河流型与沼泽型水牛LEP基因同义密码子使用特征分析

Characterization of synonymous codon usage in the LEP gene of river and swamp buffalo

为了了解影响泌乳性状的重要编码基因LEP基因的密码子使用特征,试验以27头河流型水牛和41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、山羊、小鼠和人的序列作对照,对两类水牛LEP基因的同义密码子使用偏好性及水牛与其他物种间LEP基因密码子使用的差异和进化关系进行深入分析。结果表明:两种类型水牛LEP基因密码子使用特征相似,河流型和沼泽型水牛LEP基因均有25个偏好使用的密码子;其中两类水牛LEP基因偏好性较强的密码子均为UUC、CUG、AUC、GUC、UCC、ACC、GCC、CAC、CGG、AGG和GGG(RSCU≥2.00)。河流型水牛CCA和CCG密码子的RSCU值分别为0.09和0.35,而沼泽型水牛分别为0.34和0.10。此外,所有物种LEP基因均偏好使用以G/C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。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、山羊、小鼠和人等物种相聚。在密码子使用频率上,LEP基因与小鼠密码子偏好性差异小于与大肠杆菌和酵母密码子偏好性的差异,说明小鼠更适合作为水牛LEP基因的外源表达系统。

The aim of the current study was to clarify the codon usage features of LEP gene which is an important coding gene of affecting milk trait. The data of LEP gene from 27 river buffalo and 41 swamp buffalo were used as research target, the analysis was conducted by compared with those of Bos taurus, Bos mutus, Bos bison, Ovis aries, Capra hircus, Mus musculus and Homo sapiens recruited from NCBI database. The synonymous codon usage bias in both river and swamp buffalo, and the differences in codon usage and evolutionary relationships between buffalo and other species were analyzed, respectively. The results showed that codon usage features of LEP gene in two types of buffalo were similar. The LEP gene of river and swamp buffalo had 25 biased codon. Among them, the biased codons for the LEP gene of both types of buffalo were codon UUC, CUG, AUC, GUC, UCC, ACC, GCC, CAC, CGG, AGG and GGG （RSCU^2.00）. The RSCU values of codon CCA and CCG for the river type buffalo were 0.09 and 0.35, respectively, while that of codon CCA and CCG for the swamp type buffalo were 0.34 and 0.10, respectively. Furthermore, all species in our study were bias toward the synonymous codons with G and C at the third codon position in LEP gene. However, there were differences in the types and numbers of codon usage bias among different species. Clustering analysis showed two types of buffalo gathered into one group, then in turn gathered with cattle, sheep, goat, mouse and human. The differences in synonymous co- don usage frequeficy between buffalo LEP gene and genome of Mus musculus were less than Escherichia coli and yeast genome. Therefore, Mus musculus expression systems might be more suitable for the expression of buffalo LEP gene.