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116 results for “endophytic fungi”
FIGURE 1 in Two new endophytic fungi of Colletotrichum and Diaporthe isolated from Berchemia polyphylla var. leioclada in Guizhou Province, China
FIGURE 1. Colletotrichum berchemiae (ex-type culture, GMBCC 20001). a, b Front and reverse colony on PDA. c–e Conidiomata on PDA. h–j Conidiophores. k–m Conidiogenous cells and conidia. n–p Conidia. Scale bars: f = 100 μm; g–i, n = 20 μm, j, k = 30um, l, m, o, p = 10 um.
FIGURE 3 in Two new endophytic fungi of Colletotrichum and Diaporthe isolated from Berchemia polyphylla var. leioclada in Guizhou Province, China
FIGURE 3. Results of the PHI test of Colletotrichum berchemiae and closely related species using both LogDet transformation and splits decomposition. The PHI test results (Φw) <0.05 indicate significant recombination within the dataset. The new taxa are in red.
Data from: Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi
Next-generation sequencing technologies have provided unprecedented insights into fungal diversity and ecology. However, intrinsic biases and insufficient quality control in next-generation methods can lead to difficult-to-detect errors in estimating fungal community richness, distributions, and composition. The aim of this study was to examine how tissue storage prior to DNA extraction, primer design, and various quality-control approaches commonly used in 454 amplicon pyrosequencing might influence ecological inferences in studies of endophytic and endolichenic fungi. We first contrast 454 data sets generated contemporaneously from subsets of the same plant and lichen tissues that were stored in CTAB buffer, dried in silica gel, or freshly frozen prior to DNA extraction. We show that storage in silica gel markedly limits the recovery of sequence data and yields a small fraction of the diversity observed by the other two methods. Using lichen mycobiont sequences as internal positive controls, we next show that despite careful filtering of raw reads and utilization of current best-practice OTU clustering methods, homopolymer errors in sequences representing rare taxa artificially increased estimates of richness ca. 15-fold in a model data set. Third, we show that inferences regarding endolichenic diversity can be improved by using a novel primer that reduces amplification of the mycobiont. Together, our results provide a rationale for selecting tissue treatment regimes prior to DNA extraction, demonstrate the efficacy of reducing mycobiont amplification in studies of the fungal microbiomes of lichen thalli, and highlight the difficulties in differentiating true information about fungal biodiversity from methodological artifacts.
Fig. 1. A in Bioactive terpenoids derived from plant endophytic fungi: An updated review (2011-2020)
Fig. 1. A) The proportions of terpenoids from endophytic fungi; B) the number of terpenoids reported in endophytic fungi; and, C) the most redundant endophytic fungi as terpeoid producers (2011–2020).
FIGURE 7 in Endophytic fungi associated with Coriaria nepalensis in an abandoned open-pit phosphate mine in Yunnan, P.R. China
FIGURE 7. Phylogram generated from Maximum Likelihood analysis based on a combined LSU, ITS, rpb2 and tub2 sequence datasets. The 71 strains are included in the combined gene analysis 2414 total character including gaps (LSU: 1–970 bp, ITS: 971–1476 bp, rpb2: 1477–2076 bp, tub2: 2077–2414 bp). Tree topology of the ML analysis was similar to the BI. The matrix had distinct alignment patterns, with the final ML optimization likelihood value of -10985.830126 (ln). All free model parameters were estimated by RAxML model, with 591 distinct alignment patterns and 9.91% of undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.239938, C = 0.243524, G = 0.275052, T = 0.241487, with substitution rates AC = 1.455735, AG = 5.319539, AT = 1.539293, CG = 1.013949, CT = 11.131040, GT = 1.000000. The gamma distribution shape parameter alpha = 0.665812 and the Tree-Length = 0.755110. The final average standard deviation of split frequencies at the end of total MCMC generations was calculated as 0.009112 in BI analysis. The species introduced in this study are indicated in red, and the type strains are indicated in bold. Bootstrap values greater than 60% (ML, Left) and Bayesian posterior probabilities (BI, right) greater than 0.95 are given at the nodes. Hypens (-) represent values less than 60% in ML/0.95 in BI.
