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The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature.

ABSTRACT: BACKGROUND:Ginseng is a popular traditional herbal medicine in north-eastern Asia. It has been used for human health for over thousands of years. With the rise in global temperature, the production of Korean ginseng (Panax ginseng C.A.Meyer) in Korea have migrated from mid to northern parts of the Korean peninsula to escape from the various higher temperature related stresses. Under the high ambient temperature, vegetative growth was accelerated, which resulted in early flowering. This precocious phase change led to yield loss. Despite of its importance as a traditional medicine, biological mechanisms of ginseng has not been well studied and even the genome sequence of ginseng is yet to be determined due to its complex genome structure. Thus, it is challenging to investigate the molecular biology mechanisms at the transcript level. RESULTS:To investigate how ginseng responds to the high ambient temperature environment, we performed high throughput RNA sequencing and implemented a bioinformatics pipeline for the integrated analysis of small-RNA and mRNA-seq data without a reference genome. By performing reverse transcriptase (RT) PCR and sanger sequencing of transcripts that were assembled using our pipeline, we validated that their sequences were expressed in our samples. Furthermore, to investigate the interaction between genes and non-coding small RNAs and their regulation status under the high ambient temperature, we identified potential gene regulatory miRNAs. As a result, 100,672 contigs with significant expression level were identified and 6 known, 214 conserved and 60 potential novel miRNAs were predicted to be expressed under the high ambient temperature. CONCLUSION:Collectively, we have found that development, flowering and temperature responsive genes were induced under high ambient temperature, whereas photosynthesis related genes were repressed. Functional miRNAs were down-regulated under the high ambient temperature. Among them are miR156 and miR396 that target flowering (SPL6/9) and growth regulating genes (GRF) respectively.

SUBMITTER: Jung I

PROVIDER: S-EPMC5861484 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature.

Jung Inuk I Kang Hyejin H Kim Jang Uk JU Chang Hyeonsook H Kim Sun S Jung Woosuk W

BMC systems biology 20180319 Suppl 2

<h4>Background</h4>Ginseng is a popular traditional herbal medicine in north-eastern Asia. It has been used for human health for over thousands of years. With the rise in global temperature, the production of Korean ginseng (Panax ginseng C.A.Meyer) in Korea have migrated from mid to northern parts of the Korean peninsula to escape from the various higher temperature related stresses. Under the high ambient temperature, vegetative growth was accelerated, which resulted in early flowering. This p ...[more]

PMID: 29560829

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Project description:BackgroundPanax ginseng C. A. Mey is one of famous medicinal herb plant species. Its major bioactive compounds are various ginsenosides in roots and rhizomes. It is commonly accepted that ginsenosides are synthesized from terpene precursors, IPP and DMAPP, through the cytoplasmic mevalonate (MVA) pathway. Another plastic 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway was proved also contributing to ginsenoside generation in the roots of P. ginseng by using specific chemical inhibitors recently. But their gene expression characteristics are still under reveal in P. ginseng. With the development of the high-throughput next generation sequencing (NGS) technologies, we have opportunities to discover more about the complex ginsenoside biosynthesis pathways in P. ginseng.ResultsWe carried out deep RNA sequencing and comprehensive analyses on the ginseng root samples of 1-5 years old and five different tissues of 5 years old ginseng plants. The de novo assembly totally generated 48,165 unigenes, including 380 genes related to ginsenoside biosynthesis and all the genes encoding the enzymes of the MEP pathway and the MVA pathway. We further illustrated the gene expression profiles related to ginsenoside biosynthesis among 1-5 year-old roots and different tissues of 5 year-old ginseng plants. Particularly for the first time, we revealed that the gene transcript abundances of the MEP pathway were similar to those of the MVA pathway in ginseng roots but higher in ginseng leaves. The IspD was predicated to be the rate-limiting enzyme in the MEP pathway through both co-expression network and gene expression profile analyses.ConclusionsAt the transcriptional level, the MEP pathway has similar contribution to ginsenoside biosynthesis in ginseng roots, but much higher in ginseng leaves, compared with the MVA pathway. The IspD might be the key enzyme for ginsenoside generation through the MEP pathway. These results provide new information for further synthetic biology study on ginsenoside metabolic regulation.

Project description:Panax ginseng C.A. Meyer is a shade plant, and its leaves are an important medicinal part of P. ginseng. Light intensity plays a crucial role in physiological activities and metabolite accumulation in P. ginseng. Currently, little is known about the molecular mechanisms underlying physiological changes and quality under different light intensities in P. ginseng leaves. Therefore, we investigated the changes in photosynthetic physiology, secondary metabolism, transcriptomics, and metabolomics of P. ginseng leaves under different light intensities [T20 (20 µmol m-2·s-1), T50 (50 µmol m-2·s-1), T100 (100 μmol m-2·s-1)]]. Higher light intensity positively influenced the yield, photosynthesis, and accumulation of polysaccharides, soluble sugars, terpenoids, and ginsenosides in P. ginseng leaves. The T100 treatment notably promoted the accumulation of ginsenosides in the leaves, resulting in a 68.32% and 45.55% increase in total ginsenosides compared to the T20 and T50 treatments, respectively. Ginsenosides Rg1, Re, Rb1, Rc, Rg2, Rb2, Rb3, and Rd were 1.28-, 1.47-, 2.32-, 1.64-, 1.28-, 2.59-, 1.66-, and 2.28-times higher than in the T20 treatment. Furthermore, 285 differentially accumulated metabolites (DAMs) and 4218 differentially expressed genes (DEGs) in the metabolome and transcriptome of P. ginseng leaves, respectively, were identified. 13 triterpenoid saponins were significantly upregulated, and three were downregulated. The expression of genes encoding photosystem II reaction center proteins was upregulated under the T100 treatment, thereby increasing photosynthetic activity. The T100 treatment enhanced the expression of genes involved in photosynthetic carbon and energy metabolism in P. ginseng. The expression of antenna protein synthesis genes was upregulated under the T20, which increased the ability to capture light in P. ginseng leaves. T100 upregulated the expression of HMGR, SS, CYP716A53v2, UGT74AE, PgUGT1, and UGTPg45, thereby promoting terpene and ginsenoside synthesis. In summary, 100 µmol m-2·s-1 was conducive to quality formation of P. ginseng leaves. This study elucidates molecular mechanisms underlying the photosynthetic physiology and ginsenoside synthesis in P. ginseng under varying light intensities and provides a theoretical basis for the P. ginseng cultivation and its industrial production of secondary metabolites.

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The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature.

Publications

The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature.

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