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

Zhenming Yu,Can Si,Conghui Zhao,Mingzhi Li,Jaime A Teixeira Da Silva,Mingze Zhang,Chunmei He,Jun Duan,Guihua Zhang

doi:10.1186/s12870-020-02811-8

Zhenming Yu, Can Si + Show 7 more

Open Access

https://doi.org/10.1186/s12870-020-02811-8

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Abstract

BackgroundDNA 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.ResultsIn 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.ConclusionsThese 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.

Highlights

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
Compared to DNA methylation, whose catalyzation is determined by a single DNA methyltransferase such as MET1, CMT2, CMT3 or DOMAINS REARRANGED METHYLASE2 (DRM2), active DNA demethylation requires a series of enzymes involved in excision of 5methylcytosine in the CG, CHG and CHH contexts [2]
Genome-wide identification and structural analysis of C5MTase and dMTase genes in D. officinale Blast analysis of reported A. thaliana and rice C5MTase and dMTase proteins against the whole D. officinale genome resulted in the identification of eight DoC5-MTase and three DodMTase proteins (Table 1)

Summary

Introduction

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. Compared to DNA methylation, whose catalyzation is determined by a single DNA methyltransferase such as MET1, CMT2, CMT3 or DRM2, active DNA demethylation requires a series of enzymes involved in excision of 5methylcytosine in the CG, CHG and CHH contexts [2]. In plants, this process is initially catalyzed by a bifunctional DNA glycosylase, including REPRESSOR OF SILE NCING1 (ROS1), DEMETER (DME), DEMETER-like 2 (DML2), or DEMETER-like 3 (DML3), through the base-excision repair pathway [1, 3]

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