Ontology highlight
ABSTRACT:
PROVIDER: PRJNA512054 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8375650_1.fastq.gz | Fastqsanger.gz | |||
| SRR8375650_2.fastq.gz | Fastqsanger.gz | |||
| SRR8375660_1.fastq.gz | Fastqsanger.gz | |||
| SRR8375660_2.fastq.gz | Fastqsanger.gz | |||
| SRR8375670_1.fastq.gz | Fastqsanger.gz |
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Project description:Korean ginseng (Panax ginseng Meyer) has long been cultivated as an important medicinal plant. Drought results from the moderate water loss, which primarily impairs the growth of ginseng and reduction of yield loss. However, basis of biological clues to understanding the accurate mechanisms related to drought stress in proteome level are still elusive. Therefore, we carried out label-free quantitative proteomic analysis using ginseng roots subjected to drought stress which was grown at less than 10% soil moisture for two weeks, compared with normal ginseng which was grown at 25% soil moisture. The acquired proteins were carried out label-free proteomic analysis using LC-MS/MS. This approach led to the identification of total 2,471 proteins, and out of 195 proteins showed significant modulation. Functional classification revealed that proteins related to secondary metabolites, calcium signaling, and photosynthesis were enriched in control sample (cluster_1), while proteins associated with stress responsive, redox, electron transport, and protein synthesis were mainly dominated in cluster_2 (drought stress condition). Taken together, our results provided an overview of the drought-induced proteomic changes in ginseng root, and it is correlated with physiological changes, contributing to reveal potential marker at proteome level in ginseng.
2023-09-21 | PXD028602 | Pride
Project description:In order to research the ginseng leaf-stem gene expression profiles of and dig out its function genes in the leaf-expansion period, the transcriptomic sequencing technology was set up the first time for five years the transcription of the Panax ginseng leaf-stem in the leaf-expansion period.
2012-07-31 | E-MTAB-937 | biostudies-arrayexpress
Project description:Panax ginseng C.A. Meyer is one of the most popular medicinal herbs. In order to research the genes that related to the flowering period of ginseng, and find out the antifungal proteins and transcription factors that combat various biotic and abiotic stress, a cDNA sample was prepared from the flowering period ginseng root of a five-year-old plant and sequenced using the Illumina sequencing platform. In this study, we produced nearly 40 million sequencing reads. These reads were assembled into 134,045 contigs using Trinity software (mean size: 282 bp). Based on a similarity search with known proteins, we identified 79,307 sequences with a cut-off E-value of 10-5. Assembled sequences were then annotated using gene ontology (GO) terms, clusters of orthologous group (COG) classifications and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways respectively.
2014-07-25 | E-MTAB-1239 | biostudies-arrayexpress
Project description:Panax ginseng C.A. Meyer is a precious Chinese herbal medicine belonging to the Araliaceae family. Because ginseng is extremely taboo, it seriously restricts the sustainable development of the ginseng industry. The allelopathic effect of triterpenoid saponins is one of the important incentives for continuous cropping disorders. However, there are few studies on the mechanism of allelopathic autotoxicity of triterpenoid ginsenosides. Therefore, this study took ginseng hairy roots as the research object, exogenously added ginsenoside Ro to regulate the growth of hairy roots, and measured the changes in its physiological and saponin content. It was found that ginseng hairy roots grew significantly under Ro-0.5 mg/L stress. Inhibition, the specificity of root tip cell injury was obvious, promoted the accumulation of endogenous hormones IAA and SA, and inhibited the accumulation of ABA and JA. The accumulation of ginsenosides was significantly inhibited (except Rg3) under Ro-0.5 mg/L stress. The mRNA analysis of the Ro-0.5 mg/L group and CK group showed that the differentially expressed genes were mostly concentrated in the hormone signal transduction pathway. The genes ARF7 and EFM were up-regulated, and XTH23 and ZOX1 were down-regulated, which can be used as important candidates for hormone-responsive continuous cropping disorders. Gene. 74 differentially expressed miRNAs were identified based on miRNA sequencing, of which 22 were up-regulated and 52 were down-regulated. The target genes of ptc-miR156k_L+1, mtr-miR156b-5p, gma-miR156a_R+1, and mtr-miR156e were all TRINITY_DN14567_c0_g4, TRINITY_DN14567_c0_g4 is a gene in the plant hormone signal transduction pathway, and the four miRNAs are all negatively correlated with mRNA, indicating that ptc-miR156k_L+1, mtr-miR156b-5p, gma-miR156a_R+1, and mtr-miR156e are very likely involved in ginseng Response to continuous cropping disorders and regulation of ginsenoside synthesis. Our findings will provide a useful platform for unraveling the continuous cropping barrier of ginseng and new insights into the genetic engineering of plant stress responses.
