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308 results for “fungal community”
Figure 3 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 3 NMDS ordination plot of all specimens sampled with ITS2 and LSU D1-D2, based on the fungal community composition of the individual beetles. Shapes represent forest types and colours represent beetle species. Stress for this graph fell within acceptable ranges (<0.2).
Figure 2 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 2 Top panel: The proportion of OTUs identified as members of a fungal Class determined by the ITS2 and LSU D1-D2 regions. For the spruce forest, only nine X. germanus and four X. saxesenii specimens were retained after rarefaction. Lower panel: The number of fungal OTUs per beetle specimen, separate for each beetle species and forest type, for ITS2 and LSU.
Figure 6 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 6 Order-level trees and splitting/lumping of OTUs at clustering A order-level ML trees with mixed OTU clustering thresholds (99% LSU D1-D2, 98% ITS2). Full tree in supplementary materials. Leotia lubrica was used as the outgroup (not pictured). Brackets indicate reference taxa linked to an ITS2 and/or LSUOTU, with colours indicating potential splitting/lumping (blue, splitting; green, lumping; orange, 1:1) B diagram illustrating the effects of splitting and lumping of an OTU in the fungal community on the tree inference. Four hypothetical species (A to D) in a community are treated under uniform clustering thresholds for ITS2 and LSU. This may result in deviation from the 1:1 ratio of OTUs expected if each species in the community is represented equally by both markers (species A). Threshold values may be too high, resulting in splitting of species into multiples OTUs, which is likely to affect the more variable ITS2 region (species B) or may be too low, resulting in lumping of multiple species into a single OTU, likely to affect the conservative LSU region (species C and D).
Supplementary material 4 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure S4. Binding site of ITS86 primer showing mismatched base pairs in Ophiostomatales
Figure 1 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 1 The proportion of fungi classified with IDTAXA, Protax-fungi and RDP from class to species level. "All" refers to the proportion of OTUs for which the three classifiers agreed in their classification.
Supplementary material 7 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Table S3. Number of OTUs assigned to each order based on RDP Bayesian classifier
Figure 5 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 5 ML tree of Sordariomycetes constructed from the reference sequence alignments and OTUs for both markers (clustering thresholds: 98% ITS2, 99% LSU D1-D2). Leotia lubrica (Leotiomycetes) was specified as the outgroup. The assignment of OTUs by each of the three classifiers (RDP, IDTAXA, Protax-fungi) is shown by coloured boxes. Terminals missing these boxes are the reference sequences. Coloured dots on the nodes of the tree indicate the hypothetical ancestor defining monophyletic groups corresponding to the various orders of Sordariomycetes. The extent of each order is indicated by the coloured inner ring. Note that the ancestor of an order is defined by the youngest node from which all reference sequences are descended; OTUs falling outside of the resulting clades appear as 'unassigned' by the phylogenetic analysis approach. The distribution of ITS2 (red squares) and LSU D1-D2 (blue bullets) relative to the reference set (yellow stars) on each of the tips of the tree. Note the limited presence of ITS sequences in the Ophiostomatales (in top right quadrant).
Figure 8 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 8 Proportion of OTUs assigned to each Order from metabarcoding with LSU (left panel) and ITS (right panel) markers based on the RDP classifier and the phylogenetic tree, under increasing threshold values.
Data from: Impact of local forest composition on soil fungal communities in a mixed boreal forest
[No abstract entered]
Supplementary material 2 from: Wurzbacher C, Warthmann N, Bourne EC, Attermeyer K, Allgaier M, Powell JR, Detering H, Mbedi S, Grossart H-P, Monaghan MT (2016) High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany). MycoKeys 16: 17-44. https://doi.org/10.3897/mycokeys.16.9646
List of pyrosequencing primers. : Explanation note: List of employed pyrosequencing fusion primers.
