Abstract
DNA methylation plays an important role in a wide range of developmental and physiological processes in plants. It is primarily catalyzed and regulated by cytosine-5 DNA methyltransferases (C5-MTases) and a group of DNA glycosylases that act as demethylases. To date, no genome-scale analysis of the two kiwifruit (Actinidia chinensis) families has been undertaken. In our study, nine C5-MTases and seven DNA demethylase genes were identified in the kiwifruit genome. Through selective evolution analysis, we found that there were gene duplications in C5-MTases and demethylases, which may have arisen during three genome doubling events followed by selection during evolution of kiwifruit. Expression analysis of DNA methylases (C5-MTases) and demethylases identified changes in transcripts of DNA methylation and demethylation genes during both vegetative and reproductive development. Moreover, we found that some members of the two methylase/demethylase families may also be involved in fruit ripening and the regulation of softening. Our results help to better understand the complex roles of methylation/demethylation in plants and provide a foundation for analyzing the role of DNA methylation modification in kiwifruit growth, development and ripening.
Highlights
The accurate qualitative, quantitative and temporal regulation of gene expression accomplished by cis-regulatory elements and trans-acting factors is indispensable for normal development in plants and animals
C5-MTases and DNA demethylases were identified from the kiwifruit genome using the sequences of C5-MTases and DNA demethylases of Arabidopsis as BLAST queries against the kiwifruit genome
We found that the bromineadjacent homologous domain (BAH) domain of AcCMT5 was incomplete and part of the domain was missing when compared with the BAH structural domain of AcCMT3 and AcCMT4
Summary
The accurate qualitative, quantitative and temporal regulation of gene expression accomplished by cis-regulatory elements and trans-acting factors is indispensable for normal development in plants and animals. One major epigenetic modification is DNA methylation, which occurs by the addition of methyl groups to the C-5 site of cytosine, the N6 site of adenine, and the N-7 site of guanine (Jeltsch, 2002) in DNA molecules. These epigenetic regulatory mechanisms are widely found in plants and animals (Cao et al, 2014; Wang et al, 2016) and play an important role in the regulation of gene expression. DNA methylation occurs primarily in three distinct sequence contexts: symmetric CG, CHG, and asymmetric CHH sites (where H =A, T or C) (Law and Jacobsen, 2010)
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