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36 results for “oomycete”
Hydrodynamic shape changes underpin nuclear rerouting in branched hyphae of an oomycete pathogen
<p><strong>Note:</strong> These are mp4 files. While being a widespread file format, mp4 may require additional codecs on some platforms. We recommend users to install a free media player with mp4 support such as <a href="https://www.videolan.org/vlc/index.fr.html">VLC</a>.</p> <p> </p> <p><strong>Video</strong><strong> 1. </strong>Time-lapse confocal microscopy of germinating <em>P. palmivora </em>cysts from a transgenic strain expressing a cytoplasmic tdTomato and a nuclear-localized mTFP1 (LILI-td-NT) during exploratory growth at the surface of <em>N. benthamiana</em> roots. Z-stacks were collected every 5 min. Still images corresponding to this video are displayed in <strong>Figure 1</strong>. Scale bar is 10 µm.</p> <p><strong>Video 2.</strong> Time-lapse confocal microscopy of <em>P. palmivora </em>LILI-td-NT infection structures during <em>N. benthamiana</em> root infection. The video is composed of two movies representing successful (<strong>Video 2</strong><strong>A</strong><strong>)</strong> and unsuccessful <strong>(Video 2</strong><strong>B</strong><strong>)</strong> infection events. Z-stacks were collected every 5 min. Still images corresponding to this video are displayed in <strong>Figure 2</strong>. Scale bar is 20 µm.</p> <p><strong>Video 3.</strong> Time-lapse confocal microscopy of <em>P. palmivora </em>LILI-td-NT hyphae differentiating haustoria during <em>N. benthamiana</em> leaf infection. Plastids autofluorescence is shown in magenta. Frames were collected every 6.6 s. Still images corresponding to this video are shown in <strong>Figure 3</strong>. Scale bar is 20 µm.</p> <p><strong>Video 4.</strong> Time-lapse confocal microscopy of <em>P. palmivora </em>LILI-td-NT hyphae during haustoria differentiation in <em>N</em><em>. benthamiana</em> leaf tissues. Plastids autofluorescence is shown in magenta. Frames were collected every 4 s. Still images corresponding to this video are shown in <strong>Figure 3</strong>. Scale bar is 10 µm.</p> <p><strong>Video 5.</strong> Time-lapse confocal microscopy of a <em>P. palmivora </em>LILI-td-NT hyphal tip on V8 agar plate. Frames were collected every 4.5 s. Still images corresponding to this video are displayed in <strong>Figure 3</strong>. Scale bar is 20 µm.</p> <p><strong>Video 6.</strong> Time-lapse confocal microscopy of a <em>P. palmivora </em>LILI-td-NT hyphal tip on V8 agar plate. Frames were collected every 4.8 s. Still images corresponding to this video are displayed in <strong>Figure 3</strong>. Scale bar is 20 µm.</p> <p><strong>Video </strong><strong>7</strong><strong>.</strong> Time-lapse confocal microscopy of a <em>P. palmivora </em>LILI-td-NT hyphal branch point on V8 agar plate. Frames were collected every 15 s. Still images corresponding to this video are displayed in <strong>Figure </strong><strong>5</strong>. Scale bar is 20 µm.</p> <p><strong>Video </strong><strong>8</strong><strong>.</strong> Time-lapse confocal microscopy of <em>P. palmivora </em>LILI-td-NT mycelium on V8 agar plate without (DMSO control) <strong>(Video 8</strong><strong>A</strong><strong>)</strong> or with 10 mg/L Benomyl <strong>(Video 8</strong><strong>B</strong><strong>)</strong>. Frames were collected every 12.8 s and 13 s, respectively. Still images corresponding to this video are displayed in <strong>Figure </strong><strong>6</strong>. Scale bar is 20 µm.</p> <p><strong>Video </strong><strong>9</strong><strong>.</strong> Time-lapse confocal microscopy of <em>P. palmivora </em>mycelium from a transgenic strain expressing a mCitrine-Centrin2 reporter and a nuclear-localized mTFP1 (LILI-NT-Ce) on V8 agar plate. Frames were collected every 5 s. This video is linked to <strong>Figure 7</strong>. Scale bar is 20 µm.</p>
Fungal and Oomycete cardinal temperatures (the Togashi dataset)
