Gene Expression
Nebulas
Gene Expression NebulasSummary: Legume plants form symbiotic relationships with diazotrophic bacteria called rhizobia. During such symbiosis, plants provide bacteria with preferred carbon sources such as malate and succinate in return for essential reduced nitrogen. Compatible interactions result in a series of plant root modifications that eventually result in nodule formation. Bacteria living in the nodule cells fix nitrogen via the nitrogenase enzyme complex. Interestingly, as in plant-pathogen interactions, incompatibility in legume-rhizobia associations is also regulated in a genotype-specific manner. For example, the dominant Rj2 gene is presumed to help exclude poor nitrogen-fixing or less-beneficial rhizobia such as B. japonicum USDA122 (U122). The process likely involves recognition of bacterial effectors by host receptor proteins similar to the perception of pathogenic microbes. Our results show that genetic exclusion of incompatible rhizobia in the root requires conserved molecular components of the plant immune response pathway and results in the induction of systemic signaling in the distal tissue. To better understand the mechanism underlying incompatible rhizobia-induced systemic signaling, we compared the transcriptional changes in the foliar tissue of Rj2 plants inoculated with compatible or incompatible rhizobia strains, using RNA-Seq analysis.
Overall Design: Overall, 1 control (mock), 2 treatments (treated with Incompatible Glycine max L76-1988 with Bradyrhizobium japonicum USDA122 and Glycine max L76-1988 with Sinorhizobium fredii USDA257), each with 3 replicates.
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| Growth Protocol: | Soybean (Glycine max (L.) Merr.) L76-1988 was grown in the green house with day and night temperatures of 25°C and 20°C, respectively. |
| Treatment Protocol: | Plants were grown in sterile vermiculite and roots of plants (V1 stage) were inoculated with B. japonicum USDA122 or S. fredii USDA257 (0.5 OD600). |
| Extract Protocol: | RNA from leaf tissues was extracted at 24 h post rhizobia inoculation using the TRIzol reagent (Invitrogen, Carlsbad, CA), per manufacturer’s instructions. |
| Library Construction Protocol: | RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq RNA Library Prep Kit), Paired-end |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 3000 |
| Strand-Specific: | Unspecific |
| 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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