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746 results for “Brassica”
Pathogen lifestyle determines host genetic signature of quantitative disease resistance loci in oilseed rape (Brassica napus)
<p>Supplemental datasets associated with publication: Pathogen lifestyle determines host genetic signature of quantitative disease resistance loci in oilseed rape (<em>Brassica napus</em>)</p> <p><strong>Abstract</strong></p> <ul> <li>Crops are affected by several pathogens, but these are rarely studied in parallel to identify common and unique genetic factors controlling diseases. Broad-spectrum quantitative disease resistance (QDR) is desirable for crop breeding as it confers resistance to several pathogen species.</li> <li>Here, we use associative transcriptomics (AT) to identify candidate gene loci associated with <em>Brassica napus</em> constitutive QDR to four contrasting fungal pathogens: <em>Alternaria brassicicola</em>, <em>Botrytis cinerea</em>, <em>Pyrenopeziza</em><em> brassicae</em> and <em>Verticillium longisporum. </em>We did not identify any loci associated with broad-spectrum QDR to fungal pathogens with contrasting lifestyles. Instead, we observed QDR dependent on the lifestyle of the pathogen—hemibiotrophic and necrotrophic pathogens had distinct QDR responses and associated loci, including some loci associated with early immunity. Furthermore, we identify a genomic deletion associated with resistance to <em>V. longisporum </em>and potentially broad-spectrum QDR.</li> <li>This is the first time AT has been used for several pathosystems simultaneously to identify host genetic loci involved in broad-spectrum QDR. We highlight constitutively expressed candidate loci for broad-spectrum QDR with no antagonistic effects on susceptibility to the other pathogens studies as candidates for crop breeding. In conclusion, this study represents and advancement in our understanding if broad-spectrum QDR in <em>B. napus </em>and is a significant resource for the scientific community. </li> </ul> <p><strong>Description of data files</strong></p> <p><strong>Full dataset for input into AT analysis </strong>Full datasets (infection phenotypes for <em>A. brassicicola, B. cinerea, </em>or <em>V.longisporum, </em>ROS measurements for chitin, flg22, or elf18) and link to original <em>P. brassicae </em>dataset. These datasets were used for input into the Associative Transcriptomics pipeline (Nichols, 2022, <a href="https://github.com/bsnichols/GAGA. https://zenodo.org/badge/latestdoi/512807075">https://github.com/bsnichols/GAGA. https://zenodo.org/badge/latestdoi/512807075</a>). </p> <p><strong>Table S1 </strong>Mean, normalized phenotype data for resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and <em>Verticillium longisporum</em>) and ROS response induced by PAMPS (chitin, flg22, and elf18). These data were used for association transcriptomic analysis.<strong> </strong></p> <p><strong>Table S2 </strong>Full list of single nucleotide polymorphism (SNP) markers and significance levels from genome-wide association (GWA) analyses for resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and <em>Verticillium longisporum</em>) and ROS response induced by PAMPS (chitin, flg22, and elf18). Each excel tab contains the analyses for a single trait. The best fit model for GWA analysis is indicated in the tab title. Manhattan plots showing marker-trait association are included for data visualization; x-axis indicates SNP location along the chromosome; the y-axis indicates the -log10(p) (P value). Qqplots are included to demonstrate model fit.</p> <p><strong>Table S3</strong> Full list of gene expression markers (GEMs) and significance levels from GEM analyses for resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae and Verticillium longisporum</em>) and ROS response induced by PAMPS (chitin, flg22, and elf18). Each excel tab contains the analyses for a single trait. Manhattan plots showing marker-trait association are included for data visualization; x-axis indicates GEM location along the chromosome; the y-axis indicates the -log10(p) (P value). </p> <p><strong>Table S4 </strong>184 gene expression markers (GEMs) associated with chitin-induced ROS compared with GEMs associated with resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and<em> Verticillium longisporum</em>) and ROS response induced by flg22, and elf18. Lists correspond to Venn diagrams in Fig. 2. The first tab includes all 184 GEMs associated with chitin-induced ROS. The subsequent tabs include lists of shared GEMs associated with chitin-induced ROS response and each additional trait (quantitative disease resistance (QDR) to each fungal pathogen or additional PAMP-induced ROS responses). The title of each tab indicates the data included in each comparison