Influence of soil type and vertical zonation on soil fungal communities associated with natural jack pine forests
<p>Natural jack pine forests established on sandy eskers and clayey soils represent a unique habitat in the boreal forest in northeastern Canada and are generally associated with well-differentiated soil horizons, but little is known regarding their soil fungal diversity and how soil type and vertical zonation would shape their communities. To address this question, we characterized soil fungal communities from litter, organic and mineral horizons in 18 natural jack pine forests in esker and clayey soils using ITS2 rDNA metabarcoding. Ectomycorrhizal fungi dominated the organic and mineral horizons in esker soils, while saprotrophic fungi were dominant in clayey soils. The dominance of ectomycorrhizal fungi coincided with higher C accumulation within the organic horizon in esker soils. The nutrient-poor and more acidic esker sites harbored less diverse ectomycorrhizal and saprotrophic communities than clayey soils. Several stress-tolerant and melanin-rich fungal taxa were indicators of esker soils. However, fungal communities were more distinct between horizons than soil types and soil type effects differed along the soil profile. Our findings highlight the need to fill knowledge gaps in soil fungal diversity associated with jack pine forests and pave the way for adapted and multi-resource forest management in esker forest ecosystems considering their underground fungal specificities.</p>
Figure 6 from: Wang HM, Wang Z, Liu F, Wu CX, Zhang SF, Kong XB, Decock C, Lu Q, Zhang Z (2019) Differential patterns of ophiostomatoid fungal communities associated with three sympatric Tomicus species infesting pines in south-western China, with a description of four new species. MycoKeys 50: 93-133. https://doi.org/10.3897/mycokeys.50.32653
Figure 6 Phylograms obtained from ML analysis of ITS sequences of Ophiostoma, showing fungal associates with pines infected by Tomicusyunnanensis, T.minor and T.brevipilosus in Yunnan Province, China. Novel sequences obtained in this study are printed in bold type. Bootstrap values ≥ 70% for ML and MP are indicated above branches. Bootstrap values < 70% are indicated by the symbol *. Strains representing ex-type sequences are marked with 'T'; ML, maximum likelihood; MP, maximum parsimony and the final alignment of 633 positions, including gaps.
Figure 7 from: Wang HM, Wang Z, Liu F, Wu CX, Zhang SF, Kong XB, Decock C, Lu Q, Zhang Z (2019) Differential patterns of ophiostomatoid fungal communities associated with three sympatric Tomicus species infesting pines in south-western China, with a description of four new species. MycoKeys 50: 93-133. https://doi.org/10.3897/mycokeys.50.32653
Figure 7 Phylograms obtained from ML analysis of β-tubulin sequences of OphiostomaA, B, D, E and ITS sequences of O.minus-complex C showing fungal associates with pines infected by Tomicusyunnanensis, T.minor and T.brevipilosus in Yunnan Province, China. Novel sequences obtained in this study are printed in bold type. Bootstrap values ≥ 70% for ML and MP are indicated above branches. Bootstrap values < 70% are indicated by the symbol *. Strains representing ex-type sequences are marked with 'T'; ML, maximum likelihood; MP, maximum parsimony and the final alignment of 455 (A), 430 (B), 541 (C), 378 (D), 423 (E) positions, including gaps.
Figure 5 from: Wang HM, Wang Z, Liu F, Wu CX, Zhang SF, Kong XB, Decock C, Lu Q, Zhang Z (2019) Differential patterns of ophiostomatoid fungal communities associated with three sympatric Tomicus species infesting pines in south-western China, with a description of four new species. MycoKeys 50: 93-133. https://doi.org/10.3897/mycokeys.50.32653
Figure 5 Phylograms obtained from ML analysis of ITS2-28S A β-tubulin B and elongation factor C sequences of Leptographium, showing fungal associates with pines infected by Tomicusyunnanensis and T.brevipilosus in Yunnan Province, China. Novel sequences obtained in this study are printed in bold type. Bootstrap values ≥ 70% for ML and MP are indicated above branches. Bootstrap values < 70% are indicated by the symbol *. Strains representing ex-type sequences are marked with 'T'; ML, maximum likelihood; MP, maximum parsimony and the final alignment of 641 (A), 358 (B), 639 (C) positions, including gaps.
Figure 17 from: Wang HM, Wang Z, Liu F, Wu CX, Zhang SF, Kong XB, Decock C, Lu Q, Zhang Z (2019) Differential patterns of ophiostomatoid fungal communities associated with three sympatric Tomicus species infesting pines in south-western China, with a description of four new species. MycoKeys 50: 93-133. https://doi.org/10.3897/mycokeys.50.32653
Figure 17 Venn diagram showing overlaps of the ophiostomatoid fungal communities associated with three pine shoot beetles.
