绵羊骨代谢相关基因VDR密码子偏好性分析

【目的】明确绵羊维生素D受体(vitamin D receptor,VDR)基因密码子的使用特征,探究不同物种VDR基因进化规律,为骨代谢等相关疾病动物建模提供参考依据。【方法】利用CodonW、EMBOSS、Usage Codon和DNAMAN等软件对VDR基因CDS区的同义密码子相对使用度(RSCU)、密码子碱基含量、有效密码子数(ENc)及密码子偏好指数(CBI)等参数进行统计分析,并在多物种间进行比较,同时利用ENc-Plot关联分析和中性绘图等方法分析VDR基因密码子偏好性使用的主要影响因素,并基于多物种同义密码子相对使用度数据与系统进化聚类分析探究密码子使用模式与生物进化的内在联系。【结果】绵羊VDR基因中有23个偏好使用以G/C结尾的密码子;大猩猩、鸸鹋、褐家鼠等其他14个物种在密码子使用上表现出了与之较为相似的特征,而在半胱氨酸、甘氨酸、组氨酸、丝氨酸、脯氨酸等个别氨基酸编码时,鸸鹋、褐家鼠和麻雀等部分物种显现出独有特点;ENc-Plot绘图和中性绘图分析显示,选择压力对VDR基因密码子偏好性的影响强于突变压力。【结论】以G/C结尾的密码子为VDR基因优势密码子,自然选择是导致其偏好性的主要力量,密码子偏好使用存在物种特异性,并与物种亲缘关系进化存在关联性。

Analysis of Codon Usage Bias of VDR Gene Related to Bone Metabolism in Ovis aries

【Objective】 This study was aimed to understand the codon usage characteristic and explore the evolution pattern of vitamin D receptor (VDR) gene in Ovis aries,and provide reference basis for establishing animal model related to bone metabolism diseases.【Method】 The relative synonymous codon usage (RSCU),codon composition,effective number of codons (ENc),codon bias index (CBI) and several parameters were analyzed using CodonW,EMBOSS,Usage Codon and DNAMAN softwares,and compared these parameters among multiple species,meanwhile,ENc-Plot and neutrality plot were used to analyze the main influencing factors of codon bias use of VDRgene.The internal relationship between codon use patterns and biological evolution was explored by means of relative synonymous codon usage of multiple species and cluster analysis.【Result】 There were 23 codons of VDRgene in Ovis ariespreferred to use codons ending with G/C.The other 14 species,such as Gorilla gorilla gorilla,Dromaius novaehollandiaeand Rattus norvegicusshowed similar characteristics in codon usage with Ovis aries.While,some species,such as Dromaius novaehollandiae,Rattus norvegicusand Passer montanus showed unique characteristics in the coding of Cys,Gly,His,Ser and Pro.ENc-Plot and neutrality plot analysis showed that selection pressure was stronger than mutation pressure on the codon usage bias of VDR gene.【Conclusion】 The codon ending with G/C was the dominant codon of VDR gene,the natural selection was the main force leading to the phenomenon.Meanwhile,the codon usage bias was species-specific,and there was a correlation with the evolution of genetic relationship.