亚洲草鱼群体的差异甲基化分析

Differential methylation analysis of Ctenophyngodon idella populations in Asia

为探究水产养殖过程中DNA甲基化对亚洲草鱼群体人工驯化与环境选择适应的影响,本实验对亚洲范围内8个地区的养殖和野生草鱼群体进行了全基因组甲基化测序,测序序列经质控后比对到草鱼参考基因组上,并进行差异甲基化分析和功能富集分析。结果显示,甲基化测序共获得308.15 Gbp测序数据,平均测序深度31×,平均比对率62.97%。对5个养殖群体分别与野生背景群体间进行差异甲基化分析,共发掘出76422个差异甲基化位点、3737个差异甲基化区域、1950个差异甲基化基因。功能分析发现,差异甲基化基因被注释到血管生成、神经嵴细胞迁移、T细胞分化、颅骨系统发育、肌肉细胞发育等GO功能分类中。KEGG代谢途径富集分析的结果显示,差异甲基化基因主要参与细胞黏附连接、Notch信号通路和Wnt信号通路等代谢途径。在这些功能注释的基因中,有许多与神经、免疫、骨骼和肌肉等组织发育相关的重要基因,如sema3d、sema5bb和nrg2a等。本研究进一步对表观遗传修饰在草鱼人工驯化和环境选择适应作用机制的探究奠定了基础,为保存和科学利用草鱼种质资源提供了有价值的遗传基础数据。

Ctenophyngodon idella is one of the most important aquaculture species in the world,and suffered from local adaptation during the process of introduction and aquaculture.However,most studies of C.idella local adaptation were based on genetic variation,and the effect of epimutation was still widely unknown.In order to explore how DNA methylation affects the domestication and environmental adaptation of the C.idella populations in Asia.A whole-genome bisulfite sequencing was performed between 5 farmed populations and the wild background population,followed by further differential methylation analysis and enrichment analysis.A total of 308.15 Gb sequencing data were generated with a sequencing depth of 31×and a mapping rate of 62.97%in average,where76422 differentially methylated loci(DML),3737 differentially methylated regions(DMR),and 1950 differentially methylated genes(DMG)were identified.Gene Ontology enrichment analysis showed that the DMGs were significantly enriched in development process,such as angiogenesis,neural crest cell migration,and cranial skeletal system development.Annotation with the KEGG pathway database exhibited these genes were mainly involved in adhesion junction,Notch signaling pathway,and Wnt signaling pathway.Among the DMG,some might be functional in the developmental process of neural,immunity,bone,and muscle tissues,like sema3d,sema5bb and nrg2a.This study enhances the understanding of the epigenetic mechanism of domestication and environmental adaption during the process of aquaculture and provides valuable data for the conservation and utilization of the C.idella germplasm resources.