Figure 14 from: Wang HM, Wang Z, Liu F, Wu CX, Zhang SF, Kong XB, Decock C, Lu Q, Zhang Z (2019) Differential patterns of ophiostomatoid fungal communities associated with three sympatric Tomicus species infesting pines in south-western China, with a description of four new species. MycoKeys 50: 93-133. https://doi.org/10.3897/mycokeys.50.32653
Figure 14 Morphological characters of OphiostomatingensA, B upper and reverse of cultures on 2% MEA 20 d after inoculation C–G conidiogenous cells of Sporothrix-like asexual state and conidia H–J conidiogenous cells of Pesotum-like macronematal asexual state and conidia. Scale bars: 10 μm (C–H); 50 μm (I, J).
Figure 9 from: Wang HM, Wang Z, Liu F, Wu CX, Zhang SF, Kong XB, Decock C, Lu Q, Zhang Z (2019) Differential patterns of ophiostomatoid fungal communities associated with three sympatric Tomicus species infesting pines in south-western China, with a description of four new species. MycoKeys 50: 93-133. https://doi.org/10.3897/mycokeys.50.32653
Figure 9 Phylograms obtained from ML analysis of β-tubulin A, C and calmodulin B, D sequences of Sporothrix, showing fungal associates with pines infected by Tomicusyunnanensis, T.minor and T.brevipilosus in Yunnan Province, China. Novel sequences obtained in this study are printed in bold type. Bootstrap values ≥ 70% for ML and MP are indicated above branches. Bootstrap values < 70% are indicated by the symbol *. Strains representing ex-type sequences are marked with 'T'; ML, maximum likelihood; MP, maximum parsimony and the final alignment of 284(A), 622(B), 260(C), 675(D) positions, including gaps.
Figure 13 from: Wang HM, Wang Z, Liu F, Wu CX, Zhang SF, Kong XB, Decock C, Lu Q, Zhang Z (2019) Differential patterns of ophiostomatoid fungal communities associated with three sympatric Tomicus species infesting pines in south-western China, with a description of four new species. MycoKeys 50: 93-133. https://doi.org/10.3897/mycokeys.50.32653
Figure 13 Morphological characters of Ophiostomaaggregatum sp. n. A, B upper and reverse of cultures on 2% MEA 8 d after inoculation C conidiomata on 2% MEA (bar = 50 μm) D–H conidiogenous cells of Leptographium-like asexual state and conidia. Scale bars: 20 μm (C); 10 μm (D–H).
Figure 3 from: Wang HM, Wang Z, Liu F, Wu CX, Zhang SF, Kong XB, Decock C, Lu Q, Zhang Z (2019) Differential patterns of ophiostomatoid fungal communities associated with three sympatric Tomicus species infesting pines in south-western China, with a description of four new species. MycoKeys 50: 93-133. https://doi.org/10.3897/mycokeys.50.32653
Figure 3 Phylograms obtained from ML analysis of β-tubulin A and elongation factor B sequences of Esteya, showing fungal associates with pines infected by Tomicusyunnanensis in Yunnan Province, China. Novel sequences obtained in this study are printed in bold type. Bootstrap values ≥ 70% for ML and MP are indicated above branches. Bootstrap values < 70% are indicated by the symbol *. Strains representing ex-type sequences are marked with 'T'; ML, maximum likelihood; MP, maximum parsimony and the final alignment of 320 (A), 856 (B) positions, including gaps.
Figure 15 from: Wang HM, Wang Z, Liu F, Wu CX, Zhang SF, Kong XB, Decock C, Lu Q, Zhang Z (2019) Differential patterns of ophiostomatoid fungal communities associated with three sympatric Tomicus species infesting pines in south-western China, with a description of four new species. MycoKeys 50: 93-133. https://doi.org/10.3897/mycokeys.50.32653
Figure 15 Morphological characters of Sporothrixmacroconidia sp. n. A, B Upper and reverse of cultures on 2% MEA 20 d after inoculation C–H conidiogenous cells of Sporothrix-like asexual state and conidia. Scale bars: 10 μm (C–H).
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Allen Brain Atlas
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International Brain Laboratory public data
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