Ontology highlight
ABSTRACT:
PROVIDER: PRJNA516241 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8468083_1.fastq.gz | Fastqsanger.gz | |||
| SRR8468083_2.fastq.gz | Fastqsanger.gz |
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Project description:Licorice (Glycyrrhiza uralensis Fisch) flavonoids have many pharmacological effects, as the main chemical component of licorice, its content directly affects the quality of licorice. Methyl jasmine (MeJA) is an important signaling molecule in the secondary metabolic pathway of plants, but the biological mechanisms that stimulating the production of licorice flavonoids and the related changes in transcriptome are still less studied. In this research, the expression of two key enzyme genes: Chalcone synthase (CHS) and Cinnamate 4-hydroxylase (C4H) in the biosynthesis pathway of licorice flavonoids was determined, and it was significantly different after 9 hours of MeJA induction. The transcriptome profiles of licorice cells at 9 hours after MeJA treatment were analyzed to investigate the transcriptional alterations of licorice cell in response to MeJA elicitation by “RNA-seq”. 151, 529 transcripts (200 bp in length) of cDNA from the samples were generated, and 116, 907 unigenes were found. MeJA appeared to stimulate a large number of genes involved in several relevant functional categories, such as carbohydrate metabolism and encoding transcription factors, 11 MYB transcription factors expressed significant differences were screened. This comprehensive description of gene expression information could help elucidate the molecular mechanism of MeJA-mediated biosynthesis of licorice flavonoids and MeJA-regulated network formation.
2019-08-01 | GSE128503 | GEO
Project description:Background: Dendrobium officinale, an endangered Chinese herb, has extensive therapeutic effects and contains bioactive ingredients including a large number of polysaccharides and alkaloids, and minimal flavonoids. Firstly, this study attempts to obtain the protocorm-like bodies of this plant through tissue culture to produce the main secondary metabolites whose distribution in each organelle and protocorm like bodies is analyzed. Then, analysis of the correlation between comparative transcriptome sequence and the metabolite content in different organs enables the discovery of putative genes encoding enzymes involved in the biosynthesis of polysaccharides and alkaloids, and flavonoids. Results: The optimum condition for protocorm-like bodies (PLBs) induction and propagation of D. officinale is established. For protocorm induction, we use the seed as the explant, and the optimum medium formula for PLBs propagation is 1/2 MS + α-NAA 0.5 mg·L-1 +6-BA 1.0 mg·L-1 + 2, 4-D 1.5-2.0 mg·L-1 + potato juice 100 g·L-1. The distribution of polysaccharides, alkaloids and flavonoids in D. officinale organs was clarified. Stems, PLBs and leaves have the highest content of polysaccharides, alkaloids and flavonoids, respectively. PLBs replace organs to produce alkaloids in D. officinale, and naringenin was only produced in stem. Hot water extraction (HWE) method was found outperforming the ultrasound-assisted extraction (UAE) method for polysaccharides from D. officinale. A comparative transcriptome analysis of the protocorm-like bodies and leaves of D. officinale showed genes encoding enzymes involved in polysaccharides, alkaloids and flavonoids biosynthetic pathway were differentially expressed. Putative genes encoding enzymes involved in polysaccharides, alkaloids and flavonoids synthetic pathway were identified. Notably, genes encoding enzymes of strictosidine beta-glucosidase, geissoschizine synthase and vinorine synthase in alkaloids biosynthesis of D. officinale are first reported. Conclusions: Our works, especially the identification of candidate genes encoding enzymes involved in metabolites biosynthesis will help to explore and protect the endangered genetic resources and will also facilitate further analysis of the molecular mechanism of secondary metabolites’ biosynthesis in D. officinale.
2021-04-24 | GSE155403 | GEO
Project description:Background: Hazy weather significantly increase air pollution and affect light intensity which may also affect medicinal plants growth. Syringa oblata Lindl. (S. oblata), an effective anti-biofilm medicinal plants, is also vulnerable to changes in plant photoperiods and other abiotic stress responses. Rutin, one of the flavonoids, is the main bioactive ingredient in S. oblata that inhibits Streptococcus suis biofilm formation. Thus, the present study aims to explore the biosynthesis and molecular basis of flavonoids in S. oblata in response to different light intensity. Results: In this study, it was shown that compared with natural (Z0) and 25% ~ 35% (Z2) light intensities, the rutin content of S. oblata under 50% ~ 60% (Z1) light intensity increased significantly. In addition, an integrated analysis of metabolome and transcriptome was performed using light intensity stress from two kinds of light intensities which S. oblata was subjected to: Z0 and Z1. The results revealed that differential metabolites and genes were mainly related to the flavonoid biosynthetic pathway. We found out that 13 putative structural genes and a transcription factor bHLH were significantly up-regulated in Z1. Among them, integration analysis showed that 3 putative structural genes including 4CL1, CYP73A and CYP75B1 significantly up-regulated the rutin biosynthesis, suggesting that these putative genes may be involved in regulating the flavonoid biosynthetic pathway, thereby making them key target genes in the whole metabolic process. Conclusions: The present study provided helpful information to search for the novel putative genes that are potential targets for S. oblata in response to light intensity.
