摘要
为了明确Sox9基因密码子的使用特征,揭示山羊和其他物种Sox9基因的进化规律,为建立骨科腰椎间盘退变动物模型提供基础研究试验依据,此研究利用生物信息学软件CodonW、Usage Codon和DNAMAN分析山羊Sox9基因完全编码区密码子偏爱性,比较不同物种Sox9基因密码子偏爱指标,基于完整编码区序列生成了亲缘关系进化聚类图,计算出每个物种Sox9基因的总变异值。分析显示山羊Sox9基因中有26个偏好使用密码子以G/C为第三位碱基;夜猴、家犬、原鸡、大猩猩、人、恒河猴、小家鼠、家兔、绵羊、黑猩猩、婆罗洲猩猩和褐家鼠等12个物种在密码子使用上与山羊Sox9基因基本相似,但是在编码丙氨酸、脯氨酸和苏氨酸等个别氨基酸时,原鸡和小家鼠及褐家鼠与其他物种的密码子偏爱性存在差异。Sox9基因偏好使用以G/C结尾的密码子。亲缘关系进化聚类图和不同物种RSCU值显示Sox9基因密码子偏好性与亲缘关系的远近存在关联性。
To identify the codon usage of Sox9 gene and reveal the evolutional principles of Sox9 for Carpra hircus and other species, and to provide basic research and experimental evidence for establishing an animal model of orthopedic lumbar disc degeneration, the paper analyzed the codon usage bias of the complete coding sequence of Sox9 gene in Carpra hircus by Codon W software and Codon Usage online program and DNAMAN software.The codon usage bias index of Sox9 gene in different species was compared,And the phylogenetic tree was generated based on the complete coding sequence of Sox9 gene among species, and then the value of total variation was calculated. Results showed in Sox9 gene of Capra hircus, there were 26 common preferences used codon that with G and C at the third codon position. In codon usage, Capra hircus, Aotus nancymaae, Canis lupus familiaris, Gallus gallus, Gorilla gorilla gorilla, Homo sapiens, Macaca mulatta, Mus musculus, Oryctolagus cuniculus, Ovis aries, Pan troglodytes, Pongo pygmaeus and Rattus norvegicus were similar mostly. But for the codon usage of Alanine, Proline and Threonine,Gallus gallus, Mus musculus and Rattus norvegicus existed differences. The Sox9 gene was bias toward the synonymous codons with G and C at the third codon position. The clustering relationship and the value of RSCU with Sox9 among different species demonstrated that preferences of codon has a certain relationship with genetic relationship.
作者
马建青
吴占勇
李祥龙
孔建军
吴春富
徐增年
于晶晶
MA Jianqing;WU Zhanyong;LI Xianglong;KONG Jianjun;WU Chunfu;XU Zengnian;YU Jingjing(Department of Animal Laboratory of the General Hospital of Xingtai Mining Industry Bloc,Xingtai,Hebei 054000,China;Department of Animal Laboratory,Xingtai Institute of Orthopaedics,Xingtai,Hebei 054000,China;College of Animal Science and Technology,Hebei Agricultural University,Baoding,Hebei 071001,China;Department of Zoology,Hebei Medicial University,Shijiazhuang,Hebei 050032,China;Department of Glandular Surgery,Xingtai Third Hospital,Xingtai,Hebei,054000,China)
出处
《家畜生态学报》
北大核心
2019年第12期14-21,共8页
Journal of Domestic Animal Ecology
基金
邢台市科技支撑计划项目(2018ZC121)
关键词
山羊
椎间盘退变基因
SOX9基因
密码子偏好性
Capra hircus
intervertebral disc degeneration related gene
Sox9 gene
codon bias
