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DNA methylation plays an important role in plant growth and development, gene expression regulation, and maintenance of genome stability. However, only little information regarding stress-related DNA methyltransferases (MTases) genes is available in tomato. Here, we report the analysis of nine tomato MTases, which were categorized into four known subfamilies. Structural analysis suggested their DNA methylase domains are highly conserved, whereas the N-terminals are divergent. Tissue-specific analysis of these MTase genes revealed that  SlCMT2 ,  SlCMT3 , and  SlDRM5  were expressed higher in young leaves, while  SlMET1 ,  SlCMT4 ,  SlDRM7 , and  SlDRM8  were highly expressed in immature green fruit, and their expression declined continuously with further fruit development. In contrast,  SlMETL  was highly expressed in ripening fruit and displayed an up-regulated tendency during fruit development. In addition, the expression of  SlMET1  in the ripening of mutant  rin  and  Nr  tomatoes is significantly higher compared to wild-type tomato, suggesting that  SlMET1  was negatively regulated by the ethylene signal and ripening regulator MADS-RIN. Furthermore, expression analysis under abiotic stresses revealed that these MTase genes were stress-responsive and may function diversely in different stress conditions. Overall, our results provide valuable information for exploring the regulation of tomato fruit ripening and response to abiotic stress through DNA methylation.

Molecular characterization and transcription analysis of DNA methyltransferase genes in tomato (Solanum lycopersicum)