2022-08-27 | GSE212097 | GEO
Project description:Panax ginseng roots are well known for their medicinal properties and have been used in Korean and Chinese traditional medicines for 1000s of years. However, the medicinal value of P. ginseng fruits remain poorly characterized. Using gas chromatography-time of flight mass spectrometry (GC-TOF MS), 66 metabolites including amino acids, sugars, organic acids, phenolic acids, phytosterols, tocopherols, and policosanols were identified and quantified. Some of these are well known medicinal compounds and were not previously identified in ginseng. Interestingly, the concentration of almost all metabolites was higher in the Chunpoong and Gumpoong cultivars. Parallel comparison of the four cultivars also revealed higher amounts of the medicinal metabolites in Chunpoong and Gumpoong cultivars. Taken together, our results demonstrate that ginseng fruits are a rich source of medicinal compounds with potential beneficial health effects.
2016-11-18 | MTBLS350 | MetaboLights
Project description:Nitrogen is one of the essential elements for plant growth. NH4+ and NO3- are two major forms of absorbing element N for higher plants. In this study we found that the growth of Panax notoginseng is inhibited when only adding ammonium nitrogen fertilizer, and adding nitrate fertilizer can alleviate the toxicity caused by ammonium. We use RNA-seq to identify genes that are related to the alleviated phenotypes after introducing NO3- to Panax notoginseng roots under NH4+ stresses. Twelve RNA-seq profiles in four sample groups, i.e., control, samples treated with NH4+, samples treated with NO3- only, and treated with both NH4+ and NO3- were obtained and analyzed to identify deregulated genes in samples with different treatments. ACLA-3 gene is downregulated in NH4+ treated samples, but is upregulated in samples treated with NO3- and with both NH4+ and NO3-, which is further validated in another set of samples using qRT-PCR. Our results suggest that unbalanced metabolism of nitrogen and nitrogen is the main cause of ammonium poisoning in roots of Panax notoginseng, and NO3- may significantly upregulate the activity of ACLA-3 which subsequently enhances the citrate cycle and many other metabolic pathways in Panax notoginseng root. These potentially increase the integrity of the Panax notoginseng roots. Our results suggest that introducing NO3- fertilizer is an effective means to prevent the occurrence of toxic ammonium in Panax notoginseng root.
2019-12-31 | GSE112437 | GEO
Project description:Salt stress is one of the major abiotic stresses affecting the yield of ginseng (Panax ginseng C. A. Meyer). The objective of this study was to identify proteins of ginseng, which is responsive in salt stress. In this direction, ginseng plants of different growth stages (3, 4 and 5 years), were grown in the hydroponic conditions and exposed to 5 ds/m salt concentration. The secreted proteins, collected from the water, at 0, 24, 72 and 120 hours after exposure were used for the proteome analysis using shotgun approaches. Through the shotgun proteomics, a total of 155 and 88 secreted proteins were identified by searching in two RNA-sequencing (RNA-seq) database, respectively.
2022-11-17 | PXD010322 | Pride
Project description:Here, we investigated the similarities and differences in the volatile profiles of plants and their holobionts. The VOC profiles of fruits, leaves, stems, and roots from seven plant species, including Turmeric seedlings (Curcuma longa), Artemisia capillaris, Euscaphis japonica, Panax ginseng, Clerodendrum trichotomum, Pyracantha koidzumii, and Japanese cypress (Chamaecyparis obtusa), as well as the VOCs of culturable microbial fractions characterized via GCMS-based metabolomics approaches
2025-02-19 | MSV000097162 | MassIVE
Project description:We reported the first study of transcriptome analyses using the Illumina HiSeq4000 platform for low temperature stress on callus of Panax ginseng. In total, over 546,139,358 clean reads were produced and 44,953 unigenes were assembled; Q30 results are above 95%. Differentially Expressed Gene analysis identified 9,435 and 6,345 unigenes which were expressed either higher or lower in treatment group samples(T) when compared with control group (C). We can find that the differential gene is more expressed in the T_4 vs C_4 group than in the other comparison groups, thus demonstrating that the differential gene expression is more active. Chilling treatment for 2th-6th day, the total saponin content of the treatment group was significantly higher than that of the control group, and reached the maximum on the forth day of treatment, and then gradually decreased. There is a synergistic trend between differential gene expression and saponin content at different treatment times. The accuracy of these de novo sequences was validated by RT-qPCR analysis. A number of transcription factor genes were also filtrated that presumably related to environmental cold stress. These data will enrich our knowledge of triterpenoid saponin biosynthesis and provide a theoretical foundation for molecular research on Panax ginseng.
2019-08-08 | GSE122396 | GEO