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16 results for “Hymenoscyphus fraxineus”
Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires
<p><strong>Background </strong>The dieback epidemic decimating common ash (<em>Fraxinus excelsior</em>) in Europe is caused by the invasive fungus <em>Hymenoscyphus fraxineus</em>. In this study we analyzed the genomes of <em>H. fraxineus</em> and <em>H. albidus</em>, its native but, now essentially displaced, non-pathogenic sister species, and compared them with several other members of <em>Helotiales</em>. The focus of the analyses was to identify signals in the genome that may explain the rapid establishment of <em>H. fraxineus</em> and displacement of <em>H. albidus</em>.</p> <p><strong>Results</strong> The genomes of <em>H. fraxineus</em> and <em>H. albidus </em>showed a high level of synteny and identity. The assembly of <em>H. fraxineus </em>is 13 Mb longer than that of <em>H. albidus’, </em>most of this difference can be attributed to higher dispersed repeat content ((i.e transposable elements [TEs]) in <em>H. fraxineus</em>. In general, TE families in <em>H. fraxineus</em>showed more signals of repeat-induced point mutations (RIP) than in <em>H. albidus</em>, especially in Long-terminal repeat (LTR)/Copia and LTR/Gypsy elements. Comparing gene family expansions and 1:1 orthologs, relatively few genes show signs of positive selection between species. However, several of those that did appeared to be associated with secondary metabolite genes families, including gene families containing two of the genes in the <em>H. fraxineus-</em>specific, <em>hymenosetin </em>biosynthetic gene cluster (BGC).</p> <p><strong>C</strong><strong>onclusion </strong>The genomes of <em>H. fraxineus</em> and <em>H. albidus</em> show a high degree of synteny, and are rich in both TEs and BGCs, but the genomic signatures also indicated that <em>H. albidus</em> may be less well equipped to adapt and maintain its ecological niche in a rapidly changing environment. </p> <p><strong>Data included</strong></p> <p>This post contains the alternate structural and functional annotations of the genomes of Helotealean fungi used in the study.</p>
Supplementary material 1 from: Pourmoghaddam MJ, Lambert C, Surup F, Khodaparast SA, Krisai-Greilhuber I, Voglmayr H, Stadler M (2020) Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon spp. against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture. MycoKeys 66: 105-133. https://doi.org/10.3897/mycokeys.66.50946
Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon species towards the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture
Datasets for "Meteorological factors associated with the timing and abundance of Hymenoscyphus fraxineus spore release" by Burns, Timmermann and Yearsley.
<p>======++++++++++++++++++++++++++++++==============<br> <br> # Data Files:<br> <br> File: burns_etal_preprocessed_data.Rdata<br> <br> This file contains the pre-processed spore count data and the cleaned meteorological data<br> The file contains:<br> <br> stations The longitude and latitude of the two weather stations used for the metro data<br> varStr_mean Names of the meteorological variables<br> windowStr Names of the three time windows<br> <br> emission The main data frame containing the spore and meteorological data<br> date Date of a spore count recording. (POSIXlt)<br> year Year of spore count recording<br> month Month of spore count recording <br> day Day of year of spore count recording<br> total The total daily spore count<br> peak The maximum spore count each day <br> peak_time The time (hours after midnight) of the maximum spore count each day<br> peak_time_raw Raw value for time of maximum spore count each day<br> peak_time_date Date and time (POSIXct) for maximum spore count each day<br> ===================================================<br> <br> File: results_burns_etal_daily_emission_analysis_2010_2011_prop0.8.Rdata<br> <br> This file gives the results for the total daily emission of spores<br> <br> File: results_burns_etal_daily_peaktime_analysis_2010_2011_prop0.8.Rdata<br> <br> This file gives the results for the time of the daily per in spore counts<br> <br> ================<br> Both files have the same variables, which are listed below.