Identification and characterization of the cytosine-5 DNA methyltransferase gene family in Salvia miltiorrhiza.

Jiang Li,Caili Li,Shanfa Lu

doi:10.7717/peerj.4461

Abstract

Cytosine DNA methylation is highly conserved epigenetic modification involved in a wide range of biological processes in eukaryotes. It was established and maintained by cytosine-5 DNA methyltransferases (C5-MTases) in plants. Through genome-wide identification, eight putative SmC5-MTase genes were identified from the genome of Salvia miltiorrhiza, a well-known traditional Chinese medicine material and an emerging model medicinal plant. Based on conserved domains and phylogenetic analysis, eight SmC5-MTase genes were divided into four subfamilies, including MET, CMT, DRM and DNMT2. Genome-wide comparative analysis of the C5-MTase gene family in S. miltiorrhiza and Arabidopsis thaliana, including gene structure, sequence features, sequence alignment and conserved motifs, was carried out. The results showed conservation and divergence of the members of each subfamily in plants. The length of SmC5-MTase open reading frames ranges widely from 1,152 (SmDNMT2) to 5,034 bp (SmMET1). The intron number of SmC5-MTases varies between 7 (SmDRM1) and 20 (SmCMT1 and SmCMT2b). These features were similar to their counterparts from Arabidopsis. Sequence alignment and conserved motif analysis showed the existence of highly conserved and subfamily-specific motifs in the C5-MTases analyzed. Differential transcript abundance was detected for SmC5-MTases, implying genome-wide variance of DNA methylation in different organs and tissues. Transcriptome-wide analysis showed that the transcript levels of all SmC5-MTase genes was slightly changed under yeast extract and methyl jasmonate treatments. Six SmC5-MTases, including SmMET1, SmCMT1, SmCMT2a, SmCMT2b, SmCMT3 and SmDRM1, were salicylic acid-responsive, suggesting the involvement of SmC5-MTases in salicylic acid-dependent immunity. These results provide useful information for demonstrating the role of DNA methylation in bioactive compound biosynthesis and Dao-di herb formation in medicinal plants.

Highlights

Cytosine DNA methylation, a dominating epigenetic modification mechanism, plays vital roles in gene expression regulation, transposon silencing, gene imprinting, and X chromosome inactivation (Chan, Henderson & Jacobsen, 2005; Law & Jacobsen, 2010)
Blast analysis of eleven Arabidopsis cytosine DNA methyltransferase proteins against the whole S. miltiorrhiza 99-3 genome sequence resulted in the identification of eight SmC5MTase genes
C5-MTases with two bromo adjacent homology (BAH) domains in the N-terminal belong to the MET subfamily, whereas C5-MTases having only one BAH domain belong to the CMT subfamily

Summary

Introduction

Cytosine DNA methylation, a dominating epigenetic modification mechanism, plays vital roles in gene expression regulation, transposon silencing, gene imprinting, and X chromosome inactivation (Chan, Henderson & Jacobsen, 2005; Law & Jacobsen, 2010). It. How to cite this article Li et al (2018), Identification and characterization of the cytosine-5 DNA methyltransferase gene family in Salvia miltiorrhiza. Cytosine methylation mostly occurs in CG sites with the exception of embryonic stem cells and neurons (Lister et al, 2009; Lister et al, 2013). DNA methylation in plants usually occurs at CG sites. It occurs at CHG and CHH sites, where H represents any nucleotide except G (Cokus et al, 2008)

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