<p>We collated and analysed temperature responses, specifically the minimum (T<sub>min</sub>), optimum (T<sub>opt</sub>) and maximum (T<sub>max</sub>) temperatures that comprise the 'cardinal temperatures', of various biological processes for 695 plant-associated microbes (631 fungi and 64 oomycetes) reported in "Togashi, K. (1949). <i>Biological characters of plant pathogens: temperature relations</i>. Meikundo". Cardinal temperatures can be used to derive temperature response functions, or thermal performance curves, using mathematical forms such as the beta function. The biological processes for which cardinal temperatures have been measured vary in their degree of host interaction. Experimental measurements for rates of growth in culture and often spore germination occur under axenic conditions, while infection and disease development occur as interactions with the host plant. Fruiting body formation, or fructification, and sporulation may or may not be measured in planta depending on experimental conditions.</p>
Complete telomere-to-telomere genomes uncover virulence evolution conferred by chromosome fusion in oomycete plant pathogens
<p><span>Variations in chromosome number are occasionally observed among oomycetes, a group that includes many plant pathogens, but the emergence of such variations and their effects on genome and virulence evolution remain ambiguous. We generated complete telomere-to-telomere genome assemblies for <em>Phytophthora sojae</em>, <em>Globisporangium ultimum</em>, <em>Pythium oligandrum</em>, and <em>G. spinosum</em>. Reconstructing the karyotype of the most recent common ancestor in Peronosporales revealed that frequent chromosome fusion and fission drove changes in chromosome number. Centromeres enriched with <em>Copia</em>-like transposons may contribute to chromosome fusion and fission events. Chromosome fusion facilitated the emergence of pathogenicity genes and their adaptive evolution. Effectors tended to duplicate in the sub-telomere regions of fused chromosomes, which exhibited evolutionary features distinct to the non-fused chromosomes. By integrating ancestral genomic dynamics and structural predictions, we have identified secreted Ankyrin repeat-containing proteins (ANKs) as a novel class of effectors in <em>P. sojae</em>. Phylogenetic analysis and experiments further revealed that ANK is a specifically expanded effector family in oomycetes. These results revealed chromosome dynamics in oomycete plant pathogens, and provided novel insights into karyotype and effector evolution.</span></p>
Data for: Detection of oomycete pathogens in UK peat-free growing media and implications for plant health
<p>This dataset on Zenodo accompanies the manuscript Frederickson-Matika <em>et al.</em> (2024), Detection of oomycete pathogens in UK peat-free growing media and implications for plant health.</p> <p>There are two files:</p> <ul> <li>metadata.tsv - plain text table as tab-separated variables</li> <li>raw_data.tar.gz - compressed archive of 43 paired raw FASTQ files</li> </ul> <p>This represents a subset of two complete Illumina MiSeq plates (in two dated folderes) run at the James Hutton Institute containing other environmental samples using the same protocol. Only the synthetic controls and peat-free samples are provided here.<br><br>To repeat the analysis described in the paper, first install THAPBI PICT. See <a href="https://github.com/peterjc/thapbi-pict/">https://github.com/peterjc/thapbi-pict/ </a>for instructions. At the time of the paper, v1.0.14 was the current release.</p> <p>Next, decompress the raw data into a folder of paired gzipped FASTQ files. There is no need to decompress those:</p> <pre><code> $ tar -zxvf raw_data.tar.gz<br> $ ls -1 plate_20220505/ plate_20230608/</code></pre> <p>If you wish, verify the checksums to confirm the data integrity:</p> <pre><code> $ cd plate_20220505/ $ md5sum -c MD5SUM.txt<br> $ cd ../plate_20230608/ $ md5sum -c MD5SUM.txt<br> $ cd ..</code></pre> <p>Setup output directories:</p> <pre><code><code> $ mkdir -p intermediate/ summary/</code></code></pre> <pre>Run the THAPBI PICT pipeline:</pre> <pre><code> $ thapbi_pict pipeline -m 1s3g \<br> -i plate_*/ -o summary/peat-free \<br> -y plate_*/GBL*.fastq.gz \<br> -n plate_*/GBL*.fastq.gz \<br> -s intermediate/ \<br> -t metadata.tsv -u \<br> -x 9 -c 1,2,3,4,5,6,7,8</code><br><br></pre> <p>The options here are as follows:</p> <ul> <li>-i - two input directories of paired raw FASTQ files.