<br> <br> # Setup parameters<br> use.prop Proportion of the data to use for fitting model<br> colinear_threshold The correlation threshold to identify collinear covariates<br> frost_var The name of the variable to use as a frost covariate (three possible windows)<br> k.use The dimension of the basis for the smoothing thin-plate splines in the GAM<br> nIter Number of Monte-Carlo random subsamples of the data<br> seed The random number seed at the start of the analysis<br> years The years of data to use for fitting the GAM models.<br> Leaving a year out allows it to be used as independent validation data<br> <br> # Outputs from the analysis<br> var.use The names of covariate used in the final analysis after removing collinear covariates<br> models A list (of length nIter) giving all the fitted models<br> d A data frame with a summary of the nIter model results.<br> There are nIter rows. Each row summarises the results from one GAM<br> The data frame contains:<br> r2 r-squared between the model and the validation data.<br> Validation data are the (1-use.prop) proportion not used for fitting<br> r2_fitted. r-squared for the data used to fit the model<br> dev.exp. The explained deviance from the fitted GAM<br> nTerm. The number of smooth terms in the fitted GAM<br> term1 The smooth term with the smallest p-value (number is an index for var.use)<br> term2 The smooth term with the second smallest p-value (number is an index for var.use)<br> term3 The smooth term with the third smallest p-value (number is an index for var.use)<br> termF The smooth term with the largest F-value (number is an index for var.use)<br> pValues p values for each of the smooth terms (columns) for each of the nIter models (rows)<br> FValues F values for each of the smooth terms (columns) for each of the nIter models (rows)<br> edf Estimated degrees of freedom for each of the smooth terms (columns) for each of the nIter models (rows)<br> pValue_param p values for each of the parametric terms (columns) in each of nIter models (rows)<br> tVal_param. t statistics for each of the parametric terms (columns) in each of nIter models (rows)<br> </p>
Data from: A versatile method for assessing pathogenicity of Hymenoscyphus fraxineus to ash foliage
We describe a method for inoculating rachises of Fraxinus excelsior (European or common ash) with Hymenoscyphus fraxineus, which is faster than previous methods and allows associated foliar symptoms to be assessed on replicate leaves. A total of ten ash seedlings were inoculated with five isolates of H. fraxineus and lesion development assessed over four weeks. A five‐point disease progress scale of symptom development was developed from no lesion (0), lesion on rachis (1), "pre‐top dead," with curling of distal leaflets and bending of the rachis (2), top dead, with wilting and death of distal leaflets (3) to leaf abscission (4). The method revealed variation in aggressiveness of H. fraxinus isolates and may be suitable for assessing the resistance of F. excelsior and other Fraxinus species to dieback. The in vitro growth rate of H. fraxineus isolates was highly correlated with both disease progress and the length of rachis lesions on susceptible plants, indicating that it can be used as a preliminary step in selecting isolates with high aggressiveness for use in resistance screening.
Data from: A versatile method for assessing pathogenicity of Hymenoscyphus fraxineus to ash foliage
Open the record for dataset details and reuse information.
Figure 7 from: Pourmoghaddam MJ, Lambert C, Surup F, Khodaparast SA, Krisai-Greilhuber I, Voglmayr H, Stadler M (2020) Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon spp. against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture. MycoKeys 66: 105-133. https://doi.org/10.3897/mycokeys.66.50946
Figure 7 Illustration of antagonist test by dual culture technique of Hypoxlon spp. and Hymenoscyphus fraxineus on barley-malt agar in 9-cm diam. plates A dual culture of H. rubiginosum (MUCL 47152) against Hym. fraxineus (STMA 18166) after 1 wk of incubation B dual culture of H. rubiginosum (MUCL 47152) against Hym. fraxineus (STMA 18166) after 2 wk of incubation C dual culture of H. rubiginosum (MUCL 47152) against Hym. fraxineus (STMA 18166) after 3 wk of incubation D dual culture of H. rubiginosum (MUCL 47152) against Hym. fraxineus (STMA 18166) after 4 wk of incubation E–H (Hypoxylon aff. rubiginosumMUCL 57724) against Hym. fraxineus after 1, 2, 3, 4 wk I–LH. texense (DSM 107933) against Hym. fraxineus after 1, 2, 3, 4 wk M–PH. guilanense (MUCL 57726) against Hym. fraxineus after 1, 2, 3, 4 wk.
