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Background  DNA methylation is a conserved and important epigenetic modification involved in the regulation of numerous biological processes, including plant development, secondary metabolism, and response to stresses. However, no information is available regarding the identification of cytosine-5 DNA methyltransferase ( C5-MTase ) and DNA demethylase ( dMTase ) genes in the orchid  Dendrobium officinale .    Results  In this study, we performed a genome-wide analysis of  DoC5-MTase  and  DodMTase  gene families in  D. officinale . Integrated analysis of conserved motifs, gene structures and phylogenetic analysis showed that eight DoC5-MTases were divided into four subfamilies (DoCMT, DoDNMT, DoDRM, DoMET) while three DodMTases were divided into two subfamilies (DoDML3, DoROS1). Multiple  cis -acting elements, especially stress-responsive and hormone-responsive ones, were found in the promoter region of  DoC5-MTase  and  DodMTase  genes. Furthermore, we investigated the expression profiles of  DoC5-MTase  and  DodMTase  in 10 different tissues, as well as their transcript abundance under abiotic stresses (cold and drought) and at the seedling stage, in protocorm-like bodies, shoots, and plantlets. Interestingly, most DoC5-MTases were downregulated whereas DodMTases were upregulated by cold stress. At the seedling stage,  DoC5-MTase  expression decreased as growth proceeded, but  DodMTase  expression increased.    Conclusions  These results provide a basis for elucidating the role of DoC5-MTase and DodMTase in secondary metabolite production and responses to abiotic stresses in  D. officinale .    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-020-02811-8.

bmc plant biology

Genome-wide identification and analysis of DNA methyltransferase and demethylase gene families in Dendrobium officinale reveal their potential functions in polysaccharide accumulation