Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1199194 | ENA |
REPOSITORIES: ENA
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Project description:Basil downy mildew (BDM) caused by Peronospora Belbahrii leads to losses in sweet basil cultivation across the world. Though resistant cultivars of basil exist, the formation of sterile offspring and the introduction of unwanted phenotypic and chemotypic traits slows breeding. Previous work by the Simon lab at Rutgers University identified pair of sweet basil cultivars; one resistant to BDM, MRI, and one susceptible, SB22. They predicted that three genes in MRI confer increased BDM resistance. RNA from infected MRI and SB22 plants was harvested during the first 3 days of infection at 4 timepoints in order to capture as many early phases of plant-pathogen interaction as possible. The goal is to develop resistance markers for use in breeding experiments.
2020-11-04 | GSE111387 | GEO
Project description:Applying a metatranscriptomic analysis pipeline (Guo et al. 2016 Frontiers in Plant Science), we are the first to analyze the host-pathogen metatranscriptome of the basil downy mildew system. RNA-sequencing technology was utilized to gain access to the full array of expressed transcripts from both O. basilicum and P. belbahrii. This RNA-seq workflow has allowed us to identity nearly 3,000 candidate P. belbahrii genes expressed in planta, as well as 1,267 and 2,798 candidate O. basilicum genes induced or suppressed respectively under P. belbahrii infection (five days post inoculation). Up-regulated candidate genes are highly enriched for biological processes such as biotic and abiotic stress responses whereas down-regulated genes are enriched for metabolism and photosynthesis, suggesting that basil plants actively respond to pathogen infection with transcriptome reprogramming.
2016-04-30 | GSE79807 | GEO
Project description:Plants need to adapt to fluctuating temperatures throughout their lifetime. Previous research has shown that A. thaliana retains memory of a first cold stress (priming) and improves its primed freezing tolerance even further when subjected to a second similar stress after a lag phase. This study investigates primary metabolomic (gas chromatography–mass spectrometry) and transcriptomic (RNA-Seq) changes during 24 h of cold priming or cold triggering at 4°C. During triggering higher expression of genes encoding Late Embryogenesis Abundant (LEA), antifreeze proteins or proteins function as detoxifiers of reactive oxygen species (ROS) was observed compared to cold priming. Examples of early responders to triggering were xyloglucan endotransglucosylase/hydrolase genes encoding proteins involved in cell wall remodeling while late responders were identified to act in fine-tuning of stress response and development regulation. Four transcription factors, CBF2/DREB1C, CBF4/DREB1D, DDF2/DREB1E and DDF1/DREB1F were strongly and uniquely significantly induced throughout the entire triggering response. The induction of unusual members of the DREB subfamily of ERF/AP2 transcription factors, the relatively small number of induced genes of the CBF regulon and slower accumulation of selected cold stress associated metabolites proposes that a cold triggering stimulus might be sensed as milder stress in plants compared to priming. Further, the strong induction of CBF4 throughout triggering suggests a unique function of this gene during cold stress memory.
2022-07-02 | GSE197351 | GEO
Project description:A role of chromatin in plant memory of environmental stress has been proposed. In this study ChIP-Seq was employed to investigate whether a transient mild salt treatment of Arabidopsis thaliana plant at seedling stage (M-^Qpriming treatmentM-^R: 50 mM NaCl for 24 hours) altered genome-wide profiles of four histone modifications; H3K4me2, H3K4me3, H3K9me2 and H3K27me3. Comparison of histone modification profiles between primed and non-primed plants harvested immediately after the priming treatment showed differences in all histone modifications but were strongest and most abundant for H3K27me3. We subsequently explored whether these changes were maintained over an extensive period of growth in control conditions. Additional ChIP-Seq analysis showed that differences in the H3K27me3 profiles between primed and non-primed plants were still apparent after a growth period of ten days in control conditions. The results provide first indication for a potential role of H3K27me3 in long-term somatic memory of abiotic stress events in plants. The obtained dataset was compared with RNA-seq data measured in the same plant material (see parallel submission of RNA-Seq data in ArrayExpress: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1668).
