1. Divergent DNA methylation contributes to duplicated gene evolution and chilling response in tea plants
- Author
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Fangdong Li, Ruoheng Ge, Yanli Wang, Wei-Wei Deng, Wei Tong, Ali Inayat Mallano, Yeyun Li, En-Hua Xia, Qiong Wu, Ruopei Li, Jin Huang, and Huijuan Zhao
- Subjects
0106 biological sciences ,0301 basic medicine ,Transposable element ,Plant Science ,01 natural sciences ,DNA methyltransferase ,Camellia sinensis ,Evolution, Molecular ,03 medical and health sciences ,Genome Size ,Gene Expression Regulation, Plant ,Genes, Duplicate ,Stress, Physiological ,Genetics ,Gene ,Regulation of gene expression ,DNA Methylation Regulation ,biology ,fungi ,food and beverages ,Cell Biology ,Methylation ,DNA Methylation ,Cold Temperature ,030104 developmental biology ,DNA methylation ,DNA Transposable Elements ,biology.protein ,Demethylase ,Genome, Plant ,010606 plant biology & botany - Abstract
The tea plant (Camellia sinensis) is a thermophilic cash crop and contains a highly duplicated and repeat-rich genome. It is still unclear how DNA methylation regulates the evolution of duplicated genes and chilling stress in tea plants. We therefore generated a single-base-resolution DNA methylation map of tea plants under chilling stress. We found that, compared with other plants, the tea plant genome is highly methylated in all three sequence contexts, including CG, CHG and CHH (where H = A, T, or C), which is further proven to be correlated with its repeat content and genome size. We show that DNA methylation in the gene body negatively regulates the gene expression of tea plants, whereas non-CG methylation in the flanking region enables a positive regulation of gene expression. We demonstrate that transposable element-mediated methylation dynamics significantly drives the expression divergence of duplicated genes in tea plants. The DNA methylation and expression divergence of duplicated genes in the tea plant increases with evolutionary age and selective pressure. Moreover, we detect thousands of differentially methylated genes, some of which are functionally associated with chilling stress. We also experimentally reveal that DNA methyltransferase genes of tea plants are significantly downregulated, whereas demethylase genes are upregulated at the initial stage of chilling stress, which is in line with the significant loss of DNA methylation of three well-known cold-responsive genes at their promoter and gene body regions. Overall, our findings underscore the importance of DNA methylation regulation and offer new insights into duplicated gene evolution and chilling tolerance in tea plants.
- Published
- 2021