Compatative Transcriptome Analysis Reveals Sesquiterpene Biosynthesis among 1-, 2- and 3-year Old Atractylodes Chinensis

Abstract

Background: Atractylodes chinensis (DC.) Koidz is a well-known medicinal plant containing the major bioactive compound, atrctylodin, a sesquiterpenoids. High-performance liquid chromatography (HPLC) analysis demonstrated that atrctylodin was most abundant in 3-year old A. chinensis rhizomes, compared with those from 1-year and 2-year-old plants, however, the molecular mechanisms underlying accumulation of atrctylodin in rhizomes are poorly understood. Results: In this study, we characterized the transcriptomes from 1-, 2, and 3-year old (Y1, Y2, and Y3, respectively) A. chinensis, to identify differentially expressed genes (DEGs). We identified 205 and 226 unigenes encoding the enzyme genes in the mevalonate (MVA) and methylerythritol phosphate (MEP) sesquiterpenoid biosynthesis pathways, respectively. To confirm the reliability of the RNA sequencing analysis, eleven genes key genes encoding factors involved in the sesquiterpene biosynthetic pathway, as well as in pigment, amino acid, hormone, and transcription factor functions, were selected for quantitative real time PCR (qRT-PCR) analysis. The results demonstrated similar expression patterns to those determined by RNA sequencing, with a Pearson’s correlation coefficient of 0.9 between qRT-PCR and RNA-seq data. Differential gene expression analysis of samples from different ages revealed 52 genes related to sesquiterpenoids biosynthesis. Among these, seven DEGs were identified in Y1 vs Y2, Y1 vs Y3, and Y2 vs Y3, of which five encoded four key enzymes, squalene/phytoene synthase, squalene-hopene cyclase, squalene epoxidase and dammarenediol II synthase. These four enzymes directly related to squalene biosynthesis and subsequent catalytic action. To validate the result of these seven DEGs, qRT-PCR was performed and indicated most of them displayed lower relative expression in 3-year old rhizome, similar to transcriptomic analysis. Conclusion: The enzymes SS, SHC, SE and DS down-regulated expression in 3-year old rhizome. This data corresponded to the higher content of sesquiterpenes in 3-year old rhizome, and confirmed by qRT-PCR. The results of comparative transcriptome analysis and identified key enzyme genes laid a solid foundation for investigation of production sesquiterpenoid in A. chinensis.