Ontology highlight
ABSTRACT:
PROVIDER: PRJNA609035 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11192643_1.fastq.gz | Fastqsanger.gz | |||
| SRR11192643_2.fastq.gz | Fastqsanger.gz | |||
| SRR11192644_1.fastq.gz | Fastqsanger.gz | |||
| SRR11192644_2.fastq.gz | Fastqsanger.gz | |||
| SRR11192645_1.fastq.gz | Fastqsanger.gz |
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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
Project description:Platycodon grandiflorus is a perennial traditional Chinese herb, which has more than 100 compounds including triterpenoid saponins, polysaccharides and phenolic acid etc. In this study, a (L9(34)) orthogonal experiment determined the optimal explants is stem with nodes and the optimum full medium is MS + NAA 1.0 mg/L + 6-BA 0.5 mg/L as best protocol for callus induction of P. grandiflorus.The content of platycodin D, platycoside E and total polysaccharides between callus and plant organs is significantly difference, and the distribution of platycodin D, platycoside E and total polysaccharide in whole plant has been clarified. Meanwhile, the content of platycodin D and total polysaccharide were found higher in calli than in leaves or the whole plant. While, the content of platycoside E in calli is very lower than in leaves. In order to screen candidate genes involved in platycoside E and platycodin D conversion, a RNA-Seq analysis between calli and leaves was performed. Correlating the content of platycodin D and platycoside E between calli and leaves with the gene expression level involving in triterpenoid saponin biosynthesis pathway, four cluster genes with high amino acid similarity were screened as the putative sequences of β-Glucosidase gene for converting platycoside E to platycodin D. It was found that the expression level of genes encoding enzymes involved in saponins and polysaccharides biosynthesis was co-expression with the content of the corresponding metabolite. Besides, some transcription factors predicted to regulate the expression of key enzymes involving in triterpernoid saponins and polysaccharides biosynthesis pathway of P. grandiflorus.
2020-07-15 | GSE153777 | GEO
Project description:In present study, Transcriptome analysis revealed unique differentially expressed genes (DEGs). including transcription factors (TFs), during root development in D. asperoides. In addition, α-linolenic acid metabolism, jasmonic acid (JA) biosynthesis, JA signal transduction, sesquiterpenoid and triterpenoid biosynthesis, and terpenoid backbone biosynthesis were prominently enriched.
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Project description:In hairy roots of the model legume Medicago truncatula the saponin production can be elicited by methyl jasmonate treatment. To identify genes potentially involved in saponin biosynthesis or its regulation we carried out transcript profiling by RNA-Seq of M. truncatula hairy roots treated with 100 μM of methyl jasmonate (dissolved in ethanol) for two or 24 hours. As control, M. truncatula hairy roots treated with an equivalent amount of ethanol were profiled.
2020-01-27 | E-MTAB-8697 | biostudies-arrayexpress
Project description:Purpose: Panax vietnamensis Ha et Grushv., which contains various valuable ginsenosides, is an important herbal medicine of Vietnam. However, it is an endangered species listed in Vietnam Red Data Book due to over-harvseting. Investigation about genomic or trancriptomic resources is one of the necessary activities to conserve P. vietnamensis Materials and Methods:. In this study, we sequenced the transcriptomes of 1-year-old P. vietnamensis from leaves and roots using Illumina NovaSeqTM6000 system. Results: A total of 60,254,062 and 64,588,528 reads was obtained and then assembled into 45,495 and 49,133 unigenes for leaves and roots, respectively. More than 60% unigenes from two organs were functional annotated using at least one database among Kyoto Encyclopedia of Genes and Genomes, Pfam, Gene Ontology, NCBI non-redundant Protein, and Evolutionary genealogy of genes. Further, the predominant transcripts of each cDNA library were analyzed for different gene expression identification. In addition, 457 unigenes encoding enzymes involved in triterpenoid saponin biosynthesis via the mavelonate (MVA) and the non-MVA (also named as MEP pathways) were discovered.
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2018-07-16 | PXD009352 | Pride
Project description:Purpose: To examine the gene expression within the spinach root tissues as a response to exposure to nanoparticles. Methods: Sequenced reads were processed using CLC Genomics Workbench 7.0. The reads were trimmed based on quality, length and ambiguity. Resulting reads were assembled into transcript assemblies. Sequence reads were mapped back to the constructed transcriptome. TAs were BLAST searched against a local blast database of coding sequences of Arabidopsis thaliana. Statistical analysis was performed using Baggerley’s test. Transcript assemblies were tested for gene enrichment using GO annotations and the functional categories were determined. MapMan was used to visualize gene expression data of TAs and study the biological pathways. Results: De novo assembly of the trimmed reads yielded 147,733 Transcript Assemblies (TA) with an average length of 645 bp. Largest TA was 16,379 bp. Approximately 89% of the quality trimmed reads from the different samples mapped successfully to the assembly reference. Gene expression data for spinach TAs homologous to Arabidopsis genes show upregulation of protein degradation pathways in the nano-ZnO treatment compared to the non-nanoZnO, this upregulation is coupled with a down regulation of the genes in the protein synthesis pathways crucial role in the spinach plant responses to ZnO nanoparticle exposure. Genes associated (REDOX, signaling and transcription factors) with responses to stresses (both abiotic and biotic) were upregulated upon exposure to ZnO nanoparticles. Additionally genes in biosynthesis pathways of jasmonate and gibberellins genes were up-regulated upon exposure to ZnO nanoparticles in spinach. Conclusions: A de novo transcriptome was developed for spinach. When spinach plants were exposed to ZnO nanoparticles, they seem to sense the nanoparticles similarly to external chemicals or pathogens and induced production of reactive oxygen species. Hormone signaling pathways were activated leading to the induced expression of hormones with different roles in defense.
2018-09-10 | GSE72912 | GEO
Project description:<p>Alcohol-associated fatty liver disease (AFLD) is driven by ethanol-induced metabolic dysregulation and hepatic inflammation, with gut dysbiosis and endotoxin-triggered innate immune activation implicated in disease progression. Platycodin D (PD), a triterpenoid saponin from Platycodon grandiflorum, has been reported to have antioxidant and immunomodulatory activities, but its efficacy and mechanisms in AFLD remain unclear. We hypothesized that PD alleviates AFLD by suppressing TLR4/NF-κB signaling, activating PPAR pathways, and remodeling gut microbiota and hepatic metabolites.</p>
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