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  • phylogeny  (4)
  • Microascales  (3)
  • 1
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    Unknown
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (0031-05850) vol.24 (2010) nr.1 p.18
    Publication Date: 2015-04-20
    Description: The genus Ophiostoma (Ophiostomatales) has a global distribution and species are best known for their association with bark beetles (Curculionidae: Scolytinae) on conifers. An unusual assemblage of these fungi is closely associated with the African endemic plant genus Protea (Proteaceae). Protea-associated Ophiostoma species are ecologically atypical as they colonise the fruiting structures of various serotinous Protea species. Seven species have been described from this niche in South Africa. It has been speculated that novel species may be present in other African countries where these host plants also occur. This view was corroborated by recent collections of two unknown species from Protea caffra trees in Zambia. In the present study we evaluate the species delineation of these isolates using morphological comparisons with other Protea-associated species, differential growth studies and analyses of DNA sequence data for the β-tubulin and internal transcribed spacer (ITS1, 5.8S, ITS2) regions. As a result, the species O. protea-sedis sp. nov., and O. zambiensis sp. nov. are described here as new. This study brings the number of Protea-associated Ophiostoma species to nine and highlights the need for more inclusive surveys, including additional African countries and hosts, to elucidate species diversity in this uncharacteristic niche.
    Keywords: β-tubulin ; ITS ; Ophiostoma ; phylogeny ; Protea ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
    Type: Article / Letter to the editor
    Format: application/pdf
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  • 2
    Publication Date: 2018-08-31
    Description: Ips typographus (Coleoptera, Scolytinae) is a spruce-infesting bark beetle that occurs throughout Europe and Asia. The beetle can cause considerable damage, especially when colonized trees are stressed and beetle populations increase. Although some studies have shown that populations of I. typographus in Europe, China and Japan are genetically distinct, these populations are biologically similar, including a strong association with ophiostomatoid fungi. To date, only two Leptographium spp. have been reported from the beetle in China, while 40 species have been reported from Europe and 13 from Japan. The aims of this study were to identify the ophiostomatoid fungal associates of I. typographus in north-eastern China, and to determine whether the fungal assemblages reflect the different geographical populations of the beetle. Field surveys in Jilin and Heilongjiang provinces yielded a total of 1 046 fungal isolates from 145 beetles and 178 galleries. Isolates were grouped based on morphology and representatives of each group were identified using DNA sequences of the ribosomal LSU, ITS, β-tubulin, calmodulin and elongation factor 1-α gene regions. A total of 23 species of ophiostomatoid fungi were identified, including 12 previously described species and 11 novel species, all of which are described here. The dominant species were Ophiostoma bicolor, Leptographium taigense and Grosmannia piceiperda D, representing 40.5 %, 27.8 % and 17.8 % of the isolates, respectively. Comparisons of species from China, Europe and Japan are complicated by the fact that some of the European and all the Japanese species were identified based only on morphology. However, assuming that those identifications are correct, five species were shared between Europe, Japan and China, two species were shared between China and Japan, five between Europe and China, and two between Europe and Japan. Consequently, Ips typographus populations in these different geographic areas have different fungal assemblages, suggesting that the majority of these beetle-associations are promiscuous. The results also suggested that the symbionts of the bark beetle do not reflect the population structures of the beetle. The use of fungal symbiont assemblages to infer population structures and invasion history of its vectors should thus be interpreted with circumspection.
    Keywords: 11 new taxa ; Ophiostomatales ; Microascales ; vector ; Scolytinae
    Repository Name: National Museum of Natural History, Netherlands
    Type: Article / Letter to the editor
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  • 3
    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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  • 4
    facet.materialart.
