De novo assembly and comparative analysis of root transcriptomes from different varieties of Panax ginseng C. A. Meyer grown in different environments

Abstract

Panax ginseng C. A. Meyer is an important traditional herb in eastern Asia. It contains ginsenosides, which are primary bioactive compounds with medicinal properties. Although ginseng has been cultivated since at least the Ming dynasty to increase production, cultivated ginseng has lower quantities of ginsenosides and lower disease resistance than ginseng grown under natural conditions. We extracted root RNA from six varieties of fifth-year P. ginseng cultivars representing four different growth conditions, and performed Illumina paired-end sequencing. In total, 163,165,706 raw reads were obtained and used to generate a de novo transcriptome that consisted of 151,763 contigs (76,336 unigenes), of which 100,648 contigs (66.3%) were successfully annotated. Differential expression analysis revealed that most differentially expressed genes (DEGs) were upregulated (246 out of 258, 95.3%) in ginseng grown under natural conditions compared with that grown under artificial conditions. These DEGs were enriched in gene ontology (GO) terms including response to stimuli and localization. In particular, some key ginsenoside biosynthesis-related genes, including HMG-CoA synthase (HMGS), mevalonate kinase (MVK), and squalene epoxidase (SE), were upregulated in wild-grown ginseng. Moreover, a high proportion of disease resistance-related genes were upregulated in wild-grown ginseng. This study is the first transcriptome analysis to compare wild-grown and cultivated ginseng, and identifies genes that may produce higher ginsenoside content and better disease resistance in the wild; these genes may have the potential to improve cultivated ginseng grown in artificial environments.

Development of a Validated UPLC-MS/MS Method for Analyzing Major Ginseng Saponins from Various Ginseng Species

“…In the study by Chen et al (2019), the average contents of ginsenosides indicated that the distinct volcanic pumice soil conditions of New Zealand might be more suitable for ginseng cultivation than original native locations (China and Korea) [36]. Different ginseng processing methods and cultivation environments [37] may be required due to variations in the amounts of ginsenosides [38].…”

Comparative transcriptome analyses on terpenoids metabolism in field- and mountain-cultivated ginseng roots

“…Sathiyamoorthy et al [23] firstly reported comparative transcriptome analyses of FCG and MCG, and preliminarily discussed putative isoprenoids pathways based on 6757 expressed sequence tags from hairy roots and roots of 14-year-old MCG and 4-year-old FCG. Zhen et al [24] built a set of root transcriptomes from three types of ginseng roots (i.e., roots of FCG, MCG and wild ginseng), and found that three genes encoding key terpenoids biosynthesis enzymes including HMGCR, MVK and SE were more active in wild ginseng root than in FCG’s. Wang et al [25] identified 78 genes of 13 enzymes from roots of 5-, 12-, 18- and 25-year-old MCG and 4-year-old FCG involved in biosyntheses of terpenoids backbone and triterpenoids.…”

TCMID 2.0: a comprehensive resource for TCM

“…China is vast in territory and the majority of herbs have more than one place of origin. Herbs in different districts and growth condition vary in effective composition content that is responsible for the otherness in curative effect ( 13 ). Lack of stable quality control in herbs still blocks the way of TCM modernization.…”