Q 785; S 917.4
上海海洋大学农业农村部鱼类营养与环境生态研究中心专项 (A1-3201-19-300204)；上海市科委项目 (17391900300)
为增加对刀鲚在进化过程中因核心基因家族改变而产生的特殊机制的了解。实验利用比较基因组学，通过比较刀鲚及其近缘物种斑马鱼、三刺鱼、青鳉、红鳍东方鲀和绿河鲀基因组，鉴定刀鲚基因家族；利用CAFÉ v 4.2软件进行基因家族扩张和收缩分析；最后将鉴定的扩张基因家族基因与GO、KEGG等数据库进行比对、注释和通路分析。结果显示，刀鲚具有11 872个基因家族，包含16 470个基因，有2 963个基因未形成基因家族。同其他5个物种相比，刀鲚有150个特有基因家族，包含419个基因。刀鲚扩张和收缩基因家族分析结果表明，刀鲚有1 200个基因家族扩张了，7 543个基因家族收缩了。刀鲚显著扩张的基因家族有39个，包含508个基因；显著收缩的基因家族有36个，包含21个基因。刀鲚显著扩张基因家族GO富集分析条目中鉴定较多的是，代谢过程、催化活性、细胞、细胞组分等。KEGG富集分析条目中鉴定较多的是紧密连接、心肌细胞的肾上腺素能信号、心肌收缩、细胞黏附分子等。与渗透压调节相关的通路有紧密连接、心肌收缩等；与生殖洄游行为相关的通路有GnRH信号通路、嗅觉转导通路等。对显著扩张基因家族基因进行基因组定位，结果显示23号染色体上基因数目显著多于其他染色体。定位在23号染色体的基因多为组蛋白基因，其功能与染色质结构调控有关。研究表明，刀鲚渗透调节、信号转导、代谢、性腺发育和嗅觉等方面均可能产生了适应性进化，且其染色质结构调节也可能发生改变。
Coilia nasus belongs to genus Coilia, family Engraulidae, order Clupeiformes, which is migratory fish with high nutritional and economic value in China. C. nasus has both migratory and land-locked populations, which is an excellent model for studying reproductive migration and adaptive evolution. This study identified and analyzed the expansion and contraction of gene families in C. nasus, in order to explore the special mechanism of C. nasus caused by changes in the core gene families in the evolutionary process. Comparative genomology was used to identify the C. nasus’s gene families by using the genomes of Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes and Tetraodon nigroviridis. Then CAFE V4.2 software was used for gene family expansion and contraction analysis. Finally, GO, KEGG and other database were applied for annotations and pathway analysis of the significantly expanded gene families’ genes. 11 872 gene families were identified in C. nasus, including 16 470 genes. Besides, 2 963 unclustered genes were identified. Compared with the other 5 species, 150 gene families containing 419 genes were found unique to C. nasus. In addition, 1 200 gene families of C. nasus expanded and 7 543 gene families contracted. P values of 39 expanded gene families (including 508 genes) and 36 contracted gene families (including 21 genes) are less than 0.05. 508 genes of significantly expanded gene families were utilized for pathway analysis. Metabolic process, catalytic activity, cell and cell part are the top GO terms. Tight junctions, adrenergic signaling in cardiomyocytes, cardiac muscle contraction, cell adhesion molecules (CAMs), etc. are the top KEGG pathways. Tight junctions and cardiac muscle contraction pathways are related to osmoregulation. GnRH signaling pathway and olfactory transduction pathway are involved in reproductive migration behavior. Furthermore, we mapped 508 genes of significantly expansion gene families on the genome, and found that chromosome 23 had much more genes than other chromosomes. And the genes of significantly expanded gene families located on chromosome 23 were mostly histone genes, which were related to the regulation of chromatin structure. Pathway analysis of the expansion and exclusive gene families of C. nasus indicate that the osmotic regulation, signal transduction, metabolism, gonad development and olfactory transduction may have undergone adaptive evolution, and the regulation of its chromatin structure may also have been altered. These results have strengthened our understanding of the adaptive evolution of C. nasus.
ZHANG Jinpeng, GAO Shufang, SHI Yonghai, YAN Yinlong, QI Ming, LIU Qigen. Identification and analysis of gene families expansion and contraction in Coilia nasus[J]. Journal of Fisheries of China,2022,46(6):897~905复制