Figure 4 from: Pourmoghaddam MJ, Lambert C, Surup F, Khodaparast SA, Krisai-Greilhuber I, Voglmayr H, Stadler M (2020) Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon spp. against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture. MycoKeys 66: 105-133. https://doi.org/10.3897/mycokeys.66.50946
Figure 4 Hypoxylon aff. rubiginosum (GUM 1587) A, B stromatal habit C close-up view of stromatal surface, with stromatal pigments in 10% KOHD stroma in section showing perithecia and ostioles E mature and immature asci in water F ascus in water G ascus in Melzer's reagent H ascus tip in Melzer's reagent I ascospores in 10% KOH with dehiscent perispore J ascospore in water, with germ-slit K ascospore under SEM. Scale bars: 5 mm (A, B); 1 mm (C); 0.5 mm (D); 20 µm (E–G); 10 µm (H–J); 2 µm (K).
Figure 11 from: Pourmoghaddam MJ, Lambert C, Surup F, Khodaparast SA, Krisai-Greilhuber I, Voglmayr H, Stadler M (2020) Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon spp. against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture. MycoKeys 66: 105-133. https://doi.org/10.3897/mycokeys.66.50946
Figure 11 HPLC-UV chromatograms at 210 nm from mono cultural barley-malt agar extracts of MUCL 47152 (H. rubiginosum), STMA 18166 (Hym. fraxineus), STMA 13090 (H. fuscum) and one dual culture experiment thereof. UV/Vis spectra are shown for phomopsidin (5), 10-hydroxyphomopsidin (6), orthosporin (9), daldinone B (10), 1,8-dimethoxynaphthalene (11), daldinin F (12), 5–methylmellein (13), viridiol (14) and an unidentifiable compound (UC 6) after comparison of data with internal databases. The UV signal of UC 6 was enhanced in the dual culture extract.
Figure 6 from: Pourmoghaddam MJ, Lambert C, Surup F, Khodaparast SA, Krisai-Greilhuber I, Voglmayr H, Stadler M (2020) Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon spp. against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture. MycoKeys 66: 105-133. https://doi.org/10.3897/mycokeys.66.50946
Figure 6 Hypoxylon aff. rubiginosum (GUM 1588) A stromatal habit B close-up view of stromatal surface, with stromatal pigments in 10% KOHC section of stroma showing perithecia and ostioles D ascus in Melzer's reagent E ascospores in 10% KOH with dehiscent perispore. Scale bars: 2.5 mm (A); 0.5 mm (B, C); 20 µm (D); 10 µm (E).
Figure 5 from: Pourmoghaddam MJ, Lambert C, Surup F, Khodaparast SA, Krisai-Greilhuber I, Voglmayr H, Stadler M (2020) Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon spp. against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture. MycoKeys 66: 105-133. https://doi.org/10.3897/mycokeys.66.50946
Figure 5 Culture and anamorphic structures of Hypoxylon aff. rubiginosum (GUM 1587) on OAA, B surface of colony after 1 and 8 wk of incubation (respectively, left to right) C–G general view of anamorph structure with virgariella-like branching patterns H, I conidiogenous cells and immature conidia J mature conidia. Scale bars: 20 µm (C–G); 10 µm (H–J).
Figure 3 from: Pourmoghaddam MJ, Lambert C, Surup F, Khodaparast SA, Krisai-Greilhuber I, Voglmayr H, Stadler M (2020) Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon spp. against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture. MycoKeys 66: 105-133. https://doi.org/10.3897/mycokeys.66.50946
Figure 3 Hypoxylon rubiginosum (GUM 1586) A, B stromatal habit C close-up view of stromatal surface D close-up view of stromatal surface, with stromatal pigments in 10% KOHE ascospores in 10% KOH with dehiscent perispore F mature and immature asci in water G immature ascus in water H mature ascus in water I ascus in Melzer's reagent J ascospores in water K ascus tip in Melzer's reagent. Scale bars: 2 cm (A); 1 cm (B); 4 mm (C); 2 mm (D); 10 µm (E); 20 µm (F–I), 10 µm (J, K).
