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 1436 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.

Acknowledgements

Appreciation is extended to Dr W. Wang from South China Agricultural University for providing critical insights during discussions. Apologies are expressed to those whose contributions could not be cited due to space constraints. This study was financially supported by the Guangdong Natural Science Funds for Distinguished Young Scholars (2022B1515020026), the Youth Innovation Promotion Association, Chinese Academy of Sciences (Y2021094), and the South China Botanical Garden, Chinese Academy of Sciences (QNXM-02), as well as by Science and Technology Projects in Guangzhou (No. E33309) to M.L., and the Hainan University Startup Fund (KYQD(ZR)-20101) to Z.Q.X.

Author contributions

The experimental design and planning were undertaken by M.L. and Z.Q.X. The experiments were carried out and the data analyzed by G.X.B., C.C.X., and Z.H.W. The manuscript was drafted by M.L., Z.Q.X., G.X.B., and C.C.X. All authors have reviewed and approved the final version.

Data availability

The raw data, genome assemblies, and annotations have been deposited in the National Genomics Data Center (https://ngdc.cncb.ac.cn/) under accession number PRJCA028196. The RNA-seq data are accessible via the NGDC database at https://ngdc.cncb.ac.cn/under accession number PRJCA016649.

Conflict of interest statement

The authors declare no competing interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

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