FIGURE 1 in Endophytic fungi associated with Coriaria nepalensis in an abandoned open-pit phosphate mine in Yunnan, P.R. China
FIGURE 1. Phylogram generated from Maximum Likelihood analysis based on a combined LSU, ITS, tef1-α and tub2 sequence datasets. The 22 strains are included in the combined gene analysis 2460 total character including gaps (LSU: 1–892 bp, ITS: 893–1580 bp, tef1-α: 1581–2065 bp, tub2: 2066–2598 bp). Tree topology of the ML analysis was similar to the BI. The matrix had distinct alignment patterns, with the final ML optimization likelihood value of -11028.098478 (ln). All free model parameters were estimated by RAxML model, with 982 distinct alignment patterns and 24.33% of undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.236385, C =0.275681, G = 0.277948, T = 0.209986, with substitution rates AC = 1.657800, AG = 2.641351, AT = 1.759057, CG = 1.214763, CT = 5.269496, GT = 1.000000. The gamma distribution shape parameter alpha = 0.662280 and the Tree-Length = 1.116951. The final average standard deviation of split frequencies at the end of total MCMC generations was calculated as 0.008871 in BI analysis. The species introduced in this study are indicated in red, and the type strains are indicated in bold. Bootstrap values greater than 60% (ML, Left) and Bayesian posterior probabilities (BI, right) greater than 0.95 are given at the nodes. Hypens (-) represent values less than 60% in ML/0.95 in BI.
FIGURE 4 in Endophytic fungi associated with Coriaria nepalensis in an abandoned open-pit phosphate mine in Yunnan, P.R. China
FIGURE 4. Coniella quercicola (HKAS 129063). (a,e) Obverse and reverse of colonies on PDA; (b–d) Close up of the conidiomata on PDA; (f) Conidiomata; (g) Section of conidiomata; (h) Conidiophores bearing conidiogenous cells and conidia stained by congo red reagent; (i, j) Conidia.
FIGURE 6 in Endophytic fungi associated with Coriaria nepalensis in an abandoned open-pit phosphate mine in Yunnan, P.R. China
FIGURE 6. Chaetomium cochliodes (HKAS 129064). (a,e) Obverse and reverse of colonies on PDA; (b–d) Close up of the fruiting bodies on PDA; (f,g) Ascomata; (h) Asci; (i) Asci stained by the congo red reagents; (j, k) Setae; (l) Immature ascospores stained by congo red reagent; (m, n) Ascospores.
FIGURE 2 in Endophytic fungi associated with Coriaria nepalensis in an abandoned open-pit phosphate mine in Yunnan, P.R. China
FIGURE 2. Chrysofolia kunmingensis (HKAS 129065, holotype). (a,b) Obverse and reverse of colonies on PDA; (c,d) Close up of the fruiting bodies on PDA; (e) Mycelium; (f) Conidiomata; (g–j) Conidiogenous cells bearing conidia which stained by congo red reagent; (k) Conidia stained by congo red reagent.
Data from: Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi
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Data from: Genotypic diversity in root-endophytic fungi reflects efficient dispersal and environmental adaptation
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Dark septate endophytes and arbuscular mycorrhizal fungi (Paris-morphotype) affect the stable isotope composition of ‘classically’ non-mycorrhizal plants
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Figure 6 from: Li J-L, Sun X, Zheng Y, Lü P-P, Wang Y-L, Guo L-D (2020) Diversity and community of culturable endophytic fungi from stems and roots of desert halophytes in northwest China. MycoKeys 62: 75-95. https://doi.org/10.3897/mycokeys.62.38923
Figure 6 Preferences observed in the plant-fungus associations. A Preference scores. The standardized d' estimate of preferences for fungal taxon is shown for each halophyte (column), and the standardized d' estimate of preferences for plant species is indicated for each of the fungal taxon (row). Each cell in the matrix indicates a two-dimensional preference (2DP) estimate, which measures to what extent the association of a focal plant-fungus pair was observed more/less frequently than expected by chance. P values were shown as false discovery rates (FDRs) in the plant/fungus analysis. B Relationship between 2DP and FDR-adjusted P values, 2DP values larger than 2.5 and those smaller than -2.5 represented strong preference and avoidance, respectively (PFDR < 0.05). Significance: *, P < 0.05, **, P < 0.01, ***, P < 0.001.
