National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
BMC Plant Biol. 2019 Jul 12;19(1):307. doi: 10.1186/s12870-019-1923-7.
DNA methylation is a crucial epigenetic modification, which is involved in many biological processes, including gene expression regulation, embryonic development, cell differentiation and genomic imprinting etc. And it also involves many key regulatory genes in eukaryotes. By tracing the evolutionary history of methylation-related genes, we can understand the origin and expansion time of these genes, which helps to understand the evolutionary history of plants, and we can also understand the changes of DNA methylation patterns in different species. However, most studies on the evolution of methylation-related genes failed to be carried out for the whole DNA methylation pathway.
In this study, we conducted a comprehensive identification of 33 methylation-related genes in 77 species, and investigated gene origin and evolution throughout the plant kingdom. We found that the origin of genes responsible for methylation maintenance and demethylation evolved early, while most de novo methylation-related genes appeared late. The methylation-related genes were expanded by whole genome duplication and tandem replication, but were also accompanied by a large number of gene absence events in different species. The gene length and intron length varied a lot in different species, but exon structure and functional domains were relatively conserved. The phylogenetic relationships of methylation-related genes were traced to reveal the evolution history of DNA methylation in different species. The expression patterns of methylation-related genes have changed during the evolution of species, and the expression patterns of these genes in different species can be clustered into four categories.
The study describes a global characterization of DNA methylation-related genes in the plant kingdom. The similarities and differences in origin time, gene structure and phylogenetic relationship of these genes lead us to understand the evolutionary conservation and dynamics of DNA methylation in plants.
DNA 甲基化是一种重要的表观遗传修饰，涉及许多生物学过程，包括基因表达调控、胚胎发育、细胞分化和基因组印记等。它还涉及真核生物中的许多关键调节基因。通过追踪与甲基化相关基因的进化历史，我们可以了解这些基因的起源和扩展时间，有助于理解植物的进化历史，也可以了解不同物种中 DNA 甲基化模式的变化。然而，大多数关于与甲基化相关基因进化的研究未能对整个 DNA 甲基化途径进行研究。
在这项研究中，我们在 77 个物种中全面鉴定了 33 个与甲基化相关的基因，并研究了整个植物界中基因的起源和进化。我们发现，负责甲基化维持和去甲基化的基因的起源进化较早，而大多数从头甲基化相关基因出现较晚。甲基化相关基因通过全基因组复制和串联复制得到扩展，但在不同物种中也伴随着大量基因缺失事件。不同物种中基因长度和内含子长度差异很大，但外显子结构和功能域相对保守。追踪与甲基化相关基因的系统发育关系，揭示了不同物种中 DNA 甲基化的进化历史。在物种进化过程中，与甲基化相关基因的表达模式发生了变化，并且这些基因在不同物种中的表达模式可以聚类为四个类别。
本研究描述了植物王国中 DNA 甲基化相关基因的全面特征。这些基因在起源时间、基因结构和系统发育关系上的异同，使我们能够了解植物中 DNA 甲基化的进化保守性和动态性。