</li> <li>-n - negative controls used to increase the absolute abundance threshold</li> <li>-y - synthetic controls used to increase the fractional abundance threshold</li> <li>-s - optional location to store intermediate files</li> <li>-o - output stem for reports</li> <li>-t - filename for tab-separated-variable metadata</li> <li>-u - show unsequenced samples defined in the metadata</li> <li>-x - which metadata column contains Illumina FASTQ filename stems</li> <li>-c - which metadata columns to include in the report.</li> </ul> <p>This assumes the following key default settings:</p> <ul> <li>-a 100 (default absolite abundance threshold)</li> <li>-f 0.001 (default fractional abundance threshold)</li> <li>-d -(default provided ITS1 database).</li> </ul> <p>With these settings, only synthetic sequences were found in the controls, and therefore the thresholds were not automatically increased any further.</p> <p>Opening the output file summary/peat-free.ITS1.samples.1s3g.xlsx in Excel or similar should show you a table resembling Table 1 in the paper, but one row per sequencing sample, and additional columns with per-sample per-species read counts etc.</p>
Fungal and Oomycete cardinal temperatures (the Togashi dataset)
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Data from: Population of origin and environment interact to determine oomycete infections in spotted salamander populations
Spatial variation in disease risk in wild populations can depend both on environmental and genetic factors. Understanding the various contributions of each factor requires experimental manipulation of both the environment and genetic composition of populations under natural field conditions. We first examined natural patterns of oomycete composition and infection in the eggs of 13 populations of the spotted salamander Ambystoma maculatum. We then performed a fully factorial field transplant of the eggs of six populations to separate the contributions from population of origin and the environment on oomycete resistance in spotted salamanders. Among wild ponds, we found strong variation in oomycete infections in spotted salamander populations and differences in the composition of oomycete communities. In transplant experiments, salamander populations differed in their resistance to oomycete infections via a significant interaction between population of origin and environment. However, not all populations were locally adapted to local conditions. One population was significantly adapted to its home environment, and another one was significantly maladapted. These population effects could originate from differential adaptation of salamander populations to local oomycete communities or environmental conditions that mediate resistance, local adaptation and maladaptation of oomycetes to hosts, or from maternal transmission. Accounting for both environment and population of origin will often be necessary to understand disease dynamics in wild populations.
Coexistence is stabilized by conspecific negative density dependence via fungal pathogens more than oomycete pathogens
<p>No description provided.</p>
FIGURE 3 in Achlya catenulata sp. nov., a new Saprolegniales (Oomycetes, Straminipila) from Brazilian mangrove swamp
FIGURE 3. Maximum likelihood tree inferred from LSU rDNA sequences of isolates of Achlya. Numbers next to branches indicate bootstrap support (%) and the bar shows the number of substitutions per site.
FIGURE 2 in Achlya catenulata sp. nov., a new Saprolegniales (Oomycetes, Straminipila) from Brazilian mangrove swamp
FIGURE 2. Maximum likelihood tree inferred from ITS rDNA sequences of isolates of Achlya. Numbers next to branches indicate bootstrap support (%) and the bar shows the number of substitutions per site.
FIGURE 1 A–E. Achlya catenulata. A in Achlya catenulata sp. nov., a new Saprolegniales (Oomycetes, Straminipila) from Brazilian mangrove swamp
FIGURE 1 A–E. Achlya catenulata. A. Achlyoid discharge of the zoosporangia. B. Sympodial renewal of the zoosporangia. C. Catenulate oogonia and diclinous antheridia. D–E. Oogonia, failed to mature and eccentric oospores and antheridia. Bars: 10 μm.
