Open AccessUDP and NTF2 are the most consistently expressed genes in Panax ginseng roots at different growth stages
Author(s) -
Meichen Liu,
Qun Wang,
Hongwei Xie,
Shichao Liu,
Siming Wang,
Hui Zhang,
Yu Zhao
Publication year - 2017
Publication title -
molecular medicine reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.727
H-Index - 56
eISSN - 1791-3004
pISSN - 1791-2997
DOI - 10.3892/mmr.2017.6494
Subject(s) - reference genes , biology , gene , transcriptome , gene expression , ginseng , genetics , candidate gene , real time polymerase chain reaction , computational biology , medicine , alternative medicine , pathology
Reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) analysis relies on normalization against a consistently expressed reference gene. However, it has been reported that reference gene expression levels often vary markedly between samples as they are usually selected based solely on convention. The advent of RNA sequencing technology offers the opportunity to select reference genes with the least variability in steady‑state transcript levels. To identify the most consistently stable genes, which are a prerequisite for obtaining reliable gene expression data, the present study analyzed transcriptomes from six Panax ginseng transcriptome data sets, representing six growth stages, and selected 21 candidate reference genes for screening using RT‑qPCR. Of the 21 candidate genes, 13 had not been reported previously. The geNorm, NormFinder and BestKeeper programs were used to analyze the stability of the 21 candidate reference genes. The results showed that UDP‑N‑acetylgalactosamine transporter and nuclear transport factor 2 were likely to be the optimal combination of reference genes for use in investigations of ginseng. The novel reference genes were validated by correlating the gene expression profiles of four pathogenesis‑related protein genes generated from RT‑qPCR, with their expression levels calculated from the RNA sequencing data. The expression levels were well correlated, which demonstrated their value in performing RT‑qPCR analyses in ginseng.