| 鲤trim25多拷贝基因进化和表达调控初探 |
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| 作者姓名： | 朱优秀 江炎亮 张芹 冯建新 张瀚元 吴碧银 许建 |
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| 作者单位： | 上海海洋大学 水产科学国家级实验教学示范中心 上海 201306; 中国水产科学研究院 农业农村部水生动物基因组学重点实验室 北京 100141;河南省水产科学研究院 河南 郑州 450044 |
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| 摘 要： | 天然免疫系统是硬骨鱼类抵抗病毒感染的主要防御系统，三重基序(tripartite motif, TRIM)蛋白家族作为天然免疫系统的重要组成部分，参与病毒感染的免疫网络调控，其中，TRIM25已被证实在多种鱼类的免疫反应中发挥重要作用。本研究对鲤(Cyprinus carpio) trim25基因的16个拷贝进行了序列进化分析、共线性分析和功能域结构分析，并比较了各拷贝在组织中的表达和顺式调控位点的差异。序列比对和系统进化分析结果均显示，位于鲤11和12号染色上、结构完整的TRIM25的2个拷贝与金线鲃(Sinocyclocheilus grahami)和斑马鱼(Danio rerio)的TRIM25蛋白结构高度相似，与鲤科鱼类以外的其他物种的结构差异较大。基因共线性结果显示，trim25基因上下游基因在不同物种的进化过程中相对保守。鲤TRIM25蛋白的结构分析显示，在鲤TRIM25的16个拷贝中，有6个拷贝具有完整功能结构域，其中，各有5个拷贝在鲤的肝与脑组织中高表达。在构建的表达数量性状基因座(eQTL)调控网络中，在肝和脑组织中分别筛选到5个和17个顺式调控trim25基因表达的单核苷酸多态性(SNP)位点。本研究对鲤trim25基因多个拷贝的序列差异进行了比较，并对鲤与其他物种TRIM25的序列、进化关系和共线性相似度进行了比较，揭示了鲤trim25各拷贝间的结构多样性和在组织中的表达情况，筛选出了可能调控trim25基因表达的SNP位点，为今后研究鲤TRIM25相关的调控和抗病研究提供了理论依据。
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| 关 键 词： | 鲤 TRIM25 蛋白结构 系统进化树 eQTL |
| 收稿时间： | 2021/1/27 0:00:00 |
| 修稿时间： | 2021/3/1 0:00:00 |
Gene Evolution and Expression Regulation of Multiple Copies of trim25 in Common Carp, Cyprinus carpio |
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| Authors: | ZHU Youxiu JIANG Yanliang ZHANG Qin FENG Jianxin ZHANG Hanyuan WU Biyin XU Jian |
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| Institution: | National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China;Henan Academy of Fishery Sciences, Zhengzhou, Henan 450044, China |
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| Abstract: | The innate immune system is the main defense against viral infections in teleost fish. As an important part of the innate immune system, the TRIM protein family participates in the regulation of the immune network during virus infection. Among such proteins, TRIM25 has been reported to play an important role in the immune response of many types of fish. In this study, 16 copies of the trim25 gene in common carp (Cyprinus carpio) were compared with those of other species by phylogenetic and syntenic analyses. Functional domain structures for 16 copies of the TRIM25 protein were predicted, and the expression and cis-regulatory network in tissues for each gene copy were compared. Sequence alignment and phylogenetic analysis showed that the TRIM25 protein structure of C. carpio was highly similar to that of Sinocyclocheilus grahami and Danio rerio, but distinct from that of other species beyond Cyprinidae. The results of gene synteny indicated that the upstream and downstream genes of trim25 were relatively conserved in the evolution of different species. Structural analysis of TRIM25 showed that six of the sixteen copies in C. carpio had complete functional domains; five of these copies were highly expressed in liver and brain tissue. In the expression quantitative trait loci (eQTL) regulatory network for trim25, 5 and 17 SNPs were determined to regulate trim25 expression in liver and brain tissue, respectively. In this study, the sequence differences of multiple copies of trim25 in common carp were compared, and the evolutionary relationship and synteny of trim25 were identified. The diversity of the structure and tissue expression of trim25 genes in the common carp were revealed, and the SNP sites that may regulate trim25 gene expression were identified, providing a reference for future research on trim25 related regulation and disease resistance in the C. carpio. |
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| Keywords: | Cyprinus carpio TRIM25 Protein structure Phylogenetic tree eQTL |
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