Dataset Information

SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng.

ABSTRACT: Panax notoginseng is one of the most widely used traditional Chinese herbs with particularly valued roots. Triterpenoid saponins are mainly specialized secondary metabolites, which medically act as bioactive components. Knowledge of the ginsenoside biosynthesis in P. notoginseng, which is of great importance in the industrial biosynthesis and genetic breeding program, remains largely undetermined. Here we combined single molecular real time (SMRT) and Second-Generation Sequencing (SGS) technologies to generate a widespread transcriptome atlas of P. notoginseng. We mapped 2,383 full-length non-chimeric (FLNC) reads to adjacently annotated genes, corrected 1,925 mis-annotated genes and merged into 927 new genes. We identified 8,111 novel transcript isoforms that have improved the annotation of the current genome assembly, of which we found 2,664 novel lncRNAs. We characterized more alternative splicing (AS) events from SMRT reads (20,015 AS in 6,324 genes) than Illumina reads (18,498 AS in 9,550 genes), which contained a number of AS events associated with the ginsenoside biosynthesis. The comprehensive transcriptome landscape reveals that the ginsenoside biosynthesis predominantly occurs in flowers compared to leaves and roots, substantiated by levels of gene expression, which is supported by tissue-specific abundance of isoforms in flowers compared to roots and rhizomes. Comparative metabolic analyses further show that a total of 17 characteristic ginsenosides increasingly accumulated, and roots contained the most ginsenosides with variable contents, which are extraordinarily abundant in roots of the three-year old plants. We observed that roots were rich in protopanaxatriol- and protopanaxadiol-type saponins, whereas protopanaxadiol-type saponins predominated in aerial parts (leaves, stems and flowers). The obtained results will greatly enhance our understanding about the ginsenoside biosynthetic machinery in the genus Panax.

SUBMITTER: Zhang D

PROVIDER: S-EPMC7499265 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng.

Zhang Dan D Li Wei W Chen Zhong-Jian ZJ Wei Fu-Gang FG Liu Yun-Long YL Gao Li-Zhi LZ

Scientific reports 20200917 1

Panax notoginseng is one of the most widely used traditional Chinese herbs with particularly valued roots. Triterpenoid saponins are mainly specialized secondary metabolites, which medically act as bioactive components. Knowledge of the ginsenoside biosynthesis in P. notoginseng, which is of great importance in the industrial biosynthesis and genetic breeding program, remains largely undetermined. Here we combined single molecular real time (SMRT) and Second-Generation Sequencing (SGS) technolog ...[more]

PMID: 32943706

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Project description:BackgroundTo investigate the biosynthesis and pharmacokinetic course of enteric-coated soft capsules of Panax notoginseng saponins (PNS) in a beagle dog model.MethodsTo satisfy the enteric properties of soft capsules, the PNS enteric soft gelatin capsules were prepared by formaldehyde impregnation and orthogonal experimental design. The fluidity of gelatin and the disintegration time were selected as evaluation indexes; the soft gelatin capsule content was self-emulsifying, and the Km value and the optimal prescription were determined by making three-phase diagrams; in vivo pharmacokinetics studies were performed on six beagle dogs with 3 dogs in each group. Beagle dogs were divided into two groups randomly. One group was given PNS self-emulsifying enteric capsule and the other was given market conventional capsules. Plasma samples were collected at different times. After 1 week, the crossover experiment was carried out. The plasma concentration was detected by HPLC-MS (high performance liquid chromatography-mass spectrometry). Then the pharmacokinetic parameters were calculated by non-compartment model analysis.ResultsThe range and variance analysis of the orthogonal test determined that the best prescription of total saponins of Panax notoginseng enteric soft capsule was:gelatin:glycerol:water =1:1:2, Soak the films in 1% formaldehyde for 1 hour. The contents of the soft capsule self-microemulsion are prescribed as: IPM (isopropyl myristate):Cremophor RH40:PEG400 (polyethylene glycol 400) =1:4.5:4.5 (with suitable PNS); the pharmacokinetic parameters of PNS self-emulsified enteric capsules and conventional capsules in the market are as follows: Rb1:Cmax is (18.05±0.26) and (15.50±0.51) ng/mL, Tmax is (2.00±0) and (3.00±0) h, AUC0→t is 98.49±1.16 and 34.46±2.02 (ng/mL)·h, relative bioavailability is 196.2%; Rg1: Cmax is 4.16±0.25 and 3.88±0.28 ng/mL, Tmax is 2.00±0 and 1.50±0 h, area under drug time curve (AUC)0→t is 11.80±2.93 and 10.45±2.29 (ng/mL)·h, relative bioavailability is 77.2%; R1:Cmax is 1.84±0.25 and 1.48±0.21 ng/mL, Tmax is 2.08±0.49 and 1.92±0.20 h, AUC0→t is 7.06±2.07 and 7.16±2.59 (ng/mL)·h, relative bioavailability is 117.7%.ConclusionsThe experiment in vivo showed the higher relative bioavailability of PNS self-emulsifying enteric capsule compared with market conventional capsules. This will provide a potential application prospect for the clinical research and applications of PNS.

Dataset Information

SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng.

Publications

SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng.

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