Ontology highlight
ABSTRACT:
PROVIDER: PRJNA786451 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17184301_1.fastq.gz | Fastqsanger.gz | |||
| SRR17184301_2.fastq.gz | Fastqsanger.gz | |||
| SRR17184302_1.fastq.gz | Fastqsanger.gz | |||
| SRR17184302_2.fastq.gz | Fastqsanger.gz | |||
| SRR17184303_1.fastq.gz | Fastqsanger.gz |
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Project description:transcriptome analyses reveal the flavonoids changes and biosynthesis mechanisms in different organs of Hibiseu Manihot L.
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Project description:Disanthus cercidifolius var. longipes is an important but rare tree species used in plant studies due to its highly ornamental leaves. However, its sciophilous nature and low photosynthetic efficiency make it difficult to cultivate on a large scale. In this study, we collected leaves of D. cercidifolius var. longipes at three developmental stages to assess its photosynthetic capacity and photoprotection mechanisms. Primary metabolites were quantified and separate and joint analyses of the transcriptome and metabolome were carried out. Our results revealed significant changes in the contents of flavonoids, free amino acids, and other substances during development. Metabolome and transcriptome analyses showed that the photosynthesis-related pathways changed rapidly, increasing at first and then decreasing. Under low photosynthetic capacity, flavonoids and anthocyanins were synthesized to achieve photoprotection, with synthesis of these compounds and other pathway-related genes and metabolites showing a significant increase. Total flavonoids also followed this trend. Our findings provide insights into the shade-loving plant's photoprotection mechanisms and nutrient synthesis strategy, which involve quick nutrient production over a short period. This study could aid in developing D. cercidifolius var. longipes into a street or foliage tree through selective breeding.
2024-01-29 | GSE254419 | 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.
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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.
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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.
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Project description:Metabolomic analyses reveal the specific array of metabolites present in a cell type or tissue at any given time. Multiple lines of evidence indicate that metabolites provide a readout of ongoing cellular functions, and changes in the metabolome correlate with specific biological processes1–4 as seen, for instance, during cellular differentiation. These changes are potentially associated with the regulation of signaling pathways and gene expression networks that are critical to alter cellular identity5–7. However, it is less clear whether specific metabolites or metabolic pathways can drive changes in cellular identity. To identify metabolites engaged with cell state transitions, we performed metabolomic analyses at the earliest stages of cellular differentiation and uncovered metabolites transiently upregulated just as the first transcriptional changes emerged. Specifically, we observed a wave of one-carbon metabolism conserved between three different multipotent stem cell types. Treatment of fully differentiated cells with these metabolites caused the loss of mature identity and transition toward progenitor-like states, thus demonstrating that the metabolome plays a causative role in initiating and modulating cell fate. Our studies reveal a metabolic intervention that can reprogram cellular phenotypes and could potentially be applied in regenerative medicine applications
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