Abstract
DNA methylation plays important roles in genome protection and the regulation of gene expression and it is associated with plants’ responses to environments. DNA demethylases are very important proteins in DNA methylation regulation. In this study, we performed genome-wide and deep analysis of putative demethylases (DMEs) in pear. Seven DME genes were found in the pear genome and were defined as PbDME1–7 based on their domain organization. Results were supported by the gene structural characteristics and phylogenetic analysis. The gene structure of the DME genes were relatively complex and the DME7 proteins didn’t contain the Perm_CXXC domain. The DME genes experienced a whole genome duplication event (WGD) that occurred in the ancestor genome of pear and apple before their divergence based on the Ks values. Expression results showed that high salinity stress could influence the expression level of DMEs and salt-responsive genes in Pyrus betulaefolia. Furthermore, the methylation levels of salt-responsive genes changed under salt stress treatment. Results suggested important roles of PbDME genes in response to salt stress and are useful for better understanding the complex functions of this DME genes, which will facilitate epigenetic studies in pear trees salt tolerance.
Highlights
IntroductionDNA methylation predominantly occurs at cytosines in a symmetric CG sequence context in animals; oppositely, methylation in plants commonly occurs in an asymmetrical CHH sequence context (H = A, C, or T), as well as in the symmetrical CG and CHG contexts [4,5]
DNA methylation is an important and conserved epigenetic mark that is present in animals and plants, and it is important for genome integrity, development, and environmental responses [1,2].Since it was first coined in 1942 by Conrad Waddington [3], epigenetics has become a hot research topic.DNA methylation predominantly occurs at cytosines in a symmetric CG sequence context in animals; oppositely, methylation in plants commonly occurs in an asymmetrical CHH sequence context (H = A, C, or T), as well as in the symmetrical CG and CHG contexts [4,5]
A total of seven DMEs were identified in the pear genome, all of which were confirmed by the presence of the RRM-DME domain (Table 1)
Summary
DNA methylation predominantly occurs at cytosines in a symmetric CG sequence context in animals; oppositely, methylation in plants commonly occurs in an asymmetrical CHH sequence context (H = A, C, or T), as well as in the symmetrical CG and CHG contexts [4,5]. These modifications are mainly performed by 3 cytosine-5 DNA methyltransferase (C5-MTase) families, including methyltransferases (METs), chromomethyltransferase (CMT), and domains-rearranged methyltransferases (DRMs). Active DNA demethylation in plants is initiated by a family of 5-meC DNA glycosylases/lyases
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