Environmental DNA methylation signatures in a clonal invasive crayfish

DNA methylation is an important epigenetic modification that has been repeatedly implied in organismal adaptation. However, many previous studies that have linked DNA methylation patterns to environmental factors have been limited by confounding factors, such as cell-type heterogeneity and genetic variation. In this study, we analyzed DNA methylation variation in marbled crayfish, a clonal and invasive freshwater crayfish that is characterized by a largely tissue-invariant methylome and negligible genetic variation. Using a capture-based subgenome bisulfite sequencing approach that covers a small, variably methylated portion of the marbled crayfish genome, we identified specific and highly localized DNA methylation signatures for specimens from geographically and ecologically distinct wild populations. These results were replicated both biologically and technically by re-sampling at different time points and by using independent methodology. Finally, we show specific methylation signatures for laboratory animals and for laboratory animals that were reared at a lower temperature. Our results thus demonstrate the existence of environment-dependent DNA methylation signatures in a clonal animal.

DNA甲基化（DNA methylation）是一类重要的表观遗传修饰，此前多项研究均证实其与机体适应密切相关。然而，既往诸多将DNA甲基化模式与环境因素相关联的研究，均受到混杂因素的限制，例如细胞类型异质性（cell-type heterogeneity）与遗传变异（genetic variation）。本研究针对纹螯虾（marbled crayfish）的DNA甲基化变异展开分析——该物种为克隆性入侵淡水螯虾，其甲基化组在多数组织中保持恒定，且遗传变异可忽略不计。研究团队采用基于捕获的亚基因组亚硫酸氢盐测序（capture-based subgenome bisulfite sequencing）技术，该技术可覆盖纹螯虾基因组中一小部分可变甲基化区域，最终从地理与生态特征迥异的野生种群样本中，鉴定出特异性且高度局限的DNA甲基化特征。上述结果在生物学与技术层面均得到了重复验证：通过不同时间点的重新采样以及采用独立的实验方法均可复现该结论。最后，本研究还鉴定出了实验室饲养个体以及在低温环境下饲养的实验个体的特异性甲基化特征。综上，本研究证实了克隆动物中存在环境依赖的DNA甲基化特征。