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145 results for “Basidiomycete”
Linked collectors and determiners for: Wood-inhabiting corticioid basidiomycetes in Norway.
Natural history specimen data linked to collectors and determiners held within, "Wood-inhabiting corticioid basidiomycetes in Norway". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/4dac6899-124a-40fc-90d3-aa5a872c99c0">https://bionomia.net/dataset/4dac6899-124a-40fc-90d3-aa5a872c99c0</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/4dac6899-124a-40fc-90d3-aa5a872c99c0">https://gbif.org/dataset/4dac6899-124a-40fc-90d3-aa5a872c99c0</a>. Formatted as a Frictionless Data package.
Data from: Micromphale sect. Perforantia (Agaricales, Basidiomycetes); expansion and phylogenetic placement
DNA sequences show that the traditional genus Micromphale appears to be polyphyletic. Nuclear ribosomal LSU and ITS DNA sequences place Micromphale sect. Perforantia Singer (typus sect. M. perforans) within Gymnopus, comprising a clade sister to a mixture of traditional Gymnopus taxa including G. fusipes (typus generis) plus traditional Marasmius sect. Androsacei. This study enlarges sect. Perforantia and shows that sect. Perforantia is a clade separate from those including Micromphale sect. Micromphale and sect. Rhizomorphigena. A new subsection Pinophili is proposed to include new species G. pinophilus and G. ponderosae. Eleven taxa are accepted at species rank, of which nine are proposed as new, mostly morpho-taxa.
Data from: Micromphale sect. Perforantia (Agaricales, Basidiomycetes); expansion and phylogenetic placement
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Supplementary tables S5, S7, S9, S10, original protein models fasta files used for alignments, aligned and manually curated protein modes files used for phylogenies (PHYLIP format), and phylogenetic trees of plant cell wall decomposition gene families from 44 basidiomycete genomes (.tre files)
<p><span><span><span><span><span><span><span><span><span><span><span>Litter-decomposing Agaricales play key role in terrestrial carbon cycling, but little is known about their decomposition mechanisms. We assembled datasets of 42 gene families involved in plant-cell-wall decomposition from seven newly sequenced litter decomposers and 35 other Agaricomycotina members, mostly white-rot and brown-rot species. Using sequence similarity and phylogenetics, we split the families into phylogroups and compared their gene composition across nutritional strategies. Subsequently, we used Raman spectroscopy to examine the ability of litter decomposers, white-rot fungi, and brown-rot fungi to decompose crystalline cellulose. Both litter decomposers and white-rot fungi share the enzymatic cellulose decomposition, whereas brown-rot fungi possess a distinct mechanism that disrupts cellulose crystallinity. However, litter decomposers and white-rot fungi differ with respect to hemicellulose and lignin degradation phylogroups, suggesting adaptation of the former group to the litter environment. Litter decomposers show high phylogroup diversity, which is indicative of high functional versatility within the group, whereas a set of white-rot species shows adaptation to bulk-wood decomposition. In both groups, we detected species that have unique characteristics associated with hitherto unknown adaptations to diverse wood and litter substrates. Our results suggest that the terms white-rot fungi and litter decomposers mask a much larger functional diversity.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Basidiomycete yeasts in the cortex of ascomycete macrolichens
For over 140 years, lichens have been regarded as a symbiosis between a single fungus, usually an ascomycete, and a photosynthesizing partner. Other fungi have long been known to occur as occasional parasites or endophytes, but the one lichen–one fungus paradigm has seldom been questioned. Here we show that many common lichens are composed of the known ascomycete, the photosynthesizing partner, and, unexpectedly, specific basidiomycete yeasts. These yeasts are embedded in the cortex, and their abundance correlates with previously unexplained variations in phenotype. Basidiomycete lineages maintain close associations with specific lichen species over large geographical distances and have been found on six continents. The structurally important lichen cortex, long treated as a zone of differentiated ascomycete cells, appears to consistently contain two unrelated fungi.
Data from: Extensive gene flow over Europe and possible speciation over Eurasia in the ectomycorrhizal basidiomycete Laccaria amethystina complex.