and the number of shared GEMs. Predicted <em>Arabidopsis thaliana</em> orthologs and corresponding descriptions are shown where possible. </p> <p><strong>Table S5</strong> Enrichment analyses to determine if the number of gene expression markers (GEMs) shared between different lists is greater than the number of GEMs that would be expected by chance (e.g., lists of quantitative disease resistance (QDR) GEMs for two fungal pathogens). The representation factor is the number of overlapping GEMs divided by the expected number of overlapping GEMs drawn from two independent groups (traits), considering the total number of GEMs sequenced (53884). A representation factor > 1 indicates more overlap than expected of two groups, a representation factor < 1 indicates less overlap than expected, and a representation factor of 1 indicates that the two groups by the number of genes expected for independent groups of genes. </p> <p><strong>Table S6 R</strong>esults from Weighted Co-expression Gene Network Analysis (WGCNA). The first tab indicates significant modules from WGCNA analysis. Black and magenta modules are associated with antagonistic effects on resistance/susceptibility to all four pathogens. The second tab includes a full list of the GEM markers (Table S3), which are in significant WGCNA modules. The third, fourth and, fifth tabs indicate all significant GEMs in the black module, GO terms associated with GEMs in the black module, and all GO terms associated with the black module, respectively. The sixth, seventh and, eighth tabs indicate all significant GEMs in the magenta module, GO terms associated with GEMs in the magenta module, and all GO terms associated with the magenta module, respectively.</p> <p><strong>Table S7 </strong>Shared gene expression markers (GEMs) associated with resistance to different pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and <em>Verticillium longisporum</em>). Lists correspond to matrices and Venn diagrams in Fig. 3. The first tab includes all GEMs associated quantitative disease resistance (QDR) to the fungal pathogens. The subsequent tabs include lists of shared GEMs associated with QDR to two or more fungal pathogens. The title of each tab indicates the data included in each comparison and the number of shared GEMs. Predicted <em>Arabidopsis thaliana</em> orthologs and corresponding descriptions are shown where possible. </p> <p><strong>Table S8 </strong>List of genes in linkage disequilibrium with the top marker for <em>Verticillium longisporum</em> resistance from genome-wide association (GWA) analysis on chromosome A09 (107 genes)(Tab 1) and the homoeologous region on C08 (Tab 2). Their percentage identity and query coverage in <em>Brassica napus</em> reference genotypes Quinta, Tapidor, Westar and Zhongshuang 11 compared to the <em>B. napus</em> pantranscriptome is indicated. Predicted <em>Arabidopsis thaliana</em> orthologs and corresponding descriptions are shown where possible. </p> <p> </p>
Chromosome-scale assembly of winter oilseed rape Brassica napus
<p>The files correspond to data and results referenced in research article titled "Chromosome-scale assembly of winter oilseed rape Brassica napus".</p> <p>Data files below were used in the scaffolding process of genome assembly:</p> <ol> <li>Genetic maps (csv) <ul> <li>ExR53-DH_60kSNPmap</li> <li>ExV8-DH_60kSNPmap</li> </ul> </li> </ol> <p>Result files below are assembled sequences of the genome and the predicted annotation:</p> <ol> <li>Genome assembly (Express617_v1.fa.gz)</li> <li>Predicted coding sequences (Express617_v1_cds.fa.gz)</li> <li>Predicted coding sequences (Express617_v1_gene.gff3.gz)</li> <li>Predicted protein sequences (Express617_v1_protein.fa.gz)</li> <li>Predicted repetitive elements (Express617_v1_repeats.gff.gz)</li> </ol>
Assembly and comparison of two closely related Brassica napus genomes
<p>Here we present the <em>de novo</em> assembly of the <em>B. napus</em> cultivar Tapidor and comparison with an improved assembly of the <em>B. napus</em> cultivar Darmor<em>-bzh</em>. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor<em>-bzh</em> contains a greater number of genes than the genome of Tapidor.</p>
Figs 1–6 in Nosema pieriae sp. n. (Microsporida, Nosematidae): A New Microsporidian Pathogen of the Cabbage Butterfly Pieris brassicae L. (Lepidoptera: Pieridae)
Figs 1–6. Light micrographs of the microsporidian pathogen infecting P. brassicae. 1 – intestine which is heavily infected with microsporidian spores; 2–3 – microsporidian spores in fresh smears, note that meront and sporoblast stages are easily seen and marked by arrows; 4 – tetranucleate spherical meront (schizont); 5 – binucleate oval meront; 6 – diplokaryotic sporoblast. Scale bars: 30 µm (1), 15–10 µm (2–3), 3 μm (4), 2 μm (5), 4 μm (4).