    Unknown
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 24 no. 1, pp. 18-28
    Publication Date: 2024-01-12
    Description: The genus Ophiostoma (Ophiostomatales) has a global distribution and species are best known for their association with bark beetles (Curculionidae: Scolytinae) on conifers. An unusual assemblage of these fungi is closely associated with the African endemic plant genus Protea (Proteaceae). Protea-associated Ophiostoma species are ecologically atypical as they colonise the fruiting structures of various serotinous Protea species. Seven species have been described from this niche in South Africa. It has been speculated that novel species may be present in other African countries where these host plants also occur. This view was corroborated by recent collections of two unknown species from Protea caffra trees in Zambia. In the present study we evaluate the species delineation of these isolates using morphological comparisons with other Protea-associated species, differential growth studies and analyses of DNA sequence data for the \xce\xb2-tubulin and internal transcribed spacer (ITS1, 5.8S, ITS2) regions. As a result, the species O. protea-sedis sp. nov., and O. zambiensis sp. nov. are described here as new. This study brings the number of Protea-associated Ophiostoma species to nine and highlights the need for more inclusive surveys, including additional African countries and hosts, to elucidate species diversity in this uncharacteristic niche.
    Keywords: \xce\xb2-tubulin ; ITS ; Ophiostoma ; phylogeny ; Protea ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 5
    Publication Date: 2024-01-12
    Description: Ips typographus (Coleoptera, Scolytinae) is a spruce-infesting bark beetle that occurs throughout Europe and Asia. The beetle can cause considerable damage, especially when colonized trees are stressed and beetle populations increase. Although some studies have shown that populations of I. typographus in Europe, China and Japan are genetically distinct, these populations are biologically similar, including a strong association with ophiostomatoid fungi. To date, only two Leptographium spp. have been reported from the beetle in China, while 40 species have been reported from Europe and 13 from Japan. The aims of this study were to identify the ophiostomatoid fungal associates of I. typographus in north-eastern China, and to determine whether the fungal assemblages reflect the different geographical populations of the beetle. Field surveys in Jilin and Heilongjiang provinces yielded a total of 1 046 fungal isolates from 145 beetles and 178 galleries. Isolates were grouped based on morphology and representatives of each group were identified using DNA sequences of the ribosomal LSU, ITS, \xce\xb2-tubulin, calmodulin and elongation factor 1-\xce\xb1 gene regions. A total of 23 species of ophiostomatoid fungi were identified, including 12 previously described species and 11 novel species, all of which are described here. The dominant species were Ophiostoma bicolor, Leptographium taigense and Grosmannia piceiperda D, representing 40.5 %, 27.8 % and 17.8 % of the isolates, respectively. Comparisons of species from China, Europe and Japan are complicated by the fact that some of the European and all the Japanese species were identified based only on morphology. However, assuming that those identifications are correct, five species were shared between Europe, Japan and China, two species were shared between China and Japan, five between Europe and China, and two between Europe and Japan. Consequently, Ips typographus populations in these different geographic areas have different fungal assemblages, suggesting that the majority of these beetle-associations are promiscuous. The results also suggested that the symbionts of the bark beetle do not reflect the population structures of the beetle. The use of fungal symbiont assemblages to infer population structures and invasion history of its vectors should thus be interpreted with circumspection.
    Keywords: 11 new taxa ; Ophiostomatales ; Microascales ; vector ; Scolytinae
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 6
    Publication Date: 2024-01-12
    Description: Baobabs (Adansonia spp.) are iconic trees, known for their immense size, strange forms, sources of food and as the subjects of myths and mysteries. It is thus surprising that little is known regarding the fungi that infect these trees. During a survey to determine which wound infecting fungi occur on baobabs, synnematous structures were observed and Graphium-like isolates were obtained. Culture characteristics and micro-morphology, together with DNA sequence comparisons for the SSU rRNA, rRNA-ITS and TEF-1\xce\xb1 gene regions were used to characterise these fungi. These data revealed three novel Graphium spp. and these are described as G. adansoniae, G. madagascariense and G. fabiforme.
    Keywords: Adansonia digitata ; Adansonia rubrostipa ; fungal biodiversity ; Microascales
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 7
    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
    Format: application/pdf
    Location Call Number Expected Availability
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