Difference in DNA methylation pattern and expression of active ingredients between garden ginseng and ginseng under forest.

Panax ginseng is widely used for its medicinal value. With the decline in wild ginseng resources, garden ginseng (GG) and ginseng under forest (FG) have become the main sources. Their different growth conditions and ages may account for the differences in epigenetics. The genomic DNA of Panax ginseng was digested using the methylation-insensitive enzyme Mse Ⅰ combined with the methylation-sensitive enzymes Aci Ⅰ, Pst Ⅰ, and EcoT22 Ⅰ. Then, a sequencing library of CG, CHG, and CHH methylation contexts was constructed and sequenced through amplicon sequencing. Differences in DNA methylation were observed using the methylation context-sensitive enzyme ddRAD (MCSeEd), revealing eight differentially methylated regions (DMRs). The bisulfite sequencing technology revealed that the methylation level of GG was higher than that of FG. The Plant ISOform Sequencing Database was used to predict the regulatory function of CpG island–coding region so as to estimate the relationship between methylation and effective components. The quantitative real-time polymerase chain reaction (qPCR) showed that the expression of functional genes in FG was higher than that in GG. These studies showed that the increase in GG methylation level was associated with the decrease in gene expression, providing a new perspective on epigenetic differences and gene expression in ginseng. • Analysis of the DNA methylation of ginseng by MCSeEd technic for the first time. • Based on DMPs, the garden ginseng and ginseng under forest were distinguished. • Four functional genes regulated of DMRs coding region were predicted by database. • The relationship between methylation and component production's gene was verified. [ABSTRACT FROM AUTHOR]