2013-06-01 | E-MTAB-1663 | biostudies-arrayexpress
Project description:Plant volatiles can mediate plant-plant communication in the sense that plants attacked by herbivores can signal their unattacked neighbors of danger by emitting HIPVs. We call this the priming effect. Since the plant defense response is a systematic process involving numerous pathways and genes,to characterize the priming process, a time course study using a genome-wide microarray may provide more accurate information about the priming process. Furthermore, to what extent do the priming process and direct defense share similar gene expression profiles or pathways are also not clear. We used microarray to detect the priming effect of plant volatiles to healthy Arabidopsis thaliana, and the effect of direct leafminer feeding to Arabidopsis thalianas. A system using Lima bean plants, from which HIPVs can be effectively induced by leafminer feeding, as emitters and Arabidopsis thaliana as receivers is used to track the priming process between neighbor plants. The Arabisopsis thaliana seedlings were treated by volatiles from leafminer fed lima bean for 24h or 48h for RNA extraction and hybridization on Affymetrix microarrays. The Arabisopsis thaliana seedlings fed by leafminer directly were also collected The for RNA extraction and hybridization on Affymetrix micorarrays. We want to explore the response of Arabidopsis thaliana to priming volatiles during a 24h-48h time course. We also want to compare the effect of priming and direct leafminer feeding.
2013-09-24 | E-GEOD-33505 | biostudies-arrayexpress
Project description:Salt priming A. thaliana RNA-Seq
| PRJEB1937 | ENA
Project description:Peanut (Arachis hypogaea L.) is considered as a moderately salt-sensitive species and thus soil salinity can be a limiting factor for peanut cultivation. To gain insights into peanut plant physiology in response to salt stress and alleviation, we comprehensively characterized leaf relative electrolyte leakage (REC), photosynthesis, leaf transpiration, and metabolism of plants under salt stress and plants that were subjected to salt stress followed by salt alleviation period. As expected, we found that REC levels were higher when plants were subjected to salt stress compared with the untreated plants. However, in contrast to expectations, REC was even higher compared with salt treated plants when plants were transferred from salt stress to standard conditions. To decipher REC variation in response to salt stress, especial during the recovery, metabolite, and transcript variations were analyzed by GC/MS and RNA-seq method, respectively. Ninety two metabolites, among total 391 metabolites identified, varied in response to salt and 42 metabolites responded to recovery specially. Transcriptomics data showed 1,742 in shoots and 3,281 in roots transcript varied in response to salt stress and 372 in shoots and 1,386 transcripts in roots responded specifically to recovery, but not salt stress. Finally, 95 transcripts and 1 metabolite are indicated as candidates involved in REC, photosynthesis, transpiration, and Na+ accumulation variation were revealed by using the principal component analysis (PCA) and correlation analysis. This study provides valuable information on peanut response to salt stress and recovery and may inspire further study to improve salt tolerance in peanut germplasm innovation.
2019-03-19 | MTBLS583 | MetaboLights
Project description:Ginseng is one of the well-known medicinal plants, exhibiting diverse medicinal effects. Its roots possess anticancer and anti-aging properties and are being used in the medical systems of East Asian countries. Ginseng is grown in low-light and low-temperature conditions and its growth is strongly inhibited at temperatures above 25 ℃. However, the molecular responses of ginseng to heat stress are currently poorly understood, especially at protein level. Therefore, here we utilized a shotgun proteomics approach to investigate the effect of heat stress on ginseng leaves. Total proteins were isolated from control (25 ℃) and ginseng plants exposed to 35 ℃ for 1 and 3 days and subjected to in-solution trypsin digestion. A total of 3,359 ginseng proteins were identified when searched in an in-house developed RNA-seq (PAC-BIO) database.
2018-12-11 | PXD009124 | Pride
Project description:The first GSSM of V. vinifera was reconstructed (MODEL2408120001). Tissue-specific models for stem, leaf, and berry of the Cabernet Sauvignon cultivar were generated from the original model, through the integration of RNA-Seq data. These models have been merged into diel multi-tissue models to study the interactions between tissues at light and dark phases.
2024-09-02 | MODEL2408160001 | BioModels