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  • 1
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    One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes (2015)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (0031-5850) vol.35 (2015) p.242
    Details
    Publication Date: 2016-01-08
    Description: 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.
    Keywords: DNA barcoding ; ITS supplement ; molecular taxonomy ; phylogeny ; species identification ; universal primers
    Repository Name: National Museum of Natural History, Netherlands
    Type: Article / Letter to the editor
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  • 2
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    Novel genera and species of coniothyrium-like fungi in Montagnulaceae (Ascomycota) (2014)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (0031-05850) vol.32 (2014) nr.1 p.25
    Details
    Publication Date: 2015-04-20
    Description: Based on analyses of concatenated internal transcribed spacer regions of the nrDNA operon (ITS), large subunit rDNA (LSU), γ-actin and β-tubulin gene sequences the taxonomy of coniothyrium-like fungi belonging in the family Montagnulaceae, order Pleosporales, was re-assessed. Two new genera are proposed, Alloconiothyrium, to accommodate A. aptrootii sp. nov., and Dendrothyrium for D. longisporum sp. nov. and D. variisporum sp. nov. One new species is described in Paraconiothyrium, viz. Parac. archidendri sp. nov., while two species so far classified in Paraconiothyrium are transferred to Paraphaeosphaeria, viz. Paraph. minitans comb. nov. and Paraph. sporulosa comb. nov. In Paraphaeosphaeria five new species are described based on asexual morphs, viz. Paraph. arecacearum sp. nov., Paraph. neglecta sp. nov., Paraph. sardoa sp. nov., Paraph. verruculosa sp. nov., and Paraph. viridescens sp. nov. Macro- and micromorphological characteristics are fully described.
    Keywords: γ-actin ; β-tubulin ; ITS ; LSU ; Microsphaeropsis ; Paraconiothyrium ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
    Type: Article / Letter to the editor
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  • 3
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    Fungal Planet description sheets: 558–624 (2017)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (1878-9080) vol.38 (2017) p.240
    Details
    Publication Date: 2017-06-26
    Description: Novel species of fungi described in this study include those from various countries as follows: Australia: Banksiophoma australiensis (incl. Banksiophoma gen. nov.) on Banksia coccinea, Davidiellomyces australiensis (incl. Davidiellomyces gen. nov.) on Cyperaceae, Didymocyrtis banksiae on Banksia sessilis var. cygnorum, Disculoides calophyllae on Corymbia calophylla, Harknessia banksiae on Banksia sessilis, Harknessia banksiae-repens on Banksia repens, Harknessia banksiigena on Banksia sessilis var. cygnorum, Harknessia communis on Podocarpus sp., Harknessia platyphyllae on Eucalyptus platyphylla, Myrtacremonium eucalypti (incl. Myrtacremonium gen. nov.) on Eucalyptus globulus, Myrtapenidiella balenae on Eucalyptus sp., Myrtapenidiella eucalyptigena on Eucalyptus sp., Myrtapenidiella pleurocarpae on Eucalyptus pleurocarpa, Paraconiothyrium hakeae on Hakea sp., Paraphaeosphaeria xanthorrhoeae on Xanthorrhoea sp., Parateratosphaeria stirlingiae on Stirlingia sp., Perthomyces podocarpi (incl. Perthomyces gen. nov.) on Podocarpus sp., Readeriella ellipsoidea on Eucalyptus sp., Rosellinia australiensis on Banksia grandis, Tiarosporella corymbiae on Corymbia calophylla, Verrucoconiothyrium eucalyptigenum on Eucalyptus sp., Zasmidium commune on Xanthorrhoea sp., and Zasmidium podocarpi on Podocarpus sp. Brazil: Cyathus aurantogriseocarpus on decaying wood, Perenniporia brasiliensis on decayed wood, Perenniporia paraguyanensis on decayed wood, and Pseudocercospora leandrae-fragilis on Leandra fragilis. Chile: Phialocephala cladophialophoroides on human toe nail. Costa Rica: Psathyrella striatoannulata from soil. Czech Republic: Myotisia cremea (incl. Myotisia gen. nov.) on bat droppings. Ecuador: Humidicutis dictiocephala from soil, Hygrocybe macrosiparia from soil, Hygrocybe sangayensis from soil, and Polycephalomyces onorei on stem of Etlingera sp. France: Westerdykella centenaria from soil. Hungary: Tuber magentipunctatum from soil. India: Ganoderma mizoramense on decaying wood, Hodophilus indicus from soil, Keratinophyton turgidum in soil, and Russula arunii on Pterigota alata. Italy: Rhodocybe matesina from soil. Malaysia: Apoharknessia eucalyptorum, Harknessia malayensis, Harknessia pellitae, and Peyronellaea eucalypti on Eucalyptus pellita, Lectera capsici on Capsicum annuum, and Wallrothiella gmelinae on Gmelina arborea. Morocco: Neocordana musigena on Musa sp. New Zealand: Candida rongomai-pounamu on agaric mushroom surface, Candida vespimorsuum on cup fungus surface, Cylindrocladiella vitis on Vitis vinifera, Foliocryphia eucalyptorum on Eucalyptus sp., Ramularia vacciniicola on Vaccinium sp., and Rhodotorula ngohengohe on bird feather surface. Poland: Tolypocladium fumosum on a caterpillar case of unidentified Lepidoptera. Russia: Pholiotina longistipitata among moss. Spain: Coprinopsis pseudomarcescibilis from soil, Eremiomyces innocentii from soil, Gyroporus pseudocyanescens in humus, Inocybe parvicystis in humus, and Penicillium parvofructum from soil. Unknown origin: Paraphoma rhaphiolepidis on Rhaphiolepsis indica. USA: Acidiella americana from wall of a cooling tower, Neodactylaria obpyriformis (incl. Neodactylaria gen. nov.) from human bronchoalveolar lavage, and Saksenaea loutrophoriformis from human eye. Vietnam: Phytophthora mekongensis from Citrus grandis, and Phytophthora prodigiosa from Citrus grandis. Morphological and culture characteristics along with DNA barcodes are provided.