Biogeographic patterns and large-scale genetic structure have been little studied in ectomycorrhizal fungi, despite the ecological and economic importance of ectomycorrhizal symbioses. We coupled population genetics and phylogenetic approaches to understand spatial structure in fungal populations on a continental scale. Using 9 microsatellite markers, we characterised gene flow among 16 populations of the widespread ectomycorrhizal basidiomycete Laccaria amethystina over Europe (over 2900km). We also widened our scope to two additional populations from Japan (104 km away), and compared them with European populations through microsatellite markers and multi-locus phylogenies, using 3 nuclear genes (NAR, G6PD and ribosomal DNA) and two mitochondrial ribosomal genes. European L. amethystina populations displayed limited differentiation (average FST=0.041) and very weak isolation by distance. This panmictic European pattern may result from effective aerial dispersal of spores, high genetic diversity in populations, and mutualistic interactions with multiple hosts that all facilitate migration. The multi-locus phylogeny based on nuclear genes confirmed that Japanese and European specimens were closely related but clustered on a geographical basis. By using microsatellite markers, we found that Japanese populations were strongly differentiated from the European populations (FST=0.416), more than expected by extrapolating the European pattern of isolation by distance. Population structure analyses clearly separated the populations into two clusters, European and Japanese clusters. We discuss the possibility of isolation by distance in a continuous population (considering some evidence for a ring species over the Northern Hemisphere) versus an allopatric speciation over Eurasia, making L. amethystina a promising model of intercontinental species for future studies.
Fig. 6 in Lanostane triterpenoids from cultivated fruiting bodies of basidiomycete Ganoderma mbrekobenum
Fig. 6. Computed ECD spectra of 1 (blue curve) and ent-1 (red curve) and experimental ECD spectrum (black curve). The vertical axis represents the experimental ellipticity. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 6 in Sesquiterpenes with diverse skeletons from histone deacetylase inhibitor modified cultures of the basidiomycete Cyathus stercoreus (Schwein.) De Toni HFG134
Fig. 6. (A) The four possible stereoisomers of 9. (B), (C) The comparisons of the experimental CD and calculated ECD of 9.
Data from: Extensive gene flow over Europe and possible speciation over Eurasia in the ectomycorrhizal basidiomycete Laccaria amethystina complex.
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Data from: Basidiomycete yeasts in the cortex of ascomycete macrolichens
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Data from: Molecular characterization of sexual diversity in a population of Serpula lacrymans, a tetrapolar basidiomycete
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Supplementary tables S5, S7, S9, S10, original protein models fasta files used for alignments, aligned and manually curated protein modes files used for phylogenies (PHYLIP format), and phylogenetic trees of plant cell wall decomposition gene families from 44 basidiomycete genomes (.tre files)
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Data from: Prevalence of transcription factors in ascomycete and basidiomycete fungi
Background: Gene regulation underlies fungal physiology and therefore is a major factor in fungal biodiversity. Analysis of genome sequences has revealed a large number of putative transcription factors in most fungal genomes. The presence of fungal orthologs for individual regulators has been analysed and appears to be highly variable with some regulators widely conserved and others showing narrow distribution. Although genome-scale transcription factor surveys have been performed before, no global study into the prevalence of specific regulators across the fungal kingdom has been presented. Results: In this study we have analysed the number of members for 37 regulator classes in 77 ascomycete and 31 basidiomycete fungal genomes and revealed significant differences between ascomycetes and basidiomycetes. In addition, we determined the presence of 64 regulators characterised in ascomycetes across these 108 genomes. This demonstrated that overall the highest presence of orthologs is in the filamentous ascomycetes. A significant number of regulators lacked orthologs in the ascomycete yeasts and the basidiomycetes. Conversely, of seven basidiomycete regulators included in the study, only one had orthologs in ascomycetes. Conclusions: This study demonstrates a significant difference in the regulatory repertoire of ascomycete and basidiomycete fungi, at the level of both regulator class and individual regulator. This suggests that the current regulatory systems of these fungi have been mainly developed after the two phyla diverged. Most regulators detected in both phyla are involved in central functions of fungal physiology and therefore were likely already present in the ancestor of the two phyla.
