河流型与沼泽型水牛CSN3基因密码子使用特征分析  

Analysis of Codon Use Characteristics of CSN3 Gene in River and Swamp Buffalo(Bubalus bubalis)

作　　者：范新阳[1] 邱立华[1] 罗国祥 张永云[3] 滕晓红[1] 苗永旺[1] 

机构地区：[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

出　　处：《云南农业大学学报（自然科学版）》2017年第2期238-245,共8页Journal of Yunnan Agricultural University:Natural Science

基　　金：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)

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。In this study, codon usage features of milk casein gene CSN3 for both river and swamp buf- falo, and the differences in codon usage and evolutionary relationships between buffalo and other spe- cies 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 co- don 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 spe- cies. 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.

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 

分 类 号：S823.2[农业科学—畜牧学]