Genome-wide identification of cytosine-5 DNA methyltransferases and demethylases in Solanum lycopersicum

• Published in: Gene Vol. 550; no. 2; pp. 230 - 237
• Main Authors: Cao, Dongyan, Ju, Zheng, Gao, Chao, Mei, Xiaohong, Fu, Daqi, Zhu, Hongliang, Luo, Yunbo, Zhu, Benzhong
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 25.10.2014
• Subjects: Chromosome Mapping; DNA (Cytosine-5-)-Methyltransferases - genetics; DNA Methylation; Fruit - genetics; Gene Expression Profiling; Gene Expression Regulation, Enzymologic; Gene Expression Regulation, Plant; Genome, Plant; Histone Demethylases - genetics; Lycopersicon esculentum; Lycopersicon esculentum - enzymology; Lycopersicon esculentum - genetics; Phylogenetic analyses; Phylogeny; Solanaceae; Solanum; Subcellular localization; Tomato fruit ripening; AP2a; TGS; ORF; DNMT2; CNR; BK; Mw; 1-MCP; rin; Tomato fruit ripening; NCBI; DNA methylation; TRV; MG; OsC5-MTase; SlC5-MTase; Phylogenetic analyses; DME; dsRNA; AC; DML; qRT-PCR; DAPI; siRNA; AtC5-MTase; CMT; BK+5; CMV; NOR; PSTVd; TF; C5-MTase; ROS; VIGS; Subcellular localization; CaMV; ZmC5-MTase; PI; SGN; MET; RdDM; DRM; HB-1
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2014.08.034

Recent studies have reported that decreased level of DNA cytosine methylation in the global genome was closely related to the initiation of tomato (Solanum lycopersicum) fruit ripening. However, genome-scale analysis of cytosine-5 DNA methyltransferases (C5-MTases) and demethylases in tomato has not been engaged. In this study, 7 C5-MTases and 3 demethylases were identified in tomato genome, which probably contributed to DNA cytosine methylation level in tomato. The 7 C5-MTases were categorized into 4 subgroups, and the 3 demethylases were classified into 2 subgroups based on phylogenetic analyses. Comprehensive analysis of their structure and genomic localization was also performed in this paper. According to online RNA-seq data, 4 S. lycopersicum C5-MTase (SlC5-MTase) genes (SlMET, SlDRM1L1, SlDRM5, SlMET3L) were expressed higher than others, and one DNA demethylase gene (SlDML) was significantly changed during tomato fruit development and ripening. Furthermore, all these five gene expressions at breaker (BK) stage changed with 1-methylcyclopropene (1-MCP) treatment, indicating that they were regulated by ethylene directly or indirectly in tomato fruit. In addition, subcellular localization analysis indicated that SlDRM1L1 and SlDRM5 located in the nucleus might have responsibility for RNA-directed DNA methylation (RdDM). Collectively, this paper provided a framework for gene discovery and functional characterization of C5-MTases and DNA demethylases in other Solanaceae species. •7 C5-MTases and 3 DNA demethylases were identified in tomato.•Comprehensive analysis of their structure and genomic localization were performed.•Expression patterns of tomato C5-MTase and DNA demethylase genes were analyzed.•The selected 4 SlC5-MTases and one DNA demethylases had response to ethylene.•Two DRMs of the SlC5-MTases localized to the nucleus of onion epidermal cells.