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18 results for “Zymoseptoria tritici”
A pangenome-guided manually curated library of transposable elements for Zymoseptoria tritici
<p>A manually-curated TE consensus library generated using a panel of 19 reference genomes for <em>Zymoseptoria tritici</em><sup>1-3</sup> along with reference genome assemblies for the sister species <em>Z. ardabiliae</em>, <em>Z. brevis</em>, <em>Z. pseudotritici</em>, and <em>Z. passerinii<sup>4</sup></em>. </p> <p> </p> <p><strong>Methods</strong></p> <p>Putative TE consensus sequences were first obtained by annotating all 23 genome assemblies<sup>1–4</sup> with Earl Grey with default settings (v3.0; <a href="https://github.com/TobyBaril/EarlGrey">https://github.com/TobyBaril/EarlGrey</a>)<sup>5,6</sup>. Consensus sequences generated from each reference genome were clustered using CD-Hit-Est (v4.8.1)<sup>7,8</sup> to group sequences with 90% similarity across 80% of the longer sequence length (<em>-n 8 -d 0 -aL 0.8 -c 0.90 -G 0 -g 1 -b 500 -r 1</em>) to reduce redundancy whilst preventing the collapsing of chimeric sequences. Consensus sequences <100bp were removed, as these are unlikely to represent true TE sequences. Each consensus sequence was then subject to manual curation as described by Goubert et al. (2022)<sup>9</sup>. Briefly, genomic copies of each TE were obtained using a “BLAST, Extract, Extend” process to recover genomic copies from each of the 23 reference genome assemblies with 1,000 flanking bases at either end<sup>9,10</sup>. For families with >100 BLASTN hits, the 25 longest hits were selected, along with 75 random hits. Multiple alignments were generated for each putative TE family using MAFFT (v7.505) with the --auto flag<sup>11</sup>. Columns composed of >=80% gaps were removed with T-COFFEE (v13.45.0.4846264)<sup>12</sup>. Subsequently, all sequence alignments were manually curated to define TE boundaries and remove regions of low conservation and rare insertions. Following manual curation, new majority-rule consensus sequences were generated with EMBOSS (v6.6.0.0) cons<sup>13</sup>. TE-Aid (<a href="https://github.com/clemgoub/TE-Aid/">https://github.com/clemgoub/TE-Aid/</a>) was used to aid visual inspection and to identify diagnostic features for classification of extended consensus sequences. Following this, TIRs were recorded if present, and nhmmscan (HMMER v3.3.2)<sup>14</sup> was used to identify homology to known curated elements in Dfam (v3.7). Combining this information, each TE consensus sequence was manually classified using available information following the naming convention ‘>ZymTri_2023_family_[n]#[Classification]/[Family]’. Consensus sequences classified with low confidence have a ‘?’ added to the name, as well as the string ‘_LowConf’. To reduce redundancy in the final TE library, sequences were clustered to the family-level using the 80-80-80 rule implemented in CD-hit-est<sup>9,15 </sup>(<em>-d 0 -aS 0.8 -c 0.8 -G 0 -g 1 -b 500 -r 1</em>). The representative sequence for each cluster was manually selected to select the sequence with the highest classification confidence, also defined as the ‘most intact consensus’. Chimeric sequences erroneously clustered were manually separated to retain sequences for the chimeric TE and the individual elements that generated the chimer.</p> <p> </p> <p><strong>References</strong></p> <p>1. Badet, T., Oggenfuss, U., Abraham, L., McDonald, B. A. & Croll, D. A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici. <em>BMC Biol.</em> <strong>18</strong>, 12 (2020).</p> <p>2. Goodwin, S. B. <em>et al.</em> Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis. <em>PLoS Genet.</em> <strong>7</strong>, e1002070 (2011).</p> <p>3. Plissonneau, C., Hartmann, F. E. & Croll, D. Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome. <em>BMC Biol.</em> <strong>16</strong>, 5 (2018).</p> <p>4. Feurtey, A. <em>et al.