Department of Biology, Aarhus University, Aarhus, Denmark.
Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark.
Mol Ecol. 2022 Aug;31(16):4286-4306. doi: 10.1111/mec.16586. Epub 2022 Jul 12.
The role of methylation in adaptive, developmental and speciation processes has attracted considerable interest, but interpretation of results is complicated by diffuse boundaries between genetic and non-genetic variation. We studied whole genome genetic and methylation variation in the European eel, distributed from subarctic to subtropical environments, but with panmixia precluding genetically based local adaptation beyond single-generation responses. Overall methylation was 70.9%, with hypomethylation predominantly found in promoters and first exons. Redundancy analyses involving juvenile glass eels showed 0.06% and 0.03% of the variance at SNPs to be explained by localities and environmental variables, respectively, with GO terms of genes associated with outliers primarily involving neural system functioning. For CpGs 2.98% and 1.36% of variance was explained by localities and environmental variables. Differentially methylated regions particularly included genes involved in developmental processes, with Hox clusters featuring prominently. Life stage (adult versus glass eels) was the most important source of inter-individual variation in methylation, probably reflecting both ageing and developmental processes. Demethylation of transposable elements relative to pure European eel was observed in European X American eel hybrids, possibly representing postzygotic barriers in this system characterized by prolonged speciation and ongoing gene flow. Whereas the genetic data are consistent with a role of single-generation selective responses, the methylation results underpin the importance of epigenetics in the life cycle of eels and suggest interactions between local environments, development and phenotypic variation mediated by methylation variation. Eels are remarkable by having retained eight Hox clusters, and the results suggest important roles of methylation at Hox genes for adaptive processes.
甲基化在适应、发育和物种形成过程中的作用引起了相当大的兴趣，但由于遗传和非遗传变异之间的界限模糊，结果的解释变得复杂。我们研究了分布在亚北极到亚热带环境中的欧洲鳗的全基因组遗传和甲基化变异，但由于存在单代反应之外的遗传基础上的局部适应的泛化，因此无法进行基于遗传的局部适应。总体甲基化率为 70.9%，启动子和第一外显子主要发生低甲基化。涉及幼鳗的冗余分析表明，SNP 中的 0.06%和 0.03%的方差分别由地点和环境变量解释，与异常值相关的基因的 GO 术语主要涉及神经系统功能。对于 CpG，0.06%和 0.03%的方差分别由地点和环境变量解释。差异甲基化区域特别包括参与发育过程的基因，其中 Hox 簇尤为突出。个体间甲基化差异的最重要来源是生命阶段（成年与幼鳗），这可能反映了衰老和发育过程。与纯欧洲鳗相比，欧洲鳗与美洲鳗杂交种中转座元件的去甲基化现象被观察到，这可能代表了该系统中合子后障碍的特征，该系统具有长期的物种形成和持续的基因流动。遗传数据与单代选择性反应的作用一致，而甲基化结果则为鳗鱼生命周期中表观遗传学的重要性提供了依据，并表明了环境、发育和表型变异之间通过甲基化变异相互作用的重要性。鳗鱼的特点是保留了八个 Hox 簇，结果表明甲基化在 Hox 基因的适应过程中具有重要作用。
