Combined Metabolome and Transcriptome Analysis of Creamy Yellow and Purple Colored Panax notoginseng Roots
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ABSTRACT:
SUBMITTER: He M
PROVIDER: S-EPMC10607970 | biostudies-literature | 2023 Oct
REPOSITORIES: biostudies-literature
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Project description:BackgroundPanax notoginseng (Burk.) F.H. Chen is one of the most highly valued medicinal plants in the world. The major bioactive molecules are triterpene saponins, which are also known as ginsenosides. However, its large genome size has hindered the assembly of a draft genome by whole genome sequencing. Hence, genomic and transcriptomic details about P. notoginseng, especially its biosynthetic pathways and gene expression in different parts of the plant, have remained largely unknown until now.ResultsIn this study, RNA sequencing of three different P. notoginseng tissues was performed using next generation DNA sequencing. After assembling the high quality sequencing reads into 107,340 unigenes, biochemical pathways were predicted and 9,908 unigenes were assigned to 135 KEGG pathways. Among them, 270 unigenes were identified to be involved in triterpene saponin biosynthesis. In addition, 350 and 342 unigenes were predicted to encode cytochrome P450s and glycosyltransferases, respectively, based on the annotation results, some of which encode enzymes responsible for the conversion of the triterpene saponin backbone into different ginsenosides. In particular, one unigene predominantly expressed in the root was annotated as CYP716A53v2, which probably participates in the formation of protopanaxatriol from protopanaxadiol in P. notoginseng. The differential expression of this gene was further confirmed by real-time PCR.ConclusionsWe have established a global transcriptome dataset for P. notoginseng and provided additional genetic information for further genome-wide research and analyses. Candidate genes involved in ginsenoside biosynthesis, including putative cytochrome P450s and glycosyltransferases were obtained. The transcriptomes in different plant tissues also provide invaluable resources for future study of the differences in physiological processes and secondary metabolites in different parts of P. notoginseng.
| S-EPMC4399409 | biostudies-literature
Project description:BACKGROUND:Taproot thickening is a complex biological process that is dependent on the coordinated expression of genes controlled by both environmental and developmental factors. Panax notoginseng is an important Chinese medicinal herb that is characterized by an enlarged taproot as the main organ of saponin accumulation. However, the molecular mechanisms of taproot enlargement are poorly understood. RESULTS:A total of 29,957 differentially expressed genes (DEGs) were identified during the thickening process in the taproots of P. notoginseng. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment revealed that DEGs associated with "plant hormone signal transduction," "starch and sucrose metabolism," and "phenylpropanoid biosynthesis" were predominantly enriched. Further analysis identified some critical genes (e.g., RNase-like major storage protein, DA1-related protein, and Starch branching enzyme I) and metabolites (e.g., sucrose, glucose, fructose, malate, and arginine) that potentially control taproot thickening. Several aspects including hormone crosstalk, transcriptional regulation, homeostatic regulation between sugar and starch, and cell wall metabolism, were identified as important for the thickening process in the taproot of P. notoginseng. CONCLUSION:The results provide a molecular regulatory network of taproot thickening in P. notoginseng and facilitate the further characterization of the genes responsible for taproot formation in root medicinal plants or crops.
| S-EPMC6815444 | biostudies-literature
Project description:Four new protopanaxatriol-type triterpenes (1-2) and glucosides (3-4), were isolated from the rot roots of Panax notoginseng (Burk.) Chen, along with four known ones (5-8). Their structures were elucidated on the basis of extensive spectroscopic analysis (HRESIMS, NMR, UV, IR, and OR) and acidic hydrolysis. The possible transformation pathway of these compounds were also speculated from ginsenoside Rg1. Compound 1, with a unique α,β-unsaturated ketene in its side chain, showed significant inhibitory effects against NO production on Murine macrophage cells (IC50 = 4.12 ± 0.20 μM) and comparable cytotoxicities against five human cancer cell lines (myeloid leukemia HL-60, lung cancer A-549 cells, hepatocellular carcinoma SMMC7721, breast cancer MCF-7, and colon cancer SW480) to positive control, cisplatin (DDP).
| S-EPMC6646631 | biostudies-literature
Project description: Not available
| S-EPMC10913227 | biostudies-literature
Project description:BackgroundPanax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential.MethodsRNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed.ResultsAssemblies were generated from ∼85 million and ∼77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases. We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots.ConclusionThis study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use.