Figure 5 from: Li J-L, Sun X, Zheng Y, Lü P-P, Wang Y-L, Guo L-D (2020) Diversity and community of culturable endophytic fungi from stems and roots of desert halophytes in northwest China. MycoKeys 62: 75-95. https://doi.org/10.3897/mycokeys.62.38923
Figure 5 Canonical correspondence analysis (CCA) ordination plot of endophytic fungal communities of stem and root tissues (A) and halophyte species (B). Dotted ellipses indicate 95% confidence intervals around centroids of tissue type (A) and plant species (B), B. dasyphylla = Bassia dasyphylla, C. arenarius = Ceratocarpus arenarius, K. foliatum = Kalidium foliatum, Sa. nitraria = Salsola nitraria, Su. acuminata = Suaeda acuminata, Su. salsa = Suaeda salsa, E. minor = Eragrostis minor, R. songarica = Reaumuria songarica, Se. santolinum = Seriphidium santolinum, and P. harmala = Peganum harmala.
Figure 3 from: Li J-L, Sun X, Zheng Y, Lü P-P, Wang Y-L, Guo L-D (2020) Diversity and community of culturable endophytic fungi from stems and roots of desert halophytes in northwest China. MycoKeys 62: 75-95. https://doi.org/10.3897/mycokeys.62.38923
Figure 3 Relative abundance of endophytic fungi in the stem and root tissues of the ten halophyte species.
Figure 4 from: Li J-L, Sun X, Zheng Y, Lü P-P, Wang Y-L, Guo L-D (2020) Diversity and community of culturable endophytic fungi from stems and roots of desert halophytes in northwest China. MycoKeys 62: 75-95. https://doi.org/10.3897/mycokeys.62.38923
Figure 4 Relative abundance of endophytic fungi in the stem and root of different halophyte species.
Figure 2 from: Li J-L, Sun X, Zheng Y, Lü P-P, Wang Y-L, Guo L-D (2020) Diversity and community of culturable endophytic fungi from stems and roots of desert halophytes in northwest China. MycoKeys 62: 75-95. https://doi.org/10.3897/mycokeys.62.38923
Figure 2 Endophytic fungal richness in stem, root and total (stem + root) tissues of the ten halophyte species. Data are means ± SE (n = 10). Columns without shared lowercase, uppercase, and italic letters denote significant difference in the stem, root, and total tissues among the plant species, respectively. Asterisks above bars indicate the significant difference between stem and root tissues for each halophyte species (* P<0.05, ** P < 0.01, *** P < 0.001).
Figure 1 from: Li J-L, Sun X, Zheng Y, Lü P-P, Wang Y-L, Guo L-D (2020) Diversity and community of culturable endophytic fungi from stems and roots of desert halophytes in northwest China. MycoKeys 62: 75-95. https://doi.org/10.3897/mycokeys.62.38923
Figure 1 Colonization rate of endophytic fungi in stem, root, and total (stem + root) tissues of the ten halophyte species. Data are means ± SE (n = 10). Columns without shared lowercase, uppercase, and italic letters denote the significant difference in the stem, root, and total tissues among the halophyte species, respectively. Asterisks above bars indicate significant difference between stem and root tissues for each plant species (** P < 0.01, *** P < 0.001).
Figure 7 in Bioactivity and chemical screening of endophytic fungi associated with the seaweed Ulva sp. of the Bay of Bengal, Bangladesh
Figure 7: Antioxidant and cytotoxic potential of the crude extracts of fungi associated with Ulva sp. (A) DPPH (2,2-diphenyl1-picrylhydrazyl) radical scavenging activity, and (B) brine shrimp lethality bioassay. Values are mean ± standard deviation, n = 3. Bars with different letters are significantly different according to Tukey's post hoc test at p = 0.05.
Figure 2 in Filtrates from cultures of endophytic fungi isolated from leaves of Copaifera oblongifolia (Fabaceae) affect germination and seedling development differently
Figure 2. Variations (mean ± standard error) of seedling survival (A) and its relationship with seed mass (B) of Copaifera oblongifolia as a function of treatments with inoculation of different species of endophytic fungi. Different letters on the bars indicate statistical variations between treatments (P <0.05) according contrast analysis
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.