Data from: Diversity measures in environmental sequences are highly dependent on alignment quality—data from ITS and new LSU primers targeting basidiomycetes
The ribosomal DNA comprised of the ITS1-5.8S-ITS2 regions is widely used as a fungal marker in molecular ecology and systematics but cannot be aligned with confidence across genetically distant taxa. In order to study the diversity of Agaricomycotina in forest soils, we designed primers targeting the more alignable 28S (LSU) gene, which should be more useful for phylogenetic analyses of the detected taxa. This paper compares the performance of the established ITS1F/4B primer pair, which targets basidiomycetes, to that of two new pairs. Key factors in the comparison were the diversity covered, off-target amplification, rarefaction at different Operational Taxonomic Unit (OTU) cutoff levels, sensitivity of the method used to process the alignment to missing data and insecure positional homology, and the congruence of monophyletic clades with OTU assignments and BLAST-derived OTU names. The ITS primer pair yielded no off-target amplification but also exhibited the least fidelity to the expected phylogenetic groups. The LSU primers give complementary pictures of diversity, but were more sensitive to modifications of the alignment such as the removal of difficult-to align stretches. The LSU primers also yielded greater numbers of singletons but also had a greater tendency to produce OTUs containing sequences from a wider variety of species as judged by BLAST similarity. We introduced some new parameters to describe alignment heterogeneity based on Shannon entropy and the extent and contents of the OTUs in a phylogenetic tree space. Our results suggest that ITS should not be used when calculating phylogenetic trees from genetically distant sequences obtained from environmental DNA extractions and that it is inadvisable to define OTUs on the basis of very heterogeneous alignments.
Figure 9 from: Petersen RH, Hughes KW (2016) Micromphale sect. Perforantia (Agaricales, Basidiomycetes); Expansion and phylogenetic placement. MycoKeys 18: 1-122. https://doi.org/10.3897/mycokeys.18.10007
Figure 9 - Gymnopus bulliformis. Caulocystidia from lower stipe. Standard bars = 10 µm. WTU-F-51955.
Figure 87 from: Petersen RH, Hughes KW (2016) Micromphale sect. Perforantia (Agaricales, Basidiomycetes); Expansion and phylogenetic placement. MycoKeys 18: 1-122. https://doi.org/10.3897/mycokeys.18.10007
Figure 87 - PhyML analysis of Gymnopus perforans and Gymnopus sequoiae ITS sequences. Distance measurements percent base pair differences for the ITS region only. Bootstrap support greater than 70% is given to the left of the supported node. Haplotypes are indicated as h1 or h2; clones are indicated as c1, c2, etc. North American locations are indicated by postal codes.
Figure 81 from: Petersen RH, Hughes KW (2016) Micromphale sect. Perforantia (Agaricales, Basidiomycetes); Expansion and phylogenetic placement. MycoKeys 18: 1-122. https://doi.org/10.3897/mycokeys.18.10007
Figure 81 - Gymnopus sublaccatus. A Subbasidial hyphae appearing beaded B Effete hymenial structures without collapse ("husking") C Stipe medullary hyphae. Standard bars = 10 µm. UBC 25212.
Figure 80 from: Petersen RH, Hughes KW (2016) Micromphale sect. Perforantia (Agaricales, Basidiomycetes); Expansion and phylogenetic placement. MycoKeys 18: 1-122. https://doi.org/10.3897/mycokeys.18.10007
Figure 80 - Gymnopus sublaccatus. Hymenial elements. A–D Pleurocystidia E Basidiole F–H Basidia. Standard bars = 10 µm. UBC 15356.
Figure 79 from: Petersen RH, Hughes KW (2016) Micromphale sect. Perforantia (Agaricales, Basidiomycetes); Expansion and phylogenetic placement. MycoKeys 18: 1-122. https://doi.org/10.3897/mycokeys.18.10007
Figure 79 - Gymnopus sublaccatus. Pileipellis elements. A–E Pileal hairs F Secondary septa of pileipellis hypha. Standard bars = 10 µm. UBC 25212.
Figure 77 from: Petersen RH, Hughes KW (2016) Micromphale sect. Perforantia (Agaricales, Basidiomycetes); Expansion and phylogenetic placement. MycoKeys 18: 1-122. https://doi.org/10.3897/mycokeys.18.10007
Figure 77 - Gymnopus sequoiae. Lower stipe structures. A Stipe surface free-form cells with one caulocystidium B–F Individual caulocystidia showing broad-based origin and secondary septa. Standard bars = 10 µm. TFB 14620 (TENN-F-69325).
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