Data from: Rapid response to changing environments during biological invasions: DNA methylation perspectives

Dissecting complex interactions between species and their environments has long been a research hotspot in the fields of ecology and evolutionary biology. The well-recognized Darwinian evolution has well explained long-term adaptation scenarios; however, “rapid” processes of biological responses to environmental changes remain largely unexplored, particularly moleculare mechanisms such as DNA methylation that have recently been proposed to play crucial roles in rapid environmental adaptation. Invasive species, which have capacities to successfully survive rapidly changing environments during biological invasions, provide great opportunities to study molecular mechanisms of rapid environemental adaptation. Here we used the methylation-sensitive amplified polymorphism (MSAP) technique in an invasive model ascidian, Ciona savignyi, to investigate how species interact with rapidly changing environments at the whole genome level. We detected quite rapid DNA methylation response: significant changes of DNA methylation frequency and epigenetic differentiation between treatment and control groups occurred only after 1-hour of high temperature exposure or after 3-hour of low salinity challenge. In addition, we detected time-dependent hemi-methylation changes and increased intra-group epigenetic divergence induced by environmental stresses. Interestingly, we found evidence of DNA methylation resilience, as most stress-induced DNA methylation variation maintained shortly (~48 hours) and quickly returned back to the control levels. Our findings clearly showed that invasive species could rapidly respond to acute environmental changes through DNA methylation modifications, and rapid environmental changes left significant epigenetic signatures at the whole genome level. All these results provide fundamental background to deeply investigate the contribution of DNA methylation mechanisms to rapid contemporary environmental adaptation.解析物种与环境间的复杂互作，长期以来都是生态学与进化生物学领域的研究热点。广为人知的达尔文进化论已对长期适应场景作出充分阐释，但生物针对环境变化做出响应的"快速"过程，在很大程度上仍未得到充分探索，尤其是近年来被认为在快速环境适应中发挥关键作用的DNA甲基化（DNA methylation）等分子机制。入侵物种在生物入侵过程中能够在快速变化的环境中成功存活，为研究快速环境适应的分子机制提供了绝佳契机。本研究以入侵性模式生物柄海鞘（Ciona savignyi）为研究对象，采用甲基化敏感扩增多态性（methylation-sensitive amplified polymorphism, MSAP）技术，在全基因组层面探究物种与快速变化环境间的互作机制。研究检测到极为迅速的DNA甲基化响应：仅在高温暴露1小时或低盐胁迫3小时后，处理组与对照组间的DNA甲基化频率及表观遗传分化便出现显著变化。此外，本研究还检测到时间依赖性的半甲基化变化，以及环境胁迫诱导的组内表观遗传分化加剧现象。有趣的是，本研究发现了DNA甲基化的弹性恢复现象——大多数胁迫诱导的DNA甲基化变异仅维持较短时间（约48小时），随后便快速恢复至对照组水平。本研究结果明确表明，入侵物种可通过DNA甲基化修饰快速响应急性环境变化，且快速环境变化会在全基因组层面留下显著的表观遗传印记。上述研究结果为深入探究DNA甲基化机制在当代快速环境适应中的作用提供了重要基础。