Table_1_Comparative Epigenomics Reveals Host Diversity of the Trichinella Epigenomes and Their Effects on Differential Parasitism.docx

Comparative epigenomics provides new insights on evolutionary biology in relation with complex interactions between species and their environments. In the present study, we focus on deciphering the conservation and divergence of DNA methylomes during Trichinella evolution. Whole-genome bisulfite sequencing and RNA-seq were performed on the two clades of Trichinella species, in addition to whole-genome sequencing. We demonstrate that methylation patterns of sing-copy orthologous genes (SCOs) of the 12 Trichinella species are host-related and can mirror known phylogenetic relationships. Among these SCOs, we identify a panel of genes exhibiting hyper-/hypo-methylated features in gene-bodies or respective promoters that play pivotal roles in transcriptome regulation. These hyper-/hypo-methylated SCOs are also of functional significance across developmental stages, as they are highly enriched species-specific and stage-specific expressed genes both in Ad and ML stages. We further identify a set of parasitism-related functional genes that exhibit host-related differential methylation and expression among those SCOs, including p53-like transcription factor and Cdc37 that are of functional significance for elucidating differential parasitology between the two clades of Trichinella. This comparative epigenome study can help to decipher the environmental effects on differential adaptation and parasitism of the genus Trichinella.

比较表观基因组学为探究物种与环境间复杂互作相关的进化生物学问题提供了全新视角。本研究聚焦解析旋毛虫属（Trichinella）进化过程中DNA甲基化组的保守性与分化模式。我们对两类旋毛虫支系开展了全基因组亚硫酸氢盐测序（Whole-genome bisulfite sequencing）、RNA测序（RNA-seq），同时辅以全基因组测序（Whole-genome sequencing）。研究证实，12种旋毛虫的单拷贝同源基因（single-copy orthologous genes, SCOs）的甲基化模式与宿主相关，且能够反映已知的系统发育关系。在上述SCOs中，我们筛选出一批在基因本体区或对应启动子区域呈现高/低甲基化特征的基因，这类基因在转录组调控中发挥关键作用。这些高/低甲基化的SCOs在不同发育阶段同样具有重要功能：它们在成虫（Ad）与肌幼虫（ML）阶段显著富集物种特异性及阶段特异性表达基因。我们进一步在这些SCOs中筛选出一批与寄生相关的功能基因，它们呈现出宿主相关的差异甲基化与表达模式，其中包括p53样转录因子与Cdc37，二者对于阐明两类旋毛虫支系间的寄生差异具有重要功能意义。本项比较表观基因组研究有助于解析环境因素对旋毛虫属物种差异化适应与寄生行为的影响。