Gene Expression
Nebulas
Gene Expression NebulasSummary: Purpose: To assess global changes of wheat coleoptiles gene expression in response to fusaoctaxin A which is a linear, C-terminally-reduced and D-amino acid residue-rich octapeptide, as the product of the two non-ribosomal peptide synthetases encoded by Fusarium graminearum fg3_54 cluster.Methods: For RNA seq of wheat coleoptiles, three biological replicates of mock-inoculated coleoptiles, wild-type PH-1 inoculated coleoptiles (3 dpi), ∆fg3_54 inoculated coleoptiles (3 dpi), after 3 hours fusaoctaxin A-treated coleoptiles, after 3 hours control (0.5% Tween-20) treated coleoptiles, after 24 hours fusaoctaxin A-treated coleoptiles and after 24 hours control (0.5% Tween-20) treated coleoptiles were sequenced.Results: For each sample, 33-95 M RNA-seq clean reads were obtained mapped to the Triticum aestivum Chinesespring genome sequence.Our results of RNA sequencing indicated fusaoctaxin does not induce PR gene expression, but suppress plant immunity and chloroplastc activity.Conclusions: Fusaoctaxin A represents an unprecedented virulence factor which can manipulate chloroplast and suppress host immunity.
Overall Design: Three biological replicates of mock-inoculated coleoptiles, wild-type PH-1 inoculated coleoptiles (3 dpi), ∆fg3_54 inoculated coleoptiles (3 dpi), after 3 hours fusaoctaxin A-treated coleoptiles, after 3 hours control (0.5% Tween-20) treated coleoptiles, after 24 hours fusaoctaxin A-treated coleoptiles and after 24 hours control (0.5% Tween-20) treated coleoptiles were sequenced using Illumina NovaSeq 6000 Sequencing System.
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| Growth Protocol: | Grow the wheat seedling in the growth chamber for 3 day under controlled environment conditions at 25 °C with a 12 h light/12 h dark photoperiod |
| Treatment Protocol: | For Fusarium graminearum inoculation: Mock, wild-type PH-1 and △fg3_54 inoculate wheat seedling. For compound treatment: add 2μl fusaoctaxin A (0.5mM) or 0.5% tween-20 onto wound site of wheat coleoptiles. |
| Extract Protocol: | Total RNA was isolated using EasyPure Plant RNA kit (Transgen biotech) according to the manufacturer’s protocol. RNA integrity was confirmed using the 2100 Bioanalyzer (Agilent Technologies) with a minimum RNA integrated number (RIN) value of 7. |
| Library Construction Protocol: | RNA libraries were prepared for sequencing using standard Illumina protocols |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | -; Forward |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2500; Illumina NovaSeq 6000 |
| Strand-Specific: | Unspecific; Specific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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