Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1085099 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28288861_1.fastq.gz | Fastqsanger.gz | |||
| SRR28288861_2.fastq.gz | Fastqsanger.gz | |||
| SRR28288862_1.fastq.gz | Fastqsanger.gz | |||
| SRR28288862_2.fastq.gz | Fastqsanger.gz | |||
| SRR28288863_1.fastq.gz | Fastqsanger.gz |
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Project description:Methods: Panax notoginseng was used to treat MCAO model rats, and the differentially expressed genes between Panax notoginseng group and model group were identified by RNA SEQ, and the possible mechanism of Panax notoginseng in regulating ischemic stroke was analyzed
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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.
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Project description:The total RNA were extracted from tissues of roots from several plants of Panax notoginseng under CK and Cd stress treatment by using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. The purified PCR product was sequenced using Illumina Genome Analyzer II. The qualified reads were used to study of Panax notoginseng transcriptome under CK and Cd stress treatment.
2019-12-31 | GSE108698 | GEO
Project description:Recent results demonstrated that either non-coding or coding genes generate phased secondary small interfering RNAs (phasiRNAs) guided by specific miRNAs. Till now, there is no studies for phasiRNAs in Panax notoginseng (Burk.) F.H. Chen (P. notoginseng), an important traditional Chinese herbal medicinal plant species. Here we performed a genome-wide discovery of phasiRNAs and its host PHAS loci in P. notoginseng by analyzing small RNA sequencing profiles. Degradome sequencing profile was used to identify the trigger miRNAs of these phasiRNAs and potential targets of phasiRNAs. We also used RLM 5'-RACE to validate some of the identified phasiRNA targets. After analyzing 24 small RNA sequencing profiles of P. notoginseng, 204 and 90 PHAS loci that encoded 21 and 24 nucleotide (nt) phasiRNAs were identified. Furthermore, we found that phasiRNAs produced from some pentatricopeptide repeat-contain (PPR) genes target another layer of PPR genes as validated by both the degradome sequencing profile and RLM 5'-RACE analysis. We also find that miR171 with 21 nt triggers the 21 nt phasiRNAs from its conserved targets. We validated that some phasiRNAs generated from PPRs are functional by targeting other PPRs in trans. These results provide the first set of PHAS loci and phasiRNAs in P. notoginseng, and enhance our understanding of PHAS in plants.
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Project description:Adjusting planting density is a common agricultural practice used to achieve maximum yields. However, whether the quality of medicinal herbs can be improved by implementing appropriate planting densities is still uncertain. The medicinal crop <i>Panax notoginseng</i> was used to analyze the effects of planting density on growth and ginsenoside accumulation, and the possible mechanisms of these effects were revealed through metabonomics. The results showed that <i>P. notoginseng</i> achieved high ginsenoside accumulation at high planting densities (8 × 8 and 10 × 10 cm), while simultaneously achieved high biomass and ginsenoside accumulation at moderate planting density of 15 × 15 cm. At the moderate planting density, the primary metabolism (starch and sucrose metabolism) and secondary metabolism (the biosynthesis of phytohormone IAA and ginsenoside) of the plants were significantly enhanced. However, the strong intraspecific competition at the high planting densities resulted in stress as well as the accumulation of phytohormones (SA and JA), antioxidants (gentiobiose, oxalic acid, dehydroascorbic acid) and other stress resistance-related metabolites. Interestingly, the dry biomass and ginsenoside content were significantly lower at low densities (20 × 20 and 30 × 30 cm) with low intraspecific competition, which disturbed normal carbohydrate metabolism by upregulating galactose metabolism. In summary, an appropriate planting density was benefit for the growth and accumulation of ginsenosides in <i>P. notoginseng</i> by balancing primary metabolism and secondary metabolism.
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