Data from: DNA methylation and potential for epigenetic regulation in Pygospio elegans

Transitions in developmental mode are common evolutionarily, but how and why they occur is not understood. Developmental mode describes larval phenotypes, including morphology, ecology and behavior of larvae, which typically are generalized across different species. The polychaete worm Pygospio elegans is one of few species polymorphic in developmental mode, with multiple larval phenotypes, providing a possibility to examine the potential mechanisms allowing transitions in developmental mode. We investigated the presence of DNA methylation in P. elegans, and, since maternal provisioning is a key factor determining eventual larval phenotype, we compared patterns of DNA methylation in females during oogenesis in this species. We demonstrate that intragenic CpG site DNA methylation and many relevant genes necessary for DNA methylation occur in P. elegans. Methylation-sensitive AFLP analysis showed that gravid females with offspring differing in larval developmental mode have significantly different methylation profiles and that the females with benthic larvae and non-reproductive females from the same location also differ in their epigenetic profiles. Analysis of CpG sites in transcriptome data supported our findings of DNA methylation in this species and showed that CpG observed/expected ratios differ among females gravid with embryos destined to different developmental modes. The differences in CpG site DNA methylation patterns seen among the samples suggest a potential for epigenetic regulation of gene expression (through DNA methylation) in this species.

发育模式的演化转变在进化历程中颇为常见，但其发生的具体路径与内在动因至今尚未阐明。发育模式（developmental mode）指幼虫表型范畴，涵盖幼虫的形态特征、生态习性与行为模式，此类特征通常在不同物种间具有一定的通用性。优雅偶蕊吸虫（Pygospio elegans）作为多毛纲蠕虫，是少数发育模式存在多态性的物种之一，兼具多种幼虫表型，为探究发育模式演化转变的潜在机制提供了可行的研究路径。本研究首先调查了优雅偶蕊吸虫体内DNA甲基化（DNA methylation）的存在情况；鉴于母体营养供给是决定最终幼虫表型的核心影响因素，我们同时比较了该物种雌性个体在卵子发生（oogenesis）过程中的DNA甲基化表达模式。研究证实，优雅偶蕊吸虫体内存在基因内CpG位点的DNA甲基化修饰，且具备DNA甲基化通路所需的诸多相关功能基因。甲基化敏感扩增片段长度多态性（methylation-sensitive AFLP）分析结果显示：产下幼虫发育模式存在差异的子代的怀卵雌性个体，其甲基化谱存在显著差异；且来自同一栖息地、子代以底栖幼虫为主的怀卵雌性个体与非繁殖雌性个体，其表观遗传谱同样存在显著差异。针对转录组数据（transcriptome data）中的CpG位点开展的分析验证了本研究关于该物种存在DNA甲基化的结论，同时发现，携带将发育为不同模式幼虫的胚胎的雌性个体之间，其CpG观测/预期比值存在显著差异。不同样本间观测到的CpG位点DNA甲基化模式差异，提示优雅偶蕊吸虫具备通过DNA甲基化实现基因表达表观遗传调控的潜在能力。