Integrated Genomic and DNA Methylome Analyses Reveal Epigenetic Regulation of Stevia Glycoside Biosynthesis in Stevia rebaudiana

Abstract Stevia rebaudiana, a member of the Asteraceae family, is a sugar-yielding plant abundant in stevia glycosides (SGs), which are extensively applied in sweeteners and pharmaceuticals. Although DNA methylation has been implicated in the regulation of specialized metabolite synthesis, its specific involvement in SG metabolism remains insufficiently elucidated. In this study, a chromosome-level genome assembly of S. rebaudiana was generated, including 1,436 Mb across 11 chromosomes. DNA methylation profiling indicated that the expression of UDP-glycosyltransferases may be regulated by CG methylation within gene bodies across distinct tissues of S. rebaudiana. In conclusion, this study not only delivers a high-quality reference genome for S. rebaudiana but also provides novel perspectives on the potential regulatory mechanisms by which DNA methylation influences SG biosynthesis.