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Divergent DNA methylation contributes to duplicated gene evolution and chilling response in tea plants
- Source :
- The Plant Journal. 106:1312-1327
- Publication Year :
- 2021
- Publisher :
- Wiley, 2021.
-
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.
- 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
Subjects
Details
- ISSN :
- 1365313X and 09607412
- Volume :
- 106
- Database :
- OpenAIRE
- Journal :
- The Plant Journal
- Accession number :
- edsair.doi.dedup.....fe9b2a6ca6c23b75659695fc3b14c609