Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish [RNA-seq]

The marbled crayfish (Procambarus virginalis) is a unique freshwater crayfish characterized by genetic uniformity, phenotypic variability, and substantial invasive potential. As invasion into different habitats occurs in the absence of genetic variation, epigenetic mechanisms have been suggested to mediate phenotypic adaptation. However, epigenetic regulation has not been analyzed in this organism yet. Here we show that the recently published P. virginalis draft genome sequence encodes a conserved DNA methylation system. Whole-genome bisulfite sequencing of multiple replicates and different tissues revealed a methylation pattern that is characterized by gene body methylation of housekeeping genes. Interestingly, this pattern was largely tissue-invariant, suggesting a function that is unrelated to cell-fate specification. Indeed, integrative analysis of RNA-seq datasets showed that gene body methylation correlated with stable gene expression, while unmethylated genes often showed a high degree of inter-individual expression variation. Our findings thus establish the methylome of an emerging model organism and suggest that methylation-dependent regulation of gene expression variability may facilitate the phenotypic adaptation and invasive spread of this animal. Overall design: RNA-seq data of different tissues (hepatopancreas, abdominal musculature) from 6 different P. virginalis individuals and 2 different P. fallax individuals

大理石纹螯虾（Procambarus virginalis）是一种独特的淡水螯虾，以遗传均一性、表型多样性以及极强的入侵潜能为典型特征。由于该物种可在缺乏遗传变异的情况下入侵不同生境，因此有研究推测表观遗传机制介导了其表型适应性。然而，目前尚未针对该物种开展表观遗传调控相关研究。本研究证实，近期发布的大理石纹螯虾（P. virginalis）草图基因组编码一套保守的DNA甲基化系统。对多个重复样本及不同组织开展的全基因组亚硫酸氢盐测序（Whole-genome bisulfite sequencing）结果显示，该物种存在以管家基因基因体甲基化为特征的甲基化模式。值得注意的是，该甲基化模式在多数组织中保持稳定，提示其功能与细胞命运特化无关。进一步整合RNA测序（RNA-seq）数据集进行分析后发现，基因体甲基化与基因表达稳定性呈正相关，而未发生甲基化的基因往往表现出较高的个体间表达差异。综上，本研究明确了一种新兴模式生物的甲基化组（methylome）特征，并提出依赖甲基化的基因表达变异调控机制，或可促进该物种的表型适应性与入侵扩散。实验整体设计：采集6只大理石纹螯虾（P. virginalis）与2只泽螯虾（P. fallax）的不同组织（肝胰腺、腹部肌肉）的RNA测序数据。