云南农业大学学报(自然科学)
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云南农业大学学报(自然科学) 2017, Vol. 32 Issue (2) :238-245    DOI: 10.16211/j.issn.1004-390X(n).2017.02.008
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河流型与沼泽型水牛CSN3基因密码子使用特征分析
范新阳1, 邱立华1, 罗国祥2, 张永云3, 滕晓红1, 苗永旺1
1. 云南农业大学 动物科学技术学院, 云南 昆明 650201;
2. 云南省大理州家畜繁育指导站, 云南 大理 671000;
3. 云南农业大学, 农科专业基础实验教学示范中心, 云南 昆明 650201
Analysis of Codon Use Characteristics of CSN3 Gene in River and Swamp Buffalo (Bubalus bubalis)
FAN Xinyang1, QIU Lihua1, LUO Guoxiang2, ZHANG Yongyun3, TENG Xiaohong1, MIAO Yongwang1
1. College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China;
2. Livestock Breeding Guidance Station of Dali Prefecture, Dali 671000, China;
3. Teaching Demonstration Center of the Basic Experiments of Agricultural Majors, Yunnan Agricultural University, Kunming 650201, China

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摘要 本研究以54头河流型水牛和70头沼泽型水牛为研究对象,并以从NCBI数据库中下载的普通牛、野牦牛、野牛、绵羊、小鼠和人的序列作对照,对乳成分中重要的κ-酪蛋白(kappa casein)编码基因CSN3的密码子使用偏好性及水牛与其他物种间CSN3基因密码子使用的差异和进化关系进行了深入分析。结果表明:两种类型水牛CSN3基因密码子使用特征相似,河流型水牛CSN3基因共有26个偏好使用的密码子,而沼泽型水牛共有27个;其中,两类水牛偏好性较强的密码子均为GUU、UCA、AGU、CCA、AGG、GGU和GGA(RSCU≥2),河流型水牛对Asp的两种密码子GAU、GAC没有使用偏好性,而沼泽型水牛偏好使用GAC;河流型水牛编码Asp和Cys的同义密码子RSCU值为1,而沼泽型水牛只有编码Cys的同义密码子RSCU值为1。研究发现,所有物种CSN3基因均偏好使用以A/U结尾的密码子,但不同物种之间偏好使用密码子种类和数目均有差异。在密码子使用频率上,水牛CSN3基因与其他牛科物种的差异小于与小鼠、人的差异。密码子使用偏好聚类分析表明,河流型与沼泽型水牛亲缘关系最近,聚为一类,然后依次与其他牛、绵羊、小鼠和人等物种相聚。
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范新阳
邱立华
罗国祥
张永云
滕晓红
苗永旺
关键词河流型水牛   沼泽型水牛   牛科物种   CSN3基因   密码子偏好性   聚类分析     
Abstract: In this study, codon usage features of milk casein gene CSN3 for both river and swamp buffalo, and the differences in codon usage and evolutionary relationships between buffalo and other species were analyzed based on the data of CSN3 gene from 54 river buffalo and 70 swamp buffalo, and the data of Bos taurus, Bos mutus, Bos bison, Ovis aries, Mus musculus and Homo sapiens recruited from NCBI database. The results showed that codon usage features of CSN3 gene in two types of buffalo were similar. River and swamp buffalo had 26 and 27 biased codon, respectively. Among them, strongly biased codons for both types of buffalo were codon GUU, UCA, AGU, CCA, AGG, GGU and GGA (RSCU ≥ 2). Two types of buffalo only have one difference in the use of the Asp codon, that is, the river buffalo were not bias toward codon GAU and GAC, while swamp buffalo was bias toward codon GAC. Synonymous codon RSCUs of the encoding Asp and Cys of the river type buffalo were 1, while synonymous codon RSCU of swamp buffalo only codon Cys was 1. Furthermore, CSN3 gene of all species in this study were bias toward the synonymous codons with A and U at the third codon position. However,there were differences in the types and numbers of codon usage bias among different species. The differences in codon usage frequency between buffalo and other bovine species were less than those of between buffalo and mouse, and human. Cluster analysis showed two types buffalo gathered into one group, then in turn gathered with cattle, sheep, mouse and human.
Keywordsriver buffalo   swamp buffalo   bovine species   CSN3   codon usage bias   cluster analysis     
Received 2016-08-07;
Fund:国家自然科学基金项目(31460582,30660024);云南省应用基础研究重点项目(2014FA032,2007C0003Z)。
Corresponding Authors: 苗永旺(1964-),男,内蒙古通辽人,博士,教授,博士生导师,主要从事动物遗传学研究。E-mail:yongwangmiao1@126.com     Email: yongwangmiao1@126.com
About author: 范新阳(1991-),男,河北石家庄人,硕士研究生,主要从事动物遗传学研究。E-mail:985402140@qq.com;邱立华(1990-),女,湖南涟源人,硕士研究生,主要从事动物遗传学研究。E-mail:1366033116@qq.com
引用本文:   
范新阳, 邱立华, 罗国祥, 张永云, 滕晓红, 苗永旺.河流型与沼泽型水牛CSN3基因密码子使用特征分析[J]  云南农业大学学报(自然科学), 2017,V32(2): 238-245
FAN Xinyang, QIU Lihua, LUO Guoxiang, ZHANG Yongyun, TENG Xiaohong, MIAO Yongwang.Analysis of Codon Use Characteristics of CSN3 Gene in River and Swamp Buffalo (Bubalus bubalis)[J]  Journal of Yunnan Agricultural University, 2017,V32(2): 238-245
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