FIGURE 3 in New insights into Plectospira genus (Oomycetes, Straminipila): morphological and molecular analyses
FIGURE 3. Concatenate analysis of complete ITS and partial LSU rDNA regions of Verrucalvaceae family inferred by Maximum Likelihood method. The numbers next the branches indicate the bootstrap values (%) and the scale bar the numbers of substitution per site. In bold the three Brazilian isolates of Plectospira and in grey the whole clade.
FIGURE 2. A–J. Plectospira myriandra. A–E. Plectospira myriandra CCIBt 3992. A. Lobulated zoosporangium. B. Oogonium and subcentric oospore. C in New insights into Plectospira genus (Oomycetes, Straminipila): morphological and molecular analyses
FIGURE 2. A–J. Plectospira myriandra. A–E. Plectospira myriandra CCIBt 3992. A. Lobulated zoosporangium. B. Oogonium and subcentric oospore. C. Oogonium showing pellucid spot (ps). D. Oogonium showing scattered pits in the wall (pw). E. Oogonium and abundant antheridia. F–J. Plectospira myriandra CCIBt 3372. F. Lobulated zoosporagium. G. Oogonium and antheridia. H. Oogonium and pellucid spot (ps) showed in indirect focus (arrow). I. Oogonium and subcentric oospore. J. Oogonia with pellucid spot indicated by the arrow. ps: pellucid spot. pw: scattered pits in the wall. Bars: 10 μm.
FIGURE 1. A–M. Plectospira gemmifera CCIBt 4250. A–D in New insights into Plectospira genus (Oomycetes, Straminipila): morphological and molecular analyses
FIGURE 1. A–M. Plectospira gemmifera CCIBt 4250. A–D. Different formats of gemmae. E. Lobulated zoosporangia. F–G. Zoosporangium with a long tube and zoospores cluster. H. Catenulate gemmae. I. Spherical gemmae with germinative tube. J. Oogonium and antheridia. K. Subcentric oospores. L. Empty gemmae. M. Piriform gemmae germinating. Bars: 10 μm.
Data from: Site specific distribution of oak rhizosphere associated oomycetes revealed by cytochrome c oxidase subunit II metabarcoding
The phylum Oomycota comprises important tree pathogens like Phytophthora quercina, involved in central European oak decline, and P. cinnamomi shown to affect holm oaks among many other hosts. Despite the importance to study the distribution, dispersal and niche partitioning of this phylum, metabarcoding surveys and studies considering environmental factors that could explain oomycete community patterns are still rare. We investigated oomycetes in the rhizosphere of evergreen oaks in a Spanish oak woodland using metabarcoding based on Illumina sequencing of the taxonomic marker cytochrome c oxidase subunit II (cox2). We developed an approach amplifying a 333 bp long fragment using the forward primer Hud-F (Hudspeth, Nadler, & Hudspeth, 2000) and a reverse primer found using DegePrime (Hugerth et al., 2014). Factors reflecting topo-edaphic conditions and tree health were linked to oomycete community patterns. The majority of detected OTUs belonged to the Peronosporales. Most taxa were relatives of the Pythiaceae, but relatives of the Peronosporaceae and members of the Saprolegniales were also found. The most abundant OTUs were related to Globisporangium irregulare and Phytophthora cinnamomi, both displaying strong site specific patterns. Oomycete communities were strongly correlated with the environmental factors: altitude, crown foliation, slope and soil skeleton and soil nitrogen. Our findings illustrate the significance of small scale variation in habitat conditions for the distribution of oomycetes and highlights the importance to study oomycete communities in relation to such ecological patterns.
