
                Author notes
                [] Correspondence: Margarita Hernández-Restrepo m.hernandez@ 123456westerdijkinstitute.nl
                Article
                S0166-0616(17)30022-2
                10.1016/j.simyco.2017.05.002
                5470572
                28626275
                bcb3c204-cda3-43b0-b31d-87ee7f20b871
                © 2017 Westerdijk Fungal Biodiversity Institute. Production and hosting by ELSEVIER B.V.

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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                Plant science & Botany
                biodiversity,dothideomycetes,eurotiomycetes,leotiomycetes,sordariomycetes,systematics,kirschsteiniotheliales hern.-restr., gené, r.f. castañeda & crous,lauriomycetales hern.-restr., r.f. castañeda & guarro,parasympodiellales hern.-restr., gené, r.f. castañeda & crous,vermiculariopsiellales hern.-restr., j. mena, gené & crous,xenospadicoidales hern.-restr., j. mena & gené,castanediellaceae hern.-restr., guarro & crous,lauriomycetaceae hern.-restr., r.f. castañeda & guarro,leptodontidiaceae hern.-restr., crous & gené,parasympodiellaceae hern.-restr., gené, guarro & crous,pleomonodictydaceae hern.-restr., j. mena & gené,vermiculariopsiellaceae hern.-restr., j. mena, gené & crous,xenospadicoidaceae hern.-restr., j. mena & gené,anapleurothecium hern.-restr., r.f. castañeda & gené,fuscosclera hern.-restr., j. mena & gené,neoascotaiwania hern.-restr., r.f. castañeda & guarro,paradiplococcium hern.-restr., j. mena & gené,pleomonodictys hern.-restr., j. mena & gené,pleotrichocladium hern.-restr., r.f. castañeda & gené,pseudodiplococcium hern.-restr., j. mena & gené,xenospadicoides hern.-restr., j. mena & gené,xyladictyochaeta hern.-restr., r.f. castañeda & gené,anapleurothecium botulisporum hern.-restr., r.f. castañeda & gené,brachysporiella navarrica hern.-restr., r.f. castañeda & gené,catenulostroma lignicola hern.-restr., j. mena & gené,cirrenalia iberica hern.-restr. & gené,conioscypha pleiomorpha hern.-restr., r.f. castañeda & gené,fuscosclera lignicola hern.-restr., j. mena & gené,leptodontidium aureum hern.-restr., guarro & gené,parasympodiella lauri hern.-restr., gene & guarro,pirozynskiella laurisilvatica hern.-restr., r.f. castañeda & gené,pleomonodictys descalsii hern.-restr., j. mena & gené,pseudodiplococcium ibericum hern.-restr., j. mena & gené,xyladictyochaeta lusitanica hern.-restr., r.f. castañeda & gené,zanclospora iberica hern.-restr., j. mena & gené,magnohelicospora fuscospora (linder) r.f. castañeda, hern.-restr. & gené,neoascotaiwania limnetica (h.s. chang & s.y. hsieh) hern.-restr., r.f. castañeda & gené,paradiplococcium singulare (hern.-restr., j. mena, gené & guarro) hern.-restr., j. mena & gené,pleomonodictys capensis (r.c. sinclair, boshoff & eicker) hern.-restr., j. mena & gené,pleotrichocladium opacum (corda) hern.-restr., r.f. castañeda & gené,xenospadicoides atra (corda) hern.-restr., j. mena & gené,camposporium aquaticum dudka,psilonia atra corda,sporidesmium asperum corda,sporidesmium opacum corda,magnohelicospora iberica r.f. castañeda, hern.-restr., gené & guarro,sporidesmium trigonellum sacc.,camposporium aquatium dudka
                Plant science & Botany
                biodiversity, dothideomycetes, eurotiomycetes, leotiomycetes, sordariomycetes, systematics, kirschsteiniotheliales hern.-restr., gené, r.f. castañeda & crous, lauriomycetales hern.-restr., r.f. castañeda & guarro, parasympodiellales hern.-restr., gené, r.f. castañeda & crous, vermiculariopsiellales hern.-restr., j. mena, gené & crous, xenospadicoidales hern.-restr., j. mena & gené, castanediellaceae hern.-restr., guarro & crous, lauriomycetaceae hern.-restr., r.f. castañeda & guarro, leptodontidiaceae hern.-restr., crous & gené, parasympodiellaceae hern.-restr., gené, guarro & crous, pleomonodictydaceae hern.-restr., j. mena & gené, vermiculariopsiellaceae hern.-restr., j. mena, gené & crous, xenospadicoidaceae hern.-restr., j. mena & gené, anapleurothecium hern.-restr., r.f. castañeda & gené, fuscosclera hern.-restr., j. mena & gené, neoascotaiwania hern.-restr., r.f. castañeda & guarro, paradiplococcium hern.-restr., j. mena & gené, pleomonodictys hern.-restr., j. mena & gené, pleotrichocladium hern.-restr., r.f. castañeda & gené, pseudodiplococcium hern.-restr., j. mena & gené, xenospadicoides hern.-restr., j. mena & gené, xyladictyochaeta hern.-restr., r.f. castañeda & gené, anapleurothecium botulisporum hern.-restr., r.f. castañeda & gené, brachysporiella navarrica hern.-restr., r.f. castañeda & gené, catenulostroma lignicola hern.-restr., j. mena & gené, cirrenalia iberica hern.-restr. & gené, conioscypha pleiomorpha hern.-restr., r.f. castañeda & gené, fuscosclera lignicola hern.-restr., j. mena & gené, leptodontidium aureum hern.-restr., guarro & gené, parasympodiella lauri hern.-restr., gene & guarro, pirozynskiella laurisilvatica hern.-restr., r.f. castañeda & gené, pleomonodictys descalsii hern.-restr., j. mena & gené, pseudodiplococcium ibericum hern.-restr., j. mena & gené, xyladictyochaeta lusitanica hern.-restr., r.f. castañeda & gené, zanclospora iberica hern.-restr., j. mena & gené, magnohelicospora fuscospora (linder) r.f. castañeda, hern.-restr. & gené, neoascotaiwania limnetica (h.s. chang & s.y. hsieh) hern.-restr., r.f. castañeda & gené, paradiplococcium singulare (hern.-restr., j. mena, gené & guarro) hern.-restr., j. mena & gené, pleomonodictys capensis (r.c. sinclair, boshoff & eicker) hern.-restr., j. mena & gené, pleotrichocladium opacum (corda) hern.-restr., r.f. castañeda & gené, xenospadicoides atra (corda) hern.-restr., j. mena & gené, camposporium aquaticum dudka, psilonia atra corda, sporidesmium asperum corda, sporidesmium opacum corda, magnohelicospora iberica r.f. castañeda, hern.-restr., gené & guarro, sporidesmium trigonellum sacc., camposporium aquatium dudka

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