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半滑舌鳎(Cynoglossus semilaevis)Sox基因家族生物信息学分析
高 进,马佳璐,刘 洋,邵长伟,贾晓东,陈松林
作者单位
高 进 南京农业大学无锡渔业学院 无锡 214081;农业部海洋渔业可持续发展重点实验室 中国水产科学研究院黄海水产研究所 青岛 266071;青岛海洋科学与技术国家实验室 海洋渔业科学与食物产出过程功能实验室 青岛 266200 
马佳璐 农业部海洋渔业可持续发展重点实验室 中国水产科学研究院黄海水产研究所 青岛 266071;青岛海洋科学与技术国家实验室 海洋渔业科学与食物产出过程功能实验室 青岛 266200 中国海洋大学水产学院 青岛 266003 
刘 洋 南京农业大学无锡渔业学院 无锡 214081;农业部海洋渔业可持续发展重点实验室 中国水产科学研究院黄海水产研究所 青岛 266071;青岛海洋科学与技术国家实验室 海洋渔业科学与食物产出过程功能实验室 青岛 266200 
邵长伟 农业部海洋渔业可持续发展重点实验室 中国水产科学研究院黄海水产研究所 青岛 266071;青岛海洋科学与技术国家实验室 海洋渔业科学与食物产出过程功能实验室 青岛 266200 
贾晓东 农业部海洋渔业可持续发展重点实验室 中国水产科学研究院黄海水产研究所 青岛 266071 
陈松林 南京农业大学无锡渔业学院 无锡 214081;农业部海洋渔业可持续发展重点实验室 中国水产科学研究院黄海水产研究所 青岛 266071;青岛海洋科学与技术国家实验室 海洋渔业科学与食物产出过程功能实验室 青岛 266200 
摘要:
Sox (SRY-related HMG-box)基因家族是在动物体内发现的一类编码转录因子的基因家族,广泛参与了动物生长发育、理化反应,特别是性别决定和分化等过程。本研究采用生物信息学方法,利用Sox基因高度保守的HMG-box区序列作为种子序列,检索半滑舌鳎(Cynoglossus semilaevis)基因组注释的蛋白数据库,共鉴定分离出23个Sox基因。并在全基因组水平对半滑舌鳎Sox基因家族进行了保守结构域序列、进化、基因结构、染色体定位及基因表达模式的系统分析。结果显示,通过保守结构域分析发现了半滑舌鳎Sox基因家族除CseSox32外,皆存在一段9个氨基酸残基(RPMNAFMVW)的高度保守基序;结合保守结构域及进化分析,所有半滑舌鳎Sox基因被分为B1、B2、C、D、E、F和K共7个亚族,且不同的亚族在进化上存在种间趋同性和种内特异性;基因结构分析将半滑舌鳎Sox基因分为两大类,即单外显子类和多外显子类;而染色体定位分析则显示,Sox基因在染色体上散乱分布,不存在集簇现象;不同类型性腺及幼鱼变态前后的Sox基因家族表达谱显示,半滑舌鳎Sox基因具有不同的组织表达模式,表明其在性别分化、性腺发育及早期幼鱼发育过程中可能发挥了重要作用。本研究对于今后半滑舌鳎Sox基因家族深入的功能验证及分子作用机制研究具有重要的意义,也为日益丰富的水产基因组资源的挖掘利用提供了参考。
关键词:  Sox基因  HMG结构域  半滑舌鳎  生物信息学
DOI:10.11758/yykxjz.20160115002
分类号:
基金项目:国家自然科学基金项目(31130057)、山东省自然科学基金(ZR2014CP011)、山东省农业良种工程重大课题和泰山学者攀登计划专项共同资助
Bioinformatics Analysis of Sox Gene Family in Cynoglossus semilaevis
GAO Jin,MA Jialu,LIU Yang,SHAO Changwei,JIA Xiaodong,CHEN Songlin
Abstract:
Sox genes are developmental regulators characterized by the presence of an HMG (high mobility group) DNA-binding domain, and they exist extensively in animal bodies in nature. Members of the Sox gene family have been shown to be conserved during evolution and play crucial roles in a wide variety of developmental processes, including growth and development, hemopoiesis, the development and formation of the nervous system, especially, sex determination and differentiation. Genome resources are growing faster and faster, and it provides a platform for the study gene families by scanning whole genomic sequences. We study Sox genes in Cynoglossus semilaevis by using bioinformatics analysis on the standard of whole genome. A total of 23 Sox genes were identified systematically from C. semilaevis and classified into 7 subfamilies which had not been reported yet. They are subfamily B1, B2, C, D, E, F and K, each of these groups may have distinct and specific functions. Sequence analysis of conserved domain of Sox genes in C. semilaevis shows that, all of members in the family contain 9 amino acid residues (RPMNAFMVW) as a highly conserved motif except CseSox32. On the other hand, the motif in Sox32 is identical in all specie as RPLNAF. Research on the highly conserved HMG box in C. semilaevis causes the discovery of these Sox genes, and phylogenetic analysis supports the classification of subfamily. To date, about 10 and 40 Sox genes have been identified in invertebrates and vertebrates separately. The phylogenetic analysis also suggests that the groups of Sox genes might be extended in the process of evolution. Subfamilies have got convergence between different species, and got otherness inside one of these species. Gene location results show that these 23 Sox genes were distributed randomly on 15 chromosomes, and we do not find gene cluster. The analysis of gene structure divides all of the Sox genes into two categories, evaluation on the basis of the exon numbers of the gene are less or more than two. The expression profiles of C. semilaevis Sox genes show a characteristic of different kinds of gonad and metamorphosis specific, and it indicated Sox genes may play key roles during sex determination, gonad differentiation and early development in C. semilaevis. To sum up the above, we enhance understanding of Sox genes in C. semilaevis with bioinformatics analysis, such as system evolution, gene structure, chromosomal location and gene expression patterns. Our results suggest that bioinformatics analysis may contribute to further functional verification of gene family and be good for genome resources mining and utilization.
Key words:  Sox genes  HMG motif  Cynoglossus semilaevis  Bioinformatics