Fig. 11 in Nosema pieriae sp. n. (Microsporida, Nosematidae): A New Microsporidian Pathogen of the Cabbage Butterfly Pieris brassicae L. (Lepidoptera: Pieridae)
Fig. 11. The phylogenetic analysis was carried out by Maximum Likelihood (ML) using an HKY85 substitution model of PAUP 4.0b10 software. The topology of the consensus tree was constructed and evaluated by 1000 bootstrap replications. The branches with lower than 50% confidence values were ignored.
Figs 7–10 in Nosema pieriae sp. n. (Microsporida, Nosematidae): A New Microsporidian Pathogen of the Cabbage Butterfly Pieris brassicae L. (Lepidoptera: Pieridae)
Figs 7–10. Transmission electron micrographs of microsporidian spores infecting P. brassicae. 7 – longitudinal (a) and transversal (b) sections of diplokaryotic spores, polar filament (pf), posterior vacuole (pv) and nuclei (n) are easily seen; 8 – spherical nuclei (n); 9 – polaroplast (pp) and anchoring disc (ad) structures; pp thin lamellar type polaroplast, pp thick lamellar type polaroplast; 10 – cross section of 1, 2, polar filaments; exospore (ex), endospore (en), plasmalemma (p) and polar filament (pf). Scale bars: 800 nm (7), 250 nm (8), 200 nm (9, 10).
Annotation files related to the Telomere-to-Telomere genome assembly of the clubroot pathogen Plasmodiophora brassicae (GCA_036867785.1)
<p>This repository contains annotation files related to the T2T genome aseembly of <em>Plasmodiophora brassicae</em>. Link to the NCBI genome submission- https://www.ncbi.nlm.nih.gov/bioproject/1071157</p> <p><strong>Description of the files :</strong></p> <p><strong>GCA_036867785.1_ULAVAL_Pb3A_genomic.fna</strong> - Soft-masked genome sequence FASTA file representing 20 chromosomes.</p> <p><strong>sequence_report.jsonl</strong> - Detailed information about individual chromosome seqeunce.</p> <p><strong>PBTT_annotation.gtf</strong> - GTF file corresponding to the genomic FASTA file.The GTF file was generated by BRAKER3 and contains information about all possible transcripts.</p> <p><strong>PBTT_CDS_longest_isoform.fasta</strong> - Contains 10521 FASTA sequences representing the CDS of only the longest isoform of the gene models.</p> <p><strong>PBTT_protein_longest_isoform.fasta</strong> - Contains 10521 FASTA sequences representing the amino acid sequences of only the longest isoform of the gene models.</p>
Brassica rapa (Brassicaceae) - fruit - as borne on the plant
Image of Brassica rapa (Brassicaceae) - fruit - as borne on the plant
Brassica rapa (Brassicaceae) - fruit - lateral or general close-up
Image of Brassica rapa (Brassicaceae) - fruit - lateral or general close-up
Brassica rapa (Brassicaceae) - stem - showing leaf bases
Image of Brassica rapa (Brassicaceae) - stem - showing leaf bases
Brassica rapa (Brassicaceae) - leaf - on upper stem
Image of Brassica rapa (Brassicaceae) - leaf - on upper stem
Brassica rapa (Brassicaceae) - inflorescence - lateral view of flower
Image of Brassica rapa (Brassicaceae) - inflorescence - lateral view of flower
Brassica rapa (Brassicaceae) - inflorescence - whole - unspecified
Image of Brassica rapa (Brassicaceae) - inflorescence - whole - unspecified
Brassica rapa (Brassicaceae) - whole plant - in flower - general view
Image of Brassica rapa (Brassicaceae) - whole plant - in flower - general view
Brassica rapa (Brassicaceae) - leaf - basal or on lower stem
Image of Brassica rapa (Brassicaceae) - leaf - basal or on lower stem
Brassica rapa (Brassicaceae) - fruit - as borne on the plant
Image of Brassica rapa (Brassicaceae) - fruit - as borne on the plant
Brassica rapa (Brassicaceae) - inflorescence - lateral view of flower
Image of Brassica rapa (Brassicaceae) - inflorescence - lateral view of flower
Brassica rapa (Brassicaceae) - fruit - as borne on the plant
Image of Brassica rapa (Brassicaceae) - fruit - as borne on the plant
Brassica rapa (Brassicaceae) - whole plant - juvenile
Image of Brassica rapa (Brassicaceae) - whole plant - juvenile
Brassica rapa (Brassicaceae) - whole plant - in flower - general view
Image of Brassica rapa (Brassicaceae) - whole plant - in flower - general view
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