| 鲤和草鱼IL17受体基因家族的全基因组识别、起源进化及表达分析 |
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| 引用本文： | 董传举,张江凡,李胜杰,吕红皂,聂国兴,李学军.鲤和草鱼IL17受体基因家族的全基因组识别、起源进化及表达分析[J].水产学报,2018,42(11):1693-1703. |
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| 作者姓名： | 董传举 张江凡 李胜杰 吕红皂 聂国兴 李学军 |
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| 作者单位： | 河南师范大学水产学院;中国水产科学研究院黑龙江水产研究所淡水鱼类育种国家与地方联合工程实验室;中国水产科学研究院珠江水产研究所 |
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| 基金项目： | 国家自然科学基金（31801032）；国家大宗淡水鱼产业技术体系建设项目（CARS-45-04）；淡水渔业育种国家地方联合工程实验室开放课题（KF-2016-03）；河南省科技攻关（172102210348，182102210081）；河南师范大学博士启动课题（qd16159） |
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| 摘 要： | 为了研究鲤科鱼类最具代表性的二个物种—鲤和草鱼IL17受体基因家族的起源进化,实验采用比较基因组学和生物信息学的方法,分别在鲤和草鱼基因组数据库进行序列比对和注释,然后对得到的基因进行结构域和系统发育学分析,最后在12个不同组织中进行基因表达分析研究。结果显示,在鲤和草鱼中分别注释得到9个和5个IL17受体基因家族成员。系统发育分析显示,该基因家族不存在鱼类特有的基因,在硬骨鱼类中具有一定的保守性。比较基因组学结果显示,与四足动物相比,大多数硬骨鱼类中IL17受体基因没有明显增多。鲤与草鱼等其他硬骨鱼类相比,除IL17RB以外,其余IL17受体基因家族成员均加倍。不同组织的表达分析结果显示全基因组复制后不同基因拷贝的功能发生了分化。研究表明,虽然硬骨鱼经历第三轮全基因组复制,但是由于复制发生时间久远,大多数基因已经发生改变或退化,进而在基因组中丢失。而鲤第四轮基因组复制时间发生在820万年前,复制发生时间较近,故复制后的基因基本得以保留。但是对于一些具有特殊功能的高度保守基因(例如IL17RB),也会发生在极短时间内出现丢失现象。鲤和草鱼健康组织的表达谱分析结果同样表明,鲤IL17受体基因的不同拷贝之间已经发生了快速进化及亚功能化,并且这种现象在鲤四倍体基因组中普遍存在。
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| 关 键 词： | 鲤 草鱼 IL17受体 全基因组复制 基因分化 |
| 收稿时间： | 2018/3/1 0:00:00 |
| 修稿时间： | 2018/5/27 0:00:00 |
Genome-wide identification, phylogeny, and expression of IL17 receptor genes in common carp (Cyprinus carpio) and grass carp (Ctenopharyngodon idella) |
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| DONG Chuanju,ZHANG Jiangfan,LI Shengjie,LV Hongzao,NIE Guoxing and LI Xuejun.Genome-wide identification, phylogeny, and expression of IL17 receptor genes in common carp (Cyprinus carpio) and grass carp (Ctenopharyngodon idella)[J].Journal of Fisheries of China,2018,42(11):1693-1703. |
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| Authors: | DONG Chuanju ZHANG Jiangfan LI Shengjie LV Hongzao NIE Guoxing and LI Xuejun |
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| Institution: | College of Fisheries, Henan Normal University, Xinxiang 453007, China;National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China,College of Fisheries, Henan Normal University, Xinxiang 453007, China,Pearl River Fisheries Research Institute, Chinese Acdemy of Fishery Sciences, Guangzhou 510380, China,College of Fisheries, Henan Normal University, Xinxiang 453007, China,College of Fisheries, Henan Normal University, Xinxiang 453007, China and College of Fisheries, Henan Normal University, Xinxiang 453007, China |
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| Abstract: | To gain a better understanding of the evolution and action mode of the IL17R family in common carp (Cyprinus carpio) and grass carp (Ctenopharyngodon idellus), the two representative species of Cyprinidae, we analyzed them with the method of comparative genomics and bioinformatics. Sequence alignment and annotation were conducted in the genome database of common carp and grass carp as well as the analysis of genetic structure and phylogeny respectively. Finally, gene expression analysis was performed in 12 different tissues of these two species. We identified and characterized nine and five IL17R homologues. Along with genes annotation and nomenclature, phylogenetic analysis built on amino acid sequences of the IL17R proteins in 12 species showed highly conservative and no specific genes in teleosts. Comparative genomics showed that there was no significant increase in IL17 receptor genes in most teleosts compared with tetrapods. Nevertheless, except for IL17RB genes, all of the members showed extensive gene duplications, leading to nine IL17R genes in common carp. Expression analysis of different tissues showed that the functions of different gene copies were differentiated after the whole genome duplication. Studies have shown that an additional round of duplication, also named teleost-specific (TS) WGD, or the 3R WGD, took place in the common ancestor of all extant teleosts. After duplication, one of the two redundant copies of a gene should theoretically have the freedom to degenerate and become lost from the genome without consequence. Also, it was generally hypothesized that, compared to other teleost, common carp had undergone additional whole genome duplication (the 4R WGD). The comprehensive estimation based on whole genome datasets suggested that the latest WGD event occurred around 8.2 MYA. Therefore, we postulated that the significant expansion of IL17R genes in the common carp genome may be the result of this additional WGD, which could have caused a sudden doubling of the IL17R genes and the IL17RB had been lost in their evolution history with the reason that the functions of genes were redundant and conservative. Expression profiling showed that most of the IL17R genes were expressed in a more-or-less tissue-specific fashion. |
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| Keywords: | Cyprinus carpio Ctenopharyngodon idella IL17 receptor whole genome duplication gene differentiation |
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