Figure 10 from: Pourmoghaddam MJ, Lambert C, Surup F, Khodaparast SA, Krisai-Greilhuber I, Voglmayr H, Stadler M (2020) Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon spp. against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture. MycoKeys 66: 105-133. https://doi.org/10.3897/mycokeys.66.50946
Figure 10 HPLC-UV profiles at 210 nm derived from barley-malt agar (A–C, E) and stromal (E) extracts and compound standard (F). UV/Vis spectra are shown for identified compounds in mono- and dual culture (C) experiments of STMA 18166 (Hym. fraxineus, A) and DSM 107933 (H. texense, B; UC 2, 4 – unknown compounds); stromal metabolites (4 – mitorubrinol; URg – unknown rubiginosin A derivative; 3 – rubiginosin A; 2 – mitorubrinol acetate; 7 – mitorubrin; UC2 – Unknown compound 2 of GLM-F116101 (H. texense, D), and ... ESI mass spectra of 8 in positive and negative modes... of 8 8 (rickiol A, F) identified in the mono culture extract of MUCL 54624 (H. rubiginosum, E).
Figure 2 from: Pourmoghaddam MJ, Lambert C, Surup F, Khodaparast SA, Krisai-Greilhuber I, Voglmayr H, Stadler M (2020) Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon spp. against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture. MycoKeys 66: 105-133. https://doi.org/10.3897/mycokeys.66.50946
Figure 2 Hypoxylon guilanense (Holotype GUM 989) A stromatal habit B close-up view of stromatal surface, with stromatal pigments in 10% KOHC, H, I ascospores in water, with germ-slits D, E ascospores in 10% KOH with dehiscent perispore F, G ascospore under SEMJ, K culture on 9 cm OA plates after 1 and 3 wk of incubation (left to right). Scale bars: 2.5 mm (A), 1 mm (B); 10 µm (C–E); 2 µm (F, G); 10 µm (H, I).
Figure 1 from: Pourmoghaddam MJ, Lambert C, Surup F, Khodaparast SA, Krisai-Greilhuber I, Voglmayr H, Stadler M (2020) Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon spp. against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture. MycoKeys 66: 105-133. https://doi.org/10.3897/mycokeys.66.50946
Figure 1 Phylogram of the best ML trees (lnL = −63870.651550) revealed by RAxML from an analysis of the combined ITS–LSU–rpb2–tub2 matrix of selected Xylariales. Strains in bold were sequenced in the current study. ML and MP bootstrap support above 50% are given at the first and second positions, respectively, above or below the branches.
Figure 9 from: Pourmoghaddam MJ, Lambert C, Surup F, Khodaparast SA, Krisai-Greilhuber I, Voglmayr H, Stadler M (2020) Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon spp. against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture. MycoKeys 66: 105-133. https://doi.org/10.3897/mycokeys.66.50946
Figure 9 HPLC-UV profiles at 210 nm derived from stromal extracts of strains H. rubiginosum (GUM 1586), H. guilanense (from holotype) and Hypoxylon aff. rubiginosumGUM 1587 and GUM 1588. UV/Vis spectra are shown for orsellinic acid (1), mitorubrinol acetate (2), rubiginosin A (3), an unknown rubiginosin A – like derivative (URg) and rubiginosin – like derivatives (UC 2 and UC 3). ESI mass spectra are shown for compounds URg and 2.
Figure 8 from: Pourmoghaddam MJ, Lambert C, Surup F, Khodaparast SA, Krisai-Greilhuber I, Voglmayr H, Stadler M (2020) Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon spp. against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture. MycoKeys 66: 105-133. https://doi.org/10.3897/mycokeys.66.50946
Figure 8 Chemical structures of discussed secondary metabolites. Orsellinic acid (1); mitorubrinol acetate (2); rubiginosin A (3); mitorubrinol (4); phomopsidin (5); 10-hydroxyphomopsidin (6); mitorubrin (7); rickiol A (8); orthosporin (9); daldinone B (10); 1,8-dimethoxynaphthalene (11); daldinin F (12); 5-methyl mellein (13); viridiol (14).
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