</em> Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria. <em>BMC Genomics</em> <strong>21</strong>, 588 (2020).</p> <p>5. Baril, T., Imrie, R. M. & Hayward, A. Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline. (2022) doi:10.21203/rs.3.rs-1812599/v1.</p> <p>6. Baril, T., Galbraith, J. & Hayward, A. <em>Earl Grey</em>. (Zenodo, 2023). doi:10.5281/ZENODO.8116025.</p> <p>7. Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. <em>Bioinformatics</em> <strong>22</strong>, 1658–1659 (2006).</p> <p>8. Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. <em>Bioinformatics</em> <strong>28</strong>, 3150–3152 (2012).</p> <p>9. Goubert, C. <em>et al.</em> A beginner’s guide to manual curation of transposable elements. <em>Mob. DNA</em> <strong>13</strong>, 7 (2022).</p> <p>10. Camacho, C. <em>et al.</em> BLAST+: Architecture and applications. <em>BMC Bioinformatics</em> <strong>10</strong>, 1–9 (2009).</p> <p>11. Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. <em>Mol. Biol. Evol.</em> <strong>30</strong>, 772–780 (2013).</p> <p>12. Notredame, C., Higgins, D. G. & Heringa, J. T-coffee: a novel method for fast and accurate multiple sequence alignment. <em>J. Mol. Biol.</em> <strong>302</strong>, 205–217 (2000).</p> <p>13. Rice, P., Longden, L. & Bleasby, A. EMBOSS: The European Molecular Biology Open Software Suite. <em>Trends Genet.</em> <strong>16</strong>, 276–277 (2000).</p> <p>14. Wheeler, T. J. & Eddy, S. R. nhmmer: DNA homology search with profile HMMs. <em>Bioinformatics</em> <strong>29</strong>, 2487–2489 (2013).</p> <p>15. Wicker, T. <em>et al.</em> A unified classification system for eukaryotic transposable elements. <em>Nat. Rev. Genet.</em> <strong>8</strong>, 973–982 (2007).</p>
Compatible interaction experiment with Aegilops cylindrica infected with Zymoseptoria tritici isolate Zt 469 - CSLM images and videos
<p>Microscopic images and videos from convocal laser scanning microscopy (CLSM) analysis using maximum projections of confocal z-stacks. Cell nuclei and plant tissue are visible in purple, fungal hyphae in green.</p>
ZymoSoups: A high-throughput forward genetics method for rapid identification of virulence genes in Zymoseptoria tritici
<p>These data were used to generate figures and summarise the number of mutations in 18 re-sequenced genomes of <em>Zymoseptoria tritici. </em>The isolates genotyped in this VCF file are all UV-mutegenized strains of the reference isolate IPO323.</p> <p><strong>Abstract</strong></p> <p><span><span>Septoria tritici blotch is caused by the fungus </span></span><em><span><span>Zymoseptoria</span><span> tritici</span> </span></em><span><span>and</span><span> poses a major threat to wheat </span><span>productivity</span><span>. </span><span>There are over twenty mapped loci in wheat that confer strong (gene-for-gene) resistance </span><span>against this pathogen</span><span>, h</span><span>owever</span> <span>t</span><span>he corresponding genes in </span></span><em><span><span>Z. tritici</span></span></em><span><span> that confer virulence against distinct </span></span><span><span>R</span></span><span> <span>genes </span><span>remain</span> <span>largely unknown</span><span>. </span><span>In this study, we developed a</span> <span>rapid </span><span>forward genetics </span><span>methodology</span> <span>to </span><span>identify</span><span> genes that enable </span></span><em><span><span>Z. tritici</span></span></em><span><span> to gain virulence </span><span>on </span><span>previously resistant wheat varieties. </span><span>We</span><span> used the known</span><span> gene-for-gene interaction between </span></span><span><span>Stb6</span></span><span><span> and </span></span><span><span>AvrStb6</span></span><span><span> as </span><span>a </span><span>proof of concept that this method could quickly recover single candidat</span><span>e</span><span> virulence genes</span><span>. We subjected the avirulent </span></span><em><span><span>Z. tritici</span></span></em><span><span><em> </em>strain IPO323</span><span>, which carries the recogni</span><span>z</span><span>ed </span></span><span><span>AvrStb6</span></span><span><span> allele,</span><span> to UV mutagenesis</span><span> and</span><span> generat</span><span>ed</span><span> a library of over </span><span>66</span><span>,</span><span>000 </span><span>surviving spores</span><span>. </span><span>We screen</span><span>ed</span><span> these </span><span>survivors</span><span> on leaves of the resistant wheat variety Cadenza</span><span>,</span><span> in</span><span> mixtures</span> <span>(</span><span>soups</span><span>)</span><span> ranging from </span><span>100</span><span>-</span><span>500</span> <span>survivors</span><span> per soup. </span><span>We </span><span>identified</span><span> five soups</span><span> with </span><span>a </span><span>gain</span><span>-</span><span>of</span><span>-</span><span>virulence (</span><span>GoV</span><span>)</span><span> phenotype </span><span>relative</span><span> to the IPO323 parental strain</span><span> and re-sequenced 18 individual isolates, including four control isolates and two </span><span>isolates</span><span> lacking virulence</span><span>,</span><span> when screened </span><span>individually.</span> <span>Of </span><span>the </span><span>12 </span><span>confirmed </span><span>GoV</span> <span>isolates</span><span>, o</span><span>ne had a single nucleotide polymorphism (SNP) in the </span></span><span><span>AvrStb6</span></span><span><span> coding region. </span><span>T</span><span>he other 11 </span><span>GoV</span> <span>isolates</span> <span>exhibited</span> <span>large</span><span> (~70Kb)</span> <span>deletions at the end of chromosome 5, including the </span></span><span><span>AvrStb6</span></span><span><span> locus. </span><span>Our findings </span><span>demonstrate</span><span> the </span><span>efficiency </span><span>of this forward genetic approach in elucidating the genetic basis of qualitative resistance to </span></span><span><span>Z. tritici</span></span><span><span> and the </span><span>potential </span><span>to rapidly </span><span>identify</span><span> other</span><span>,</span><span> currently unknown</span><span>,</span> </span><span><span>Avr</span></span><span><span> genes in this pathogen. </span></span></p> <p><span><strong>Analysis pipeline</strong></span></p> <p><span>The pipeline used to generate this filtered vcf file and tab delimited file is publicly available at https://github.com/megancamilla/GATK4_Zymoseptoria</span></p> <p><span><strong>Isolate Data Accessibility</strong></span></p> <p><span><span>The individual fastq files for each isolate included in this study have been uploaded to NCBI's Short Read Archive (SRA), project number PRJNA1017776. This project </span><span>contains</span><span> 18 re-sequenced samples (SAMN37407989-SAMN37407972),</span> <span>which are UV mutagenized IPO323. Short Read Archive (SRA) accession numbers are SRR26072101-SRR26072118. </span> </span></p>
Incompatible interaction experiment with Aegilops cylindrica infected with Zymoseptoria tritici isolate Zt 244 (IPO323) - CSLM images and videos
<p>Microscopic images and videos from convocal laser scannning microscopy (CLSM) analysis using maximum projections of confocal z-stacks. Cell nuclei and plant tissue are visible in purple, fungal hyphae in green.</p>
Multi-reference genome and K-mer based association mapping in Zymoseptoria tritici
<p>Data tables for a study of multi-reference genome and K-mer based association mapping of the fungal wheat pathogen <em>Zymoseptoria tritici</em></p>
Zymoseptoria tritici pangenome resources
<p>This repository is a collection of reference-quality genomes available for the fungal wheat pathogen Zymoseptoria tritici.</p>
Denovo SPAdes assemblies for isolates included in the 1000-genome panel of Zymoseptoria tritici
