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

## TL;DR

This study identifies DNA methylation-related genes in Sophora tonkinensis and shows how they help the plant cope with cadmium and drought stress.

## Contribution

The first genome-wide characterization of DNA methylation-related genes in S. tonkinensis under abiotic stress.

## Key findings

- Four C5-MTases and eight dMTases were identified and analyzed for stress response.
- StCMT1 and StMET2 were induced by Cd and drought stress but declined after rehydration.
- Overexpression of StCMT1 and StROSlike3 improved plant growth under stress conditions.

## Abstract

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.