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6 results for “Rhynchosporium commune”
Improved genome annotation of Rhynchosporium commune isolate UK7 using Illumina short reads of in vitro and in plantae conditions
<p>Improved genome annotation of the <em>Rhynchosporium commune</em> isolate UK7 using Illumina short reads of <em>in vitro</em> and <em>in plantae</em> conditions. The short reads used for the annotation are available at <a href="https://doi.org/10.5281/zenodo.5729968">https://doi.org/10.5281/zenodo.5729968</a> and <a href="https://doi.org/10.5281/zenodo.5729863">https://doi.org/10.5281/zenodo.5729863</a>.To create the gene models, we used tophat v. 2.0.14 to align short reads to the UK7 reference genome (Trapnell et al., 2009). The Intron splice site hints were generated using bam2hints, included in the AUGUSTUS v. 3.2.1 software (Stanke et al., 2006). Due to the very high RNA-sequencing depth available, intron splice hints were filtered for a minimum coverage of 20 reads to avoid an impact of spurious splice signals on gene prediction. To produce <em>ab initio </em>gene models, the BRAKER v. 1.0 pipeline (Hoff et al., 2016) combining GeneMark-ET <em>ab initio </em>gene model predictions and AUGUSTUS v. 3.2.1. GeneMark-ET was trained using the RNA-seq-based splice information as hints. AUGUSTUS was automatically trained using <em>ab initio </em>gene models that were fully supported by splice information. Finally, AUGUSTUS was used to predict gene models using both RNA-seq splice information and coding sequence hints based on exonerate protein alignments as extrinsic evidence.</p>
Transposable element annotation Rhynchosporium commune isolate UK7
<p>To obtain a consensus sequence for each TE family, RepeatModeler v. open-4.0.7 (http://www.repeatmasker.org/RepeatModeler/) was run on the <em>R. commune</em> UK7 reference genome. The classification was based on the GIRI Repbase (v. 2018) using RepeatMasker v. open-4.0.7. (Smit, Hubley, and P. 2015; Bao, Kojima, and Kohany 2015). We used WICKERsoft to finalize the classification of TE consensus sequences (Breen et al. 2010). Specifically, we used WICKERsoft to screen for copies of known consensus sequences from other fungal species with blastn filtering for sequence identity > 80% and sequence length > 80%. (Altschul et al. 1997). Then, using WICKERsoft, flanks of 10000 bp were added and visually inspected for sequence similarity and terminal repeats with dot plots. Subsequent multiple sequence alignments were performed with 10-15 sequences using ClustalW (Thompson, Higgins, and Gibson 1994). Alignment boundaries were visually inspected in WICKERsoft and trimmed if necessary. Using WICKERsoft, consensus sequences were classified according to the presence and type of terminal repeats, as well as homology of the encoded proteins based on blastx against the NCBI protein database. Consensus sequences were named according to the three-letter classification system (Wicker et al. 2007). The reference genome was annotated with the curated consensus sequences using RepeatMasker v. open-4.0.7 with a cut-off value of 250 (Smit, Hubley, and P. 2015). Simple repeats, low complexity regions and annotated elements shorter than 100 bp were filtered out and adjacent identical TEs overlapping by more than 100 bp were merged as belonging to the same TE family. Different TE families overlapping by more than 100 bp were considered as nested insertions and were renamed accordingly. Identical elements separated by less than 200 bp are indicative of interrupted elements and were grouped into a single element. TEs overlapping genes were recovered using the bedtools v. 2.27.1 suite and the “overlap” function (Quinlan and Hall 2010).</p>
Illumina TruSeq stranded mRNA sequences of Rhynchosporium commune isolate UK7 in plantae
<p>Transcription profiles were generated from the <em>Rhynchosporium commune</em> isolate UK7. RNA-seq experiments were conducted <em>in plantae</em> on the barley cultivar Beatrix (Viskosa 9 Pasadena, Saaten Union, breeders’ Reference NS01/2449). Leaves were collected at 9 and at 13 days post infection (dpi). All experiments were conducted in triplicates. Total RNA was extracted using TRIzol (Invitrogen Inc.) following the manufacturer’s recommendations. RNA integrity and quantity was assessed on a Bioanalyzer 2100 (Agilent) and a Qubit fluorometer (Life Technologies) and a Bioanalyzer 2100. Libraries were prepared using the TruSeq stranded mRNA sample prep kit (Illumina Inc.). Total RNA was ribosome-depleted by using polyA selection and reverse-transcribed into double-stranded cDNA.</p>
Illumina TruSeq stranded mRNA sequences of Rhynchosporium commune isolate UK7 in vitro
<p>Transcription profiles were generated from the <em>Rhynchosporium commune</em> isolate UK7. Cultures were grown either on Luria-Bertani (LBA) or Potato Dextrose Broth (PDB) media. Total RNA was extracted using TRIzol (Invitrogen Inc.) following the manufacturer’s recommendations. Experiments were conducted in triplicates. RNA integrity and quantity was assessed on a Bioanalyzer 2100 (Agilent) and a Qubit fluorometer (Life Technologies) and a Bioanalyzer 2100. Libraries were prepared using the TruSeq stranded mRNA sample prep kit (Illumina Inc.). Total RNA was ribosome-depleted by using polyA selection and reverse-transcribed into double-stranded cDNA.</p>
Data from: Local adaptation and evolutionary potential along a temperature gradient in the fungal pathogen Rhynchosporium commune
To predict the response of plant pathogens to climate warming, data are needed on current thermal adaptation, the pathogen's evolutionary potential and the link between them. We conducted a common garden experiment using isolates of the fungal pathogen Rhynchosporium commune from nine barley populations representing climatically diverse locations. Clonal replicates of 126 genetically distinct isolates were assessed for their growth rate at 12°C, 18°C and 22°C. Populations originating from climates with higher monthly temperature variation had higher growth rate at all three temperatures compared to populations from climates with less temperature fluctuation. Population differentiation in growth rate (Q_ST) was significantly higher at 22°C than population differentiation for neutral microsatellite loci (G_ST), consistent with local adaptation for growth at higher temperatures. At 18°C we found evidence for stabilizing selection for growth rate as Q_ST was significantly lower than G_ST. Heritability of growth rate under the three temperatures was substantial in all populations (0.58-0.76). Genetic variation was lower in populations with higher growth rate at the three temperatures and evolvability increased under heat stress in seven out of nine populations. Our findings imply that the distribution of this pathogen is unlikely to be genetically limited under climate warming, due to its high genetic variation and plasticity for thermal tolerance.
Data from: Local adaptation and evolutionary potential along a temperature gradient in the fungal pathogen Rhynchosporium commune
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