Genome-Wide Identification and Comparative Analysis of Cytosine-5 DNA Methyltransferase and Demethylase Families in Wild and Cultivated Peanut.

Pengfei Wang,Chuanzhi Zhao,Xiaotong Bian,Han Xia,Lei Hou,Shubo Wan,Shuzhen Zhao,Chao Gao,Hui Song,Xingjun Wang

doi:10.3389/fpls.2016.00007

Pengfei Wang, Chuanzhi Zhao + Show 8 more

Open Access

https://doi.org/10.3389/fpls.2016.00007

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Abstract

DNA methylation plays important roles in genome protection, regulation of gene expression and is associated with plants development. Plant DNA methylation pattern was mediated by cytosine-5 DNA methyltransferase and demethylase. Although the genomes of AA and BB wild peanuts have been fully sequenced, these two gene families have not been studied. In this study we report the identification and analysis of putative cytosine-5 DNA methyltransferases (C5-MTases) and demethylases in AA and BB wild peanuts. Cytosine-5 DNA methyltransferases in AA and BB wild peanuts could be classified in MET, CMT, and DRM2 groups based on their domain organization. This result was supported by the gene and protein structural characteristics and phylogenetic analysis. We found that some wild peanut DRM2 members didn't contain UBA domain which was different from other plants such as Arabidopsis, maize and soybean. Five DNA demethylase encoding genes were found in AA genome and five in BB genome. The selective pressure analysis showed that wild peanut C5-MTase genes mainly underwent purifying selection but many positive selection sites can be detected. Conversely, DNA demethylase genes mainly underwent positive selection during evolution. Additionally, the expression dynamic of cytosine-5 DNA methyltransferase and demethylase genes in different cultivated peanut tissues were analyzed. Expression result showed that cold, heat or PEG stress could influence the expression level of C5-MTase and DNA demethylase genes in cultivated peanut. These results are useful for better understanding the complexity of these two gene families, and will facilitate epigenetic studies in peanut in the future.

Highlights

DNA methylation is a process that DNA methyltransferase transfer the methyl group from the methyl donor S-adenosylmethionine (SAMe) to cytosine residues and generate Sadenosylhomocysteine (SAH) (Lu and Mato, 2012)
The results showed that cold, heat or PEG stress could influence the expression level of cultivated peanut C5-MTase and DNA demethylase genes
The results showed that peanut C5-MTases were located in nucleus which was consisted with other species (Cao et al, 2014; Garg et al, 2014)

Summary

Introduction

DNA methylation is a process that DNA methyltransferase transfer the methyl group from the methyl donor S-adenosylmethionine (SAMe) to cytosine residues and generate Sadenosylhomocysteine (SAH) (Lu and Mato, 2012). DNA methylation is a conserved epigenetic gene regulation mechanism in plants and animals (Zhong et al, 2014). Peanut C5-MTases and DNA Demethylases through transferring the methyl group from S-adenosyl methionine into the 5′ position of the pyrimidine (Bender, 2004). Small RNAs could direct methylation through recruitment of methyltransferase. It is called RNA-directed DNA methylation (RdDM) pathway (Matzke and Mosher, 2014). The small interfering RNAs (siRNA) were found to be a group of small RNAs that could direct the occurrence of DNA methylation. The silence of many transposable elements (TEs) was due to siRNA-directed DNA methylation (Slotkin et al, 2009). It is confirmed that microRNAs (miRNA) and piwiinteracting RNAs (piRNA) could direct RdDM (Wu et al, 2010)

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