Genome-Wide Identification and Functional Analysis of DNA Methylation-Related Genes in Sophora tonkinensis Under Cadmium and Drought Stress

Sophora tonkinensis is a valuable medicinal plant whose cultivation is constrained by drought and cadmium (Cd) contamination. DNA methylation, mediated by cytosine-5 DNA methyltransferases (C5-MTases) and DNA demethylases (dMTases), contributes to plant stress response; however, these gene families have remained uncharacterized in S. tonkinensis. Here, we identified 12 methylation-related genes (four StC5-MTases and eight StdMTases) and analyzed their phylogeny, duplication, promoter cis-elements, and expression patterns under Cd exposure and drought/rehydration. Most duplicated pairs showed Ka/Ks < 1, consistent with purifying selection. StCMT1 and StMET2 were induced by both Cd and drought stress but declined after rehydration, whereas StROS1b and StROSlike3 responded rapidly to both stresses. Heterologous overexpression in Nicotiana benthamiana improved growth under Cd stress for StCMT1 lines and under PEG-induced osmotic stress for StROSlike3 lines, as reflected by plant height and whole-plant fresh weight. Together, these findings establish a genome-wide resource for DNA methylation machinery in S. tonkinensis and provide candidate genes for investigating epigenetic regulation of abiotic stress adaptation.