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张曼曼,冯兵,罗双双,王卫民,周小云.二倍体和四倍体泥鳅全基因组DNA甲基化的比较[J].华中农业大学学报,2018,37(5):95-103
二倍体和四倍体泥鳅全基因组DNA甲基化的比较
Comparative studies on DNA methylation variation between diploid and tetraploid Misgurnus anguillicaudatus
投稿时间:2018-01-22  
DOI:
中文关键词:  泥鳅  二倍体  四倍体  DNA甲基化  MethylRAD-Seq
英文关键词:Misgurnus anguillicaudatus  diploid  tetraploid  DNA methylation  MethylRAD-Seq
基金项目:国家自然科学基金项目(31472267)
作者单位E-mail
张曼曼 华中农业大学水产学院/农业动物遗传育种与繁育教育部重点实验室武汉 430070 1527050643@qq.com 
冯兵 华中农业大学水产学院/农业动物遗传育种与繁育教育部重点实验室武汉 430070  
罗双双 华中农业大学水产学院/农业动物遗传育种与繁育教育部重点实验室武汉 430070  
王卫民 华中农业大学水产学院/农业动物遗传育种与繁育教育部重点实验室武汉 430070  
周小云 华中农业大学水产学院/农业动物遗传育种与繁育教育部重点实验室武汉 430070 zhouxy@mail.hzau.edu.cn 
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中文摘要:
      以二倍体和四倍体泥鳅为研究对象,采用甲基化修饰依赖性内切酶测序技术(MethylRAD-Seq)在全基因组水平上分析泥鳅的DNA甲基化特点及倍性间的DNA甲基化变异。测序结果共得到302 111 684条Methyl RAD序列标签。与参考基因组比对结果显示,泥鳅的甲基化位点主要分布在基因体区(gene body),其次为内含子区(intron)和基因间区(intergenic),而在其他功能元件上的分布较少。四倍体泥鳅的整体甲基化水平比二倍体高,尤其是在第一外显子区(1st Exon)和转录起始位点上游1 500 bp至200 bp区(TSS1500),且倍性间差异极显著(P<0.01)。但在启动子区,四倍体泥鳅的甲基化水平略低于二倍体。在二倍体和四倍体泥鳅间共筛选到1 268个差异甲基化CmCGG位点和14个差异甲基化CmCWGG位点,这些位点主要分布于内含子、基因体和基因间区。比较各基因的甲基化水平,共得到684个倍性间差异甲基化基因。KEGG分析结果显示,倍性间差异甲基化基因主要富集到与生长发育、免疫及错配修复等相关通路上。
英文摘要:
      Using MethylRAD-Seq method, we analyzed DNA methylation distribution in the genome of Misgurnus anguillicaudatus and compared DNA methylation variation between the diploids and tetraploids. In total, 302 111 684 MethyRAD sequence tags were obtained and mapped to the reference genome. The results showed that, the DNA methylated sites distributed mainly in gene body, followed by intron and intergenic, but fewer methylated sites were found in other functional elements. Total DNA methylation level in the tetraploids was higher than that in the diploids, especially significant differences (P<0.01) of DNA methylation level existed in 1st Exon and upstream 200-1 500 bp region of the transcription start site (TSS 1500). However, in the promoter region, DNA methylation level in the tetraploids was lower than that in the diploids. For DNA methylation level of each sites, 1 268 CmCGG and 14 CmCWGG sites showed significant difference between the diploids and tetraploids, which mainly distributed in intron, gene body and intergenic. A total of 684 genes exhibited significant methylation variations between ploidy. KEGG Pathway enrichment analysis showed that, the genes with DNA methylation variation between ploidy enriched mainly in the growth development, immunity and mismatch repair related signaling pathways.
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