绵羊骨代谢相关基因VDR密码子偏好性分析

doi:10.16431/j.cnki.1671-7236.2022.08.005

中国畜牧兽医 ›› 2022, Vol. 49 ›› Issue (8): 2888-2898.doi: 10.16431/j.cnki.1671-7236.2022.08.005

绵羊骨代谢相关基因VDR密码子偏好性分析

马建青¹, 杨清芳², 宋占锋¹, 贾丁丁¹, 吴东蔚¹, 莫秀芳³, 徐增年⁴, 杨克¹, 吴占勇¹, 籍颖⁵, 周荣艳⁵

1. 华北医疗健康集团邢台总医院骨科实验室, 邢台 054000;
2. 邢台市动物疫病预防控制中心, 邢台 054001;
3. 华北理工大学护理与康复学院, 唐山 063210;
4. 河北医科大学实验动物学部, 石家庄 050017;
5. 河北农业大学, 保定 071001

收稿日期:2022-02-18 出版日期:2022-08-05 发布日期:2022-07-21
通讯作者: 籍颖, 周荣艳 E-mail:hdjiying@163.com;rongyanzhou@126.com
作者简介:马建青,E-mail:majianqing2006@126.com。
基金资助:
河北省自然科学基金资助项目(H2021108006);邢台市科技支撑计划项目(2018ZC121)

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

MA Jianqing¹, YANG Qingfang², SONG Zhanfeng¹, JIA Dingding¹, WU Dongwei¹, MO Xiufang³, XU Zengnian⁴, YANG Ke¹, WU Zhanyong¹, JI Ying⁵, ZHOU Rongyan⁵

1. Department of Orthopedic Laboratory, North China Medical & Health Group Xingtai General Hospital, Xingtai 054000, China;
2. Xingtai Animal Disease Prevention and Control Center, Xingtai 054001, China;
3. College of Nursing and Rehabilitation, North China University of Science and Technology, Tangshan 063210, China;
4. Deparment of Zoology, Hebei Medical University, Shijiazhuang 050017, China;
5. Hebei Agricultural University, Baoding 071001, China

Received:2022-02-18 Online:2022-08-05 Published:2022-07-21

摘要/Abstract

摘要： 【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。

关键词: 绵羊; VDR基因; 密码子偏好性; 骨代谢

Abstract: 【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.

Key words: Ovis aries; VDR gene; codon bias; bone metabolism

中图分类号:

马建青, 杨清芳, 宋占锋, 贾丁丁, 吴东蔚, 莫秀芳, 徐增年, 杨克, 吴占勇, 籍颖, 周荣艳. 绵羊骨代谢相关基因VDR密码子偏好性分析[J]. 中国畜牧兽医, 2022, 49(8): 2888-2898.

MA Jianqing, YANG Qingfang, SONG Zhanfeng, JIA Dingding, WU Dongwei, MO Xiufang, XU Zengnian, YANG Ke, WU Zhanyong, JI Ying, ZHOU Rongyan. Analysis of Codon Usage Bias of VDR Gene Related to Bone Metabolism in Ovis aries[J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 2888-2898.

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绵羊骨代谢相关基因VDR密码子偏好性分析

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

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