2019-11-25 | GSE137862 | GEO
Project description:The study assigns a key regulatory role of FaGAMYB in the initiation of strawberry receptacle ripening and acting upstream of the known regulator ABA. Down-regulation of FaGAMYB caused an arrest in the ripening of receptacle and inhibited colour formation. Consistent with this, several transcription factors associated to the regulation of flavonoids biosynthetic pathway showed altered expression. FaGAMYB silencing also caused a reduction of ABA biosynthesis and sucrose content. Interestingly exogenous ABA application to RNAi transformed receptacle reversed most defects caused by FaGAMYB down53 regulation. Transient silencing of FaGAMYB using RNAi and further determination of changes in (1) global gene expression by RNAseq, and (2) composition of primary and secondary metabolites has been used to investigate the role played by this gene during the development of the receptacle.
2015-04-14 | E-MTAB-3496 | biostudies-arrayexpress
Project description:Scutellaria baicalensis Georgi, a perennial herb, is an important medicinal plant that possesses broad pharmacological actions and contains flavonoids with good bioactivities such as anti-inflammation, anti-bacteria and anti-tumor. However, little is known on the molecular processes responsible for the medical properties of this species, owing to the absence of genomic resources such as available sequences of key enzyme genes in biosynthetic pathways. In this study, the RNA sequencing data of S. baicalensis were first generated and used for transcriptome analysis.
2022-05-31 | GSE132061 | GEO
Project description:Dendrobium huoshanense C.Z. Tang et S.J. Cheng is a perennial epiphytic herb of family Orchidaceae, which main metabolites are polysaccharides, flavonoids, etc. Low temperature is the main environmental factor that limits the growth and development of plants, and even threatens the survival of plants. However, Changes that occur at the molecular level in response to low temperatures are poorly understood in D. huoshanense. To understand the molecular mechanism of cold tolerance, we performed transcriptomic analysis on two time points of 0 d (control group) and 7 d (cold stress group). A total of 37.63 Gb transcriptomic data were generated using the MGI 2000 platform. These reads were assembled into 170,754 transcripts, and 23,724 differentially expressed genes (DEGs) were obtained. Pathway analysis indicated that “flavonoid biosynthesis”, “anthocyanin biosynthesis”, “flavone and flavonol biosynthesis”, and “plant hormone signal transduction” might play a vital role in D. huoshanense responses to cold stress. Several important pathways genes such as genes encoding polysaccharides, flavonoid, and plant hormone-signaling transduction kinase were identified under cold stress. In addition, the contents of mannose and total flavonoids increased under cold stress. Twelve DEGs in polysaccharides, flavonoid, and hormone pathways were selected from transcriptome analysis for quantitative real-time PCR (qRT-PCR) validation. Our results provide a transcriptome database and candidate genes for further study of D. huoshanense cold stress.
2022-11-10 | GSE217439 | GEO
Project description:Transcript analysis of Calotropis procera seedling for elucidation of biosynthetic pathway
| PRJNA257023 | ENA
Project description:Metabolic syndrome is an important public concern and demand for effective therapeutic strategies. Abdominal obesity, especially an increase in the visceral adipose tissue, is the main cause of this syndrome. Flavonoids are expected to improve risk factors for metabolic syndrome. Bilberry, original species of blueberry containing anthocyanidin flavonoids have been used for centuries in Europe to ameliorate the symptoms of diabetes, but their effects and the mechanisms on lipid accumulation of adipocyte cells are not well defined. In the present study, we investigated effects of the Bilberry extract on differentiation of adipocytes using 3T3-L1 adipocyte cell line. Exposure to Bilberry extract during the early period of adipogenesis (6 days) was significantly inhibited adipocyte differentiation of 3T3-L1. During this period, Bilberry extract greatly down-regulated the mRNA levels of the key adipogenesis-associated markers peroxisome proliferator-activated receptor-γ (PPARγ). Furthermore, Bilberry extract significantly decreased expression of the transcription factor Sterol Regulatory Element Binding Protein 1c (SREBP1c), which plays a central role in adipocyte differentiation including the induction of PPARγ. The expression of SREBP1c is remarkably enhanced in response to insulin, thus raises the possibility that Bilberry extract might inhibit the Insulin pathway. So, We investigated whether Billberry extract and anthocyanidines turned the insulin signaling pathway using microarray. As a result, Gene Set Enrichment Analysis (GSEA) shows that these additives turned insulin signaling pathway certainly.
2011-04-01 | GSE21157 | GEO
Project description:In vivo assembly of sorgoleone biosynthetic pathway
| PRJNA660791 | ENA