    Keywords: ITS nrDNA barcodes ; LSU ; novel fungal species ; systematics
    Repository Name: National Museum of Natural History, Netherlands
    Type: Article / Letter to the editor
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  • 4
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    A new species concept for the clinically relevant Mucor circinelloides complex (2019)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 44, pp. 67-97
    Details
    Publication Date: 2024-01-12
    Description: Mucor species are common soil fungi but also known as agents of human infections (mucormycosis) \nand used in food production and biotechnology. Mucor circinelloides is the Mucor species that is most frequently \nisolated from clinical sources. The taxonomy of Mucor circinelloides and its close relatives (Mucor circinelloides \ncomplex \xe2\x80\x93 MCC) is still based on morphology and mating behaviour. The aim of the present study was a revised \ntaxonomy of the MCC using a polyphasic approach. Using a set of 100 strains molecular phylogenetic analysis of \nfive markers (ITS, rpb1, tsr1, mcm7, and cfs, introduced here) were performed, combined with phenotypic studies, \nmating tests and the determination of the maximum growth temperatures. The multi-locus analyses revealed 16 \nphylogenetic species of which 14 showed distinct phenotypical traits and were recognised as discrete species. \nFive of these species are introduced as novel taxa: M. amethystinus sp. nov., M. atramentarius sp. nov., M. variicolumellatus sp. nov., M. pseudocircinelloides sp. nov., and M. pseudolusitanicus sp. nov. The former formae of \nM. circinelloides represent one or two separate species. In the MCC, the simple presence of well-shaped zygospores \nonly indicates a close relation of both strains, but not necessarily conspecificity. Seven species of the MCC have \nbeen implemented in human infection: M. circinelloides, M. griseocyanus, M. janssenii, M. lusitanicus, M. ramosissimus, M. variicolumellatus, and M. velutinosus
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; mating tests ; maximum growth temperature ; Mucor ; mucormycosis ; new taxa ; phylogeny ; taxonomy ; zygospore formation
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 5
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    One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes (2015)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 35, pp. 242-263
    Details
    Publication Date: 2024-02-03
    Description: 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. Ampli\xef\xac\x81cation ef\xef\xac\x81ciencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across 〉\xe2\x80\xaf1\xe2\x80\xaf500 species (1\xe2\x80\xaf931 strains or specimens) and the outcomes of almost twenty thousand (19\xe2\x80\xaf577) 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\xe2\x80\x93D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial \xce\xb2-tubulin II (TUB2); iv) \xce\xb3-actin (ACT); v) translation elongation factor 1-\xce\xb1 (TEF1\xce\xb1); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5\xe2\x80\x936). Their PCR ef\xef\xac\x81ciencies were compared with novel candidate primers corresponding to: i) the fungal-speci\xef\xac\x81c 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 TEF1\xce\xb1. 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-speci\xef\xac\x81c variation that make them attractive barcodes for species identi\xef\xac\x81cation. Among these gene sections, a novel high \xef\xac\x81delity primer pair for TEF1\xce\xb1, 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.
