Whole-genome methylation analysis reveals epigenetic differences in the occurrence and recovery of hyperhydricity in Dendrobium officinale plantlets

DNA methylation is one of the important contents of epigenetics research, and it is inseparable from the occurrence of various biological processes. To explore the epigenetic mechanism of hyperhydricity development and recovery in Dendrobium officinale , whole-genome bisulfite sequencing was performed to systematically analyze the extent and patterns of cytosine methylation in the normal plantlets (Normal), hyperhydric plantlets (HH), and hyperhydric plantlets cultured with K 2 SiO 3 (HH-Si). The CHH context accounted for the largest proportion of methylated cytosine site in D. officinale . There was no significant difference in the degree of methylation in the CG context among the HH vs . Normal, HH-Si vs . HH, and HH-Si vs. Normal. The methylation level in the CHH context decreased with hyperhydricity, while the exogenous addition of silicon increased the methylation level of hyperhydric plantlets. In addition, 36,944 differentially methylated regions were detected in our study. GO enrichment analysis of differentially methylated genes revealed that various methylation sites were involved in different processes and pathways. In HH vs. Normal and HH-Si vs. HH, CHH-DMGs are closely related to the redox system. A cointegration analysis of transcriptome sequencing and methylation data showed that the expression levels of most differentially expressed genes were positively correlated to the methylation level. Our research provides references for an in-depth understanding of plant oxidative stress response mechanisms, as well as new insights into the epigenetic regulation of gene expression in the occurrence and restoration of hyperhydricity.