Dataset Information

Selection of reference genes for quantitative real-time PCR normalization in Panax ginseng at different stages of growth and in different organs.

ABSTRACT: Quantitative real-time reverse transcription PCR (qRT-PCR) has become a widely used method for gene expression analysis; however, its data interpretation largely depends on the stability of reference genes. The transcriptomics of Panax ginseng, one of the most popular and traditional ingredients used in Chinese medicines, is increasingly being studied. Furthermore, it is vital to establish a series of reliable reference genes when qRT-PCR is used to assess the gene expression profile of ginseng. In this study, we screened out candidate reference genes for ginseng using gene expression data generated by a high-throughput sequencing platform. Based on the statistical tests, 20 reference genes (10 traditional housekeeping genes and 10 novel genes) were selected. These genes were tested for the normalization of expression levels in five growth stages and three distinct plant organs of ginseng by qPCR. These genes were subsequently ranked and compared according to the stability of their expressions using geNorm, NormFinder, and BestKeeper computational programs. Although the best reference genes were found to vary across different samples, CYP and EF-1? were the most stable genes amongst all samples. GAPDH/30S RPS20, CYP/60S RPL13 and CYP/QCR were the optimum pair of reference genes in the roots, stems, and leaves. CYP/60S RPL13, CYP/eIF-5A, aTUB/V-ATP, eIF-5A/SAR1, and aTUB/pol IIa were the most stably expressed combinations in each of the five developmental stages. Our study serves as a foundation for developing an accurate method of qRT-PCR and will benefit future studies on gene expression profiles of Panax Ginseng.

SUBMITTER: Liu J

PROVIDER: S-EPMC4230945 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Selection of reference genes for quantitative real-time PCR normalization in Panax ginseng at different stages of growth and in different organs.

Liu Jing J Wang Qun Q Sun Minying M Zhu Linlin L Yang Michael M Zhao Yu Y

PloS one 20141113 11

Quantitative real-time reverse transcription PCR (qRT-PCR) has become a widely used method for gene expression analysis; however, its data interpretation largely depends on the stability of reference genes. The transcriptomics of Panax ginseng, one of the most popular and traditional ingredients used in Chinese medicines, is increasingly being studied. Furthermore, it is vital to establish a series of reliable reference genes when qRT-PCR is used to assess the gene expression profile of ginseng. ...[more]

PMID: 25393243

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Project description:Background:Ginseng berries (GBs) show temporal metabolic variations among different maturation stages, determining their organoleptic and functional properties. Methods:We analyzed metabolic variations concomitant to five different maturation stages of GBs including immature green (IG), mature green (MG), partially red (PR), fully red (FR), and overmature red (OR) using mass spectrometry (MS)-based metabolomic profiling and multivariate analyses. Results:The partial least squares discriminant analysis score plot based on gas chromatography-MS datasets highlighted metabolic disparity between preharvest (IG and MG) and harvest/postharvest (PR, FR, and OR) GB extracts along PLS1 (34.9%) with MG distinctly segregated across PLS2 (18.2%). Forty-three significantly discriminant primary metabolites were identified encompassing five developmental stages (variable importance in projection > 1.0, p < 0.05). Among them, most amino acids, organic acids, 5-C sugars, ethanolamines, purines, and palmitic acid were detected in preharvest GB extracts, whereas 6-C sugars, phenolic acid, and oleamide levels were distinctly higher during later maturation stages. Similarly, the partial least squares discriminant analysis based on liquid chromatography-MS datasets displayed preharvest and harvest/postharvest stages clustered across PLS1 (11.1 %); however, MG and PR were separated from IG, FR, and OR along PLS2 (5.6 %). Overall, 24 secondary metabolites were observed significantly discriminant (variable importance in projection > 1.0, p < 0.05), with most displaying higher relative abundance during preharvest stages excluding ginsenosides Rg1 and Re. Furthermore, we observed strong positive correlations between total flavonoid and phenolic metabolite contents in GB extracts and antioxidant activity. Conclusion:Comprehending the dynamic metabolic variations associated with GB maturation stages rationalize their optimal harvest time per se the related agroeconomic traits.

Dataset Information

Selection of reference genes for quantitative real-time PCR normalization in Panax ginseng at different stages of growth and in different organs.

Publications

Selection of reference genes for quantitative real-time PCR normalization in Panax ginseng at different stages of growth and in different organs.

Similar Datasets

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