<p>SPAdes draft assemblies for isolates included in the 1000-genome panel of <em>Zymoseptoria tritici</em></p> <p> </p> <p>For methods, please refer to: <a href="https://doi.org/10.1038/s41467-023-36674-y"><span>https://doi.org/10.1038/s41467-023-36674-y</span></a></p> <div> <div> </div> </div> <p>Original abstract: </p> <div> <div> <p>Human activity impacts the evolutionary trajectories of many species worldwide. Global trade of agricultural goods contributes to the dispersal of pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how pathogens surmount control strategies and cope with new climates is crucial to predicting the future impact of crop pathogens. Here, we address this by assembling a global thousand-genome panel of <em>Zymoseptoria tritici</em>, a major fungal pathogen of wheat reported in all production areas worldwide. We identify the global invasion routes and ongoing genetic exchange of the pathogen among wheat-growing regions. We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. Finally, we find significant standing variation for adaptation to new climates encountered during the global spread. Our work shows how large population genomic panels enable deep insights into the evolutionary trajectory of a major crop pathogen.</p> </div> </div>
Transcriptome analyses of three Zymoseptoria tritici isolates during infection of Triticum aestivum
GEO Series GSE106136. Triticum aestivum; Zymoseptoria tritici. 24 samples. Type: Expression profiling by high throughput sequencing.
Fungal plant pathogen “mutagenomics” reveals tagged and untagged mutations in Zymoseptoria tritici and identifies SSK2 as key morphogenesis and stress-responsive virulence factor
GEO Series GSE225623. Zymoseptoria tritici IPO323; Triticum aestivum. 12 samples. Type: Expression profiling by high throughput sequencing.
Next generation RNA sequencing to identify overexpressed transporter genes in Zymoseptoria tritici field strains
GEO Series GSE58672. Zymoseptoria tritici. 12 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome sequencing at early stage infection of the wheat pathogen Zymoseptoria tritici reveals chromosomal differences in transcription patterns and host specific gene expression.
GEO Series GSE54874. Zymoseptoria tritici. 3 samples. Type: Expression profiling by high throughput sequencing.
Data from: QTL mapping of temperature sensitivity reveals candidate genes for thermal adaptation and growth morphology in the plant pathogenic fungus Zymoseptoria tritici
Open the record for dataset details and reuse information.
Deciphering defense mechanisms primed by a rhamnolipid in wheat towards Zymoseptoria tritici
GEO Series GSE178704. Triticum aestivum. 18 samples. Type: Expression profiling by array.
Deciphering immune responses primed by a bacterial lipopeptide in wheat towards Zymoseptoria tritici
GEO Series GSE169298. Triticum aestivum. 18 samples. Type: Expression profiling by array.
Wheat resistance response triggered upon recognition of the avirulence factor AvrStb6 hinders the penetration of Zymoseptoria tritici through stomata
GEO Series GSE250605. Zymoseptoria tritici; Triticum aestivum. 36 samples. Type: Expression profiling by high throughput sequencing.
Improved genome annotation of the fungal wheat pathogen Zymoseptoria tritici IPO323 using Iso-Seq and RNA-Seq data
GEO Series GSE218898. Zymoseptoria tritici. 38 samples. Type: Expression profiling by high throughput sequencing.
Responses to temperature shocks in Zymoseptoria tritici reveal specific transcriptional reprogramming and novel candidate genes for thermal adaptation
GEO Series GSE284056. Zymoseptoria tritici. 18 samples. Type: Expression profiling by high throughput sequencing.
Zymoseptoria tritici suppresses the host immune response and facilitates the success of avirulent strains in mixed infections
GEO Series GSE232243. Triticum aestivum. 24 samples. Type: Expression profiling by high throughput sequencing.
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