Data from: Site specific distribution of oak rhizosphere associated oomycetes revealed by cytochrome c oxidase subunit II metabarcoding
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Data from: Comparison and validation of Oomycetes metabarcoding primers for Phytophthora high throughput sequencing
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Data from: Population of origin and environment interact to determine oomycete infections in spotted salamander populations
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Supplementary materials for "Effect of cesium ions on the mycelium growth and zoospores motility in the oomycete Phytophthora infestans" article
<p>This archive contains supplementary materials for Safonov et al. (2020) article.</p> <p>Each of the three subfolders (series a-c) contains data regarding the corresponding series of zoospore tracking experiments: “video fragments” subfolder with analyzed recordings and “excluded regions” subfolder with ROI-files. ROI-files contain ROIs needed to exclude certain parts of a video frame from analysis (for example, if they contain any debris that can be falsely recognized by the program as a zoospore). Each ROI-file corresponds to its video fragment: for example, “excluded regions control 3 mM a” is a ROI-file for “control 3 mM a”.</p>
Data from: A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models
Background: Molecular clock methodologies allow for the estimation of divergence times across a variety of organisms; this can be particularly useful for groups lacking robust fossil histories, such as microbial eukaryotes with few distinguishing morphological traits. Here we have used a Bayesian molecular clock method under three distinct clock models to estimate divergence times within oomycetes, a group of fungal-like eukaryotes that are ubiquitous in the environment and include a number of devastating pathogenic species. The earliest fossil evidence for oomycetes comes from the Lower Devonian (~400 Ma), however the taxonomic affinities of these fossils are unclear. Results: Complete genome sequences were used to identify orthologous proteins among oomycetes, diatoms, and a brown alga, with a focus on conserved regulators of gene expression such as DNA and histone modifiers and transcription factors. Our molecular clock estimates place the origin of oomycetes by at least the mid-Paleozoic (~430-400 Ma), with the divergence between two major lineages, the peronosporaleans and saprolegnialeans, in the early Mesozoic (~225-190 Ma). Divergence times estimated under the three clock models were similar, although only the strict and random local clock models produced reliable estimates for most parameters. Conclusions: Our molecular timescale suggests that modern pathogenic oomycetes diverged well after the origin of their respective hosts, indicating that environmental conditions or perhaps horizontal gene transfer events, rather than host availability, may have driven lineage diversification. Our findings also suggest that the last common ancestor of oomycetes possessed a full complement of eukaryotic regulatory proteins, including those involved in histone modification, RNA interference, and tRNA and rRNA methylation; interestingly no match to canonical DNA methyltransferases could be identified in the oomycete genomes studied here.
Data from: Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes
The kingdom Stramenopile includes diatoms, brown algae, and oomycetes. Plant pathogenic oomycetes, including Phytophthora, Pythium and downy mildew species, cause devastating diseases on a wide range of host species and have a significant impact on agriculture. Here, we report comparative analyses on the genomes of thirteen straminipilous species, including eleven plant pathogenic oomycetes, to explore common features linked to their pathogenic lifestyle. We report the sequencing, assembly, and annotation of six Pythium genomes and comparison with other stramenopiles including photosynthetic diatoms, and other plant pathogenic oomycetes such as Phytophthora species, Hyaloperonospora arabidopsidis, and Pythium ultimum var. ultimum. Novel features of the oomycete genomes include an expansion of genes encoding secreted effectors and plant cell wall degrading enzymes in Phytophthora species and an over-representation of genes involved in proteolytic degradation and signal transduction in Pythium species. A complete lack of classical RxLR effectors was observed in the seven surveyed Pythium genomes along with an overall reduction of pathogenesis-related gene families in H. arabidopsidis. Comparative analyses revealed fewer genes encoding enzymes involved in carbohydrate metabolism in Pythium species and H. arabidopsidis as compared to Phytophthora species, suggesting variation in virulence mechanisms within plant pathogenic oomycete species. Shared features between the oomycetes and diatoms revealed common mechanisms of intracellular signaling and transportation. Our analyses demonstrate the value of comparative genome analyses for exploring the evolution of pathogenesis and survival mechanisms in the oomycetes. The comparative analyses of seven Pythium species with the closely related oomycetes, Phytophthora species and H. arabidopsidis, and distantly related diatoms provide insight into genes that underlie virulence.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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