    Keywords: DNA barcoding ; ITS supplement ; molecular taxonomy ; phylogeny ; species identi\xef\xac\x81cation ; universal primers
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 6
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    Fungal Planet description sheets: 558\xe2\x80\x93624 (2017)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 38, pp. 240-384
    Details
    Publication Date: 2024-02-03
    Description: Novel species of fungi described in this study include those from various countries as follows: Australia: Banksiophoma australiensis (incl. Banksiophoma gen. nov.) on Banksia coccinea, Davidiellomyces australiensis (incl. Davidiellomyces gen. nov.) on Cyperaceae, Didymocyrtis banksiae on Banksia sessilis var. cygnorum, Disculoides calophyllae on Corymbia calophylla, Harknessia banksiae on Banksia sessilis, Harknessia banksiae-repens on Banksia repens, Harknessia banksiigena on Banksia sessilis var. cygnorum, Harknessia communis on Podocarpus sp., Harknessia platyphyllae on Eucalyptus platyphylla, Myrtacremonium eucalypti (incl. Myrtacremonium gen. nov.) on Eucalyptus globulus, Myrtapenidiella balenae on Eucalyptus sp., Myrtapenidiella eucalyptigena on Eucalyptus sp., Myrtapenidiella pleurocarpae on Eucalyptus pleurocarpa, Paraconiothyrium hakeae on Hakea sp., Paraphaeosphaeria xanthorrhoeae on Xanthorrhoea sp., Parateratosphaeria stirlingiae on Stirlingia sp., Perthomyces podocarpi (incl. Perthomyces gen. nov.) on Podocarpus sp., Readeriella ellipsoidea on Eucalyptus sp., Rosellinia australiensis on Banksia grandis, Tiarosporella corymbiae on Corymbia calophylla, Verrucoconiothyrium eucalyptigenum on Eucalyptus sp., Zasmidium commune on Xanthorrhoea sp., and Zasmidium podocarpi on Podocarpus sp. Brazil: Cyathus aurantogriseocarpus on decaying wood, Perenniporia brasiliensis on decayed wood, Perenniporia paraguyanensis on decayed wood, and Pseudocercospora leandrae-fragilis on Leandra fragilis. Chile: Phialocephala cladophialophoroides on human toe nail. Costa Rica: Psathyrella striatoannulata from soil. Czech Republic: Myotisia cremea (incl. Myotisia gen. nov.) on bat droppings. Ecuador: Humidicutis dictiocephala from soil, Hygrocybe macrosiparia from soil, Hygrocybe sangayensis from soil, and Polycephalomyces onorei on stem of Etlingera sp. France: Westerdykella centenaria from soil. Hungary: Tuber magentipunctatum from soil. India: Ganoderma mizoramense on decaying wood, Hodophilus indicus from soil, Keratinophyton turgidum in soil, and Russula arunii on Pterigota alata. Italy: Rhodocybe matesina from soil. Malaysia: Apoharknessia eucalyptorum, Harknessia malayensis, Harknessia pellitae, and Peyronellaea eucalypti on Eucalyptus pellita, Lectera capsici on Capsicum annuum, and Wallrothiella gmelinae on Gmelina arborea. Morocco: Neocordana musigena on Musa sp. New Zealand: Candida rongomai-pounamu on agaric mushroom surface, Candida vespimorsuum on cup fungus surface, Cylindrocladiella vitis on Vitis vinifera, Foliocryphia eucalyptorum on Eucalyptus sp., Ramularia vacciniicola on Vaccinium sp., and Rhodotorula ngohengohe on bird feather surface. Poland: Tolypocladium fumosum on a caterpillar case of unidentified Lepidoptera. Russia: Pholiotina longistipitata among moss. Spain: Coprinopsis pseudomarcescibilis from soil, Eremiomyces innocentii from soil, Gyroporus pseudocyanescens in humus, Inocybe parvicystis in humus, and Penicillium parvofructum from soil. Unknown origin: Paraphoma rhaphiolepidis on Rhaphiolepsis indica. USA: Acidiella americana from wall of a cooling tower, Neodactylaria obpyriformis (incl. Neodactylaria gen. nov.) from human bronchoalveolar lavage, and Saksenaea loutrophoriformis from human eye. Vietnam: Phytophthora mekongensis from Citrus grandis, and Phytophthora prodigiosa from Citrus grandis. Morphological and culture characteristics along with DNA barcodes are provided.
    Keywords: ITS nrDNA barcodes ; LSU ; novel fungal species ; systematics
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 7
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    Novel genera and species of coniothyrium-like fungi in Montagnulaceae (Ascomycota) (2014)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 32 no. 1, pp. 25-51
    Details
    Publication Date: 2024-01-12
    Description: Based on analyses of concatenated internal transcribed spacer regions of the nrDNA operon (ITS), large subunit rDNA (LSU), \xce\xb3-actin and \xce\xb2-tubulin gene sequences the taxonomy of coniothyrium-like fungi belonging in the family Montagnulaceae, order Pleosporales, was re-assessed. Two new genera are proposed, Alloconiothyrium, to accommodate A. aptrootii sp. nov., and Dendrothyrium for D. longisporum sp. nov. and D. variisporum sp. nov. One new species is described in Paraconiothyrium, viz. Parac. archidendri sp. nov., while two species so far classified in Paraconiothyrium are transferred to Paraphaeosphaeria, viz. Paraph. minitans comb. nov. and Paraph. sporulosa comb. nov. In Paraphaeosphaeria five new species are described based on asexual morphs, viz. Paraph. arecacearum sp. nov., Paraph. neglecta sp. nov., Paraph. sardoa sp. nov., Paraph. verruculosa sp. nov., and Paraph. viridescens sp. nov. Macro- and micromorphological characteristics are fully described.
    Keywords: \xce\xb3-actin ; \xce\xb2-tubulin ; ITS ; LSU ; Microsphaeropsis ; Paraconiothyrium ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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