Dynamic DNA methylation landscapes in plants from a whole-genome perspective: characteristics and future perspectives

DNA methylation, an important epigenetic modification, has been confirmed to act as a key regulator of gene expression and genome stability in plants. This review aimed to analyze DNA methylation landscapes in plants by integrating genome-wide DNA methylation data from 105 plant species, among which 53 species possess quantitative methylation levels for downstream analyses. We found that the levels of DNA methylation in plants are both interspecific and tissue-specific. Environmental stresses and evolutionary processes such as polyploidization, domestication, and de-domestication can influence DNA methylation levels at both the whole-genome and single-gene levels. Finally, this study reviewed functional genes related to DNA methylation changes and highlighted recent advances in multi-omics approaches (e.g., single-cell bisulfite sequencing, transcriptome sequencing, and chromosome conformation capture-based technologies) for an improved interpretation of DNA methylation dynamics among plants and its roles in environmental adaptation.