盐碱水环境对脊尾白虾基因组DNA甲基化的影响  

Effects of Saline-Alkaline Water Environment on DNA Methylation of Exopalaemon carinicauda

作　　者：秦桢 李吉涛[2] 李明栋 王佳佳[2] 葛倩倩[2] 刘萍[2] 李健[2] QIN Zhen;LI Jitao;LI Mingdong;WANG Jiajia;GE Qianqian;LIU Ping;LI Jian(National Experimental Teaching Demonstration Center of Aquatic Science,Shanghai Ocean University,Shanghai 201306,China;Yellow Sea Fisheries Research Institute,Chinese Academy of Fishery Sciences,Key Laboratory of Sustainable Development of Marine Fisheries,Ministry of Agriculture and Rural Affairs,Laboratory for Marine Fisheries Science and Food Production Processes,Pilot National Laboratory for Marine Science and Technology(Qingdao),Qingdao,Shandong 266071,China)

机构地区：[1]上海海洋大学水产科学国家级实验教学示范中心,上海201306 [2]中国水产科学研究院黄海水产研究所农业农村部海洋渔业可持续发展重点实验室青岛海洋科学与技术试点国家实验室海洋渔业科学与食物产出过程功能实验室,山东青岛266071

出　　处：《渔业科学进展》2022年第4期33-50,共18页Progress in Fishery Sciences

基　　金：国家重点研发计划课题(2019YFD0900404-03);国家自然科学基金项目(32072974);财政部和农业农村部:国家现代农业产业技术体系和中国水产科学研究院基本科研业务费项目(2020TD46)共同资助。

摘　　要：为探讨盐碱水环境对脊尾白虾(Exopalaemon carinicauda)基因组DNA甲基化的影响,本研究利用MethylRAD-Seq技术探究了长期盐碱水养殖组(SAS)和正常海水养殖对照组(SW)脊尾白虾鳃组织中的DNA甲基化水平,并对关键通路和基因进行了差异表达分析。结果显示,脊尾白虾鳃组织基因组中CG和CWG位点(W=A或T)分别检测到2347003和416176处甲基化,甲基化普遍存在于基因组的基因间区和内含子区域,共筛选到8805个(8189个CG-DMSs和616个CWG-DMSs)差异甲基化位点,盐碱水环境下DNA甲基化水平略有增强。通过KEGG富集分析发现,DMS所在差异表达基因显著富集在HIF-1信号通路和剪接体通路,通路中hif-p、hk和sf3b1等关键基因在脊尾白虾盐碱水环境适应中可能发挥着重要作用;对SW和SAS组差异甲基化基因(DMG)进行筛选,得到158个CG-DMGs和94个CWG-DMGs,其中,富集到脂质代谢和囊泡介导的转运通路中的DMG最多;此外,有一些DNA甲基化位点与基因表达呈负相关,表明DNA甲基化与基因调控之间存在复杂的联系,大部分基因组DNA甲基化对基因表达有正调控效应。本研究结果首次分析了在盐碱水环境下脊尾白虾鳃组织的DNA甲基化水平特征,为解析甲壳类盐碱水环境适应机制提供了基础信息。The global levels of soil and water salinization and alkalinization are increasing with the influence of climate and topography changes,as well as other natural and human factors.Saline-alkaline water(SAW)all over the world has specific characteristics such as high alkalinity,high pH,and complex water quality types,which inhibits the survival and culture of common aquatic animals.The ridgetail white prawn Exopalaemon carinicauda is an economically important marine shrimp with many advantages,such as widely environmental adaptability,rapid growth,and good reproductive capability.It is potentially suitable for large-scale culture in SAW;however,its adaptability to this environment remains unclear.Exploring the E.carinicauda adaptability mechanism to SAW will help to guide culture management for marine crustaceans.In this study,the DNA methylomes of the E.carinicauda gill tissue cultured in SAW and normal seawater(SW)were analyzed and the impact on gene regulation was investigated by MethylRAD sequencing.The results showed 2347003 and 416176 methylations at the CG and CWG sites(W=A or T),respectively.Comparing the SAW and SW groups,the CG and CWG loci in the SAW group increased slightly,indicating that SAW induced more DNA methylation in the gill cells that activated or inhibited pathways and played a crucial role in the environmental changes adaption.Methylation was prevalent in the exon,intron,splice site,and upstream and downstream regions of the E.carinicauda gill genes,as well as in the intergenic regions.DNA methylation sites were mostly distributed in the Genebody.The DNA methylation distribution curve peaked in the downstream sequence of the transcription start site and upstream sequence of the transcription termination site.The methylation label frequency was significantly higher in these regions in relation to other sequences.A total of 8805 differential methylation sites(DMSs)were screened,including 8189 CG DMSs and 616 CWG DMSs.Obviously,the CG DMS was significantly higher than the CWG DMS.The intergenic

关 键 词：脊尾白虾 盐碱水环境 DNA甲基化 差异表达基因 

分 类 号：S917.4[农业科学—水产科学]