| S-EPMC4213845 | biostudies-literature
Project description:Panax notoginseng (P. notoginseng) is an invaluable perennial medicinal herb. However, the roots of P. notoginseng are frequently subjected to severe damage caused by root-knot nematode (RKN) infestation. Although we have observed that P. notoginseng possessed adult-plant resistance (APR) against RKN disease, the defense response mechanisms against RKN disease in different age groups of P. notoginseng remain unexplored. We aimed to elucidate the response mechanisms of P. notoginseng at different stages of development to RKN infection by employing transcriptome, metabolome, and histochemistry analyses. Our findings indicated that distinct age groups of P. notoginseng may activate the phenylpropanoid and flavonoid biosynthesis pathways in varying ways, leading to the synthesis of phenolics, flavonoids, lignin, and anthocyanin pigments as both the response and defense mechanism against RKN attacks. Specifically, one-year-old P. notoginseng exhibited resistance to RKN through the upregulation of 5-O-p-coumaroylquinic acid and key genes involved in monolignol biosynthesis, such as PAL, CCR, CYP73A, CYP98A, POD, and CAD. Moreover, two-year-old P. notoginseng enhanced the resistance by depleting chlorogenic acid and downregulating most genes associated with monolignol biosynthesis, while concurrently increasing cyanidin and ANR in flavonoid biosynthesis. Three-year-old P. notoginseng reinforced its resistance by significantly increasing five phenolic acids related to monolignol biosynthesis, namely p-coumaric acid, chlorogenic acid, 1-O-sinapoyl-D-glucose, coniferyl alcohol, and ferulic acid. Notably, P. notoginseng can establish a lignin barrier that restricted RKN to the infection site. In summary, P. notoginseng exhibited a potential ability to impede the further propagation of RKN through the accumulation or depletion of the compounds relevant to resistance within the phenylpropanoid and flavonoid pathways, as well as the induction of lignification in tissue cells.
| S-EPMC10539906 | biostudies-literature
Project description:Colored potatoes with red and purple skin or flesh possess significant nutritional value and health benefits due to their rich anthocyanin content. To investigate the genetic mechanisms underlying color formation, the high-anthocyanin-content purple-skinned and purple-fleshed potato line 15-12-16, and the white-skinned and white-fleshed Xiazhai 65 variety were used for ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS) analysis, which was conducted to identify and quantify anthocyanins. RNA sequencing was performed to analyze the transcriptome. The results indicated a significant upregulation of genes within the anthocyanidin biosynthesis pathway in the purple potato, while these genes were either downregulated or absent in the white potato. The bHLH, MYB, and WRKY gene families exhibited a greater number of regulatory members, suggesting their pivotal role in color formation. Integrated analysis of the transcriptional and metabolic revealed that 12 differentially expressed genes (DEGs) related to the anthocyanidin biosynthetic had a significant correlation with 18 anthocyanin metabolites. Notably, the key gene St5GT in the anthocyanidin biosynthesis pathway was markedly upregulated in the purple skin and flesh. Furthermore, the overexpression of St5GT (PGSC0003DMG400004573) in tobacco contributed to anthocyanin accumulation. The expression of 10 DEGs was validated through quantitative real-time PCR. In conclusion, these findings provide new insights into anthocyanin biosynthesis and accumulation in purple potatoes, offering valuable candidate genes for the future breeding of colored potatoes.
| S-EPMC11641821 | biostudies-literature
Project description:Purple turnip Brassica rapa ssp. rapa is highly appreciated by consumers but the metabolites and molecular mechanisms underlying the root skin pigmentation remain open to study. Herein, we analyzed the anthocyanin composition in purple turnip (PT) and green turnip (GT) at five developmental stages. A total of 21 anthocyanins were detected and classified into the six major anthocynanin aglycones. Distinctly, PT contains 20 times higher levels of anthocyanins than GT, which explain the difference in the root skin pigmentation. We further sequenced the transcriptomes and analyzed the differentially expressed genes between the two turnips. We found that PT essentially diverts dihydroflavonols to the biosynthesis of anthocyanins over flavonols biosynthesis by strongly down-regulating one flavonol synthase gene, while strikingly up-regulating dihydroflavonol 4-reductase (DFR), anthocyanidin synthase and UDP-glucose: flavonoid-3-O-glucosyltransferase genes as compared to GT. Moreover, a nonsense mutation identified in the coding sequence of the DFR gene may lead to a nonfunctional protein, adding another hurdle to the accumulation of anthocyanin in GT. We also uncovered several key members of MYB, bHLH and WRKY families as the putative main drivers of transcriptional changes between the two turnips. Overall, this study provides new tools for modifying anthocyanin content and improving turnip nutritional quality.
| S-EPMC6769466 | biostudies-literature
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:Although Panax notoginseng (PN) roots in raw and steamed forms were historically supposed to be different in the efficacies, the raw materials and steamed ones were often undifferentiated in the use and market circulation, which might bring unstable curative effects or even adverse reactions. To uncover chemical constituents responsible to different activities of raw and steamed PN, chemometrics analyses including partial least squares regression (PLSR) and multi-linear regression analysis (MLRA) were used to establish the relationships between the chromatographic fingerprints and activities of PN samples. Chemical fingerprints of PN were determined by HPLC. Anticoagulant and antioxidant activities were evaluated by the thromboplastin inhibiting test and hydroxyl radical scavenging assay, respectively. Results showed that there was a significant difference in the chemical composition between raw and steamed PN, which could be discriminated by principle component analysis according to different steaming temperatures. Compared with the steamed PN, raw PN exhibited stronger anticoagulation and weaker antioxidation. By chemometrics analyses, notoginsenoside R1, ginsenosides Rg1, Re, Rb1, and Rd were found to be the major active constituents of raw PN, whereas ginsenosides Rh1, Rk3, Rh4, and 20(R)-Rg3 had the key role in the activities of steamed PN, which could be used as new markers for the quality control (QC) of steamed PN.
| S-EPMC5651511 | biostudies-literature