Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| Racetosa454.bam | Bam | |||
| Racetosa454.bam.bai | Bam | |||
| Rpalustris454.bam | Bam | |||
| Rpalustris454.bam.bai | Bam |
Items per page: 5 1 - 5 of 7 |
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Project description:Two wild plant species regulate flooding survival through distinct mechanisms. TSA of Rumex palustris, ERS203005
| PRJEB1524 | ENA
Project description:Two wild plant species regulate flooding survival through distinct mechanisms- TSA assembly of Rumex acetosa, ERS203002
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Project description:Two super-enhancers regulate Nanog expression through distinct mechanisms [45del]
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Project description:Flooding stress is a major environmental threat for many terrestrial plants. The detrimental effects of flooding stress, however, vary between different plant species. Whereas many crops are rather sensitive to flooding, some wild species from flood-prone areas are well adapted to excess water conditions. Morphological adaptations like adventitious roots and aerenchyma formation, or the ability to elongate rapidly the above-ground organs, allow these plants to thrive in water. The focus of this research is Nasturtium officinale, also known as watercress, which is an auto-tetraploid, dicotyledonous and stem-growing Brassicaceae species. Its natural habitat is near rivers and streams, but absent from stagnant water. Submergence induces underwater elongation of stems and growth suppression of petioles in Nasturtium officinale. By using the RNA sequencing technique, we aimed to uncover the underlying mechanisms for these contrasting responses. Combining submergence experiments with hormone manipulations revealed that ABA degradation is required for stem elongation.
2019-12-04 | GSE138020 | GEO
Project description:Most crop species cannot survive flooding events for a long period of time. However, within the Cardamineae tribe of the Brassicaceae family, there exist several wild species with high flooding tolerance. Here, Rorippa islandica was identified as a genetically accessible diploid species with high submergence tolerance. Another diploid species from the same genus, R. stylosa, showed similar submergence sensitivity compared with Arabidopsis. Both species exhibited a strong and partially overlapping transcriptomic response to submergence within the first 48 hours of stress, including carbon-starvation and ethylene-responsive marker genes. We demonstrate that R. islandica can be transformed via floral dip, but with rather low frequency. The successful CRISPR-Cas9-mediated knockout of RiBCA3 confirms the suitability of this species for genetic transformation. However, although it was hypothesized that RiBCA3 might have an important function in carbon fixation under water, no differences in submergence survival or underwater photosynthesis were observed between wildtype and bca3 knockout lines. The molecular mechanisms of submergence tolerance of Rorippa islandica are therefore not understood yet. The data indicate that illumination and therefore photosynthesis-associated processes must be the basis for superior submergence survival. This work suggests that Rorippa islandica is a promising dicot model to further investigate the underlying tolerance mechanisms.
2025-12-31 | GSE295090 | GEO
Project description:Phosphorylation-mediated signaling transduction plays a crucial role in the regulation of plant defense mechanisms against environmental stresses. In order to address the high complexity and dynamic range of plant proteomes and phosphoproteomes, we present a universal sample preparation procedure to facilitate profiling plant phosphoproteomes. This advanced workflow significantly improves phosphopeptide identifications, enabling deep insight into plant phosphoproteomes. We then applied the workflow to study the phosphorylation events involved in tomato cold tolerance mechanisms. Phosphoproteomic changes of two tomato species (N135 Green Gage and Atacames) with distinct cold tolerance phenotypes were profiled under cold stress. In total, we identified more than 30,000 unique phosphopeptides from tomato leaves, representing about 5,500 phosphoproteins, as the largest tomato phosphoproteomic resource. The data, along with the validation through in vitro kinase reactions, allowed us to identify kinases involved in cold tolerant signaling and discover distinctive kinase-substrate events in two tomato species under cold environment. In particular, the activation of SnRK2s and their direct substrates may assist N135 Green Gage tomatoes in surviving long-term cold stress. Taken together, the streamlined approach and the resulting deep phosphoproteomic analyses revealed a global view of tomato cold-induced signaling mechanisms.
2019-03-08 | PXD009130 | JPOST Repository
Project description:Phosphorylation-mediated signaling transduction plays a crucial role in the regulation of plant defense mechanisms against environmental stresses. To address the high complexity and dynamic range of plant proteomes and phosphoproteomes, we present a universal sample preparation procedure that facilitates plant phosphoproteomic profiling. This advanced workflow significantly improves phosphopeptide identifications, enabling deep insight into plant phosphoproteomes. We then applied the workflow to study the phosphorylation events involved in tomato cold tolerance mechanisms. Phosphoproteomic changes of two tomato species (N135 Green Gage and Atacames) with distinct cold tolerance phenotypes were profiled under cold stress. In total, we identified more than 30,000 unique phosphopeptides from tomato leaves, representing about 5,500 phosphoproteins, thereby creating the largest tomato phosphoproteomic resource to date. The data, along with the validation through in vitro kinase reactions, allowed us to identify kinases involved in cold tolerant signaling and discover distinctive kinase-substrate events in two tomato species in response to a cold environment. In particular, the activation of SnRK2s and their direct substrates may assist N135 Green Gage tomatoes in surviving long-term cold stress. Taken together, the streamlined approach and the resulting deep phosphoproteomic analyses revealed a global view of tomato cold-induced signaling mechanisms.
2018-09-20 | PXD010310 | JPOST Repository
Project description:Heavy rainfall causes flooding of natural ecosystems as well as farmland, negatively affecting crop performance and yield. While the response of the wild model organism Arabidopsis thaliana to such stress conditions is well understood, we hardly know anything about the response of its relative, the important oil crop plant Brassica napus. Here, we analyzed the molecular response of leaves of rapeseed seedlings to full submergence under illumination. RNAseq experiments revealed a strong carbon starvation response under submergence, but no indication for a low-oxygen response. We used two cultivars in this study, one Asian flooding-tolerant cultivar and one European hybrid cultivar, but those genotypes did not show strong differences in their responses to submergence.
2020-10-28 | GSE140828 | GEO
Project description:To decipher stress responses under flooding and drought as well as flooding-tolerant mechanisms in soybean, the mathematic biological approach of simulation model was applied. Furthermore, wild-type soybean with ABA treatment and flooding-tolerant mutant line, which displayed flooding tolerance, were used as the flooding-tolerant materials. Proteins acquired by gel-free/label-free proteomic technique were used for simulation model of responses under different stresses and flooding tolerant.
2018-10-26 | PXD005680 | Pride
Project description:Plasma membrane NADPH oxidases (NOXs) are major producers of reactive oxygen species (ROS) in plant cells under normal growth and stress conditions. Rice NOXs have multiple homologs but their functional mechanisms are largely unknown. We used microarrays to detail the global gene expression profiles in rice wild-type (WT, Dongjin) and a mutant osnox2 which loss the functions of OsNOX2 protein under drought and identified distinct classes of genes between the two type rice plants under both normal growth and drought stressed conditions.
2015-12-31 | GSE54466 | GEO