水牛瘦素受体基因密码子使用偏好性分析

Analysis of Codon Usage Bias of Leptin Receptor Gene in Buffalo

试验选取27头河流型水牛和41头沼泽型水牛,以从NCBI数据库中下载的家牛、野牦牛、野牛、绵羊、山羊、小鼠和人的序列作对照,对编码瘦素受体(leptin receptor,LEPR)基因的密码子偏好性及水牛与其他物种间密码子使用的差异和进化关系进行了深入分析。结果发现,所有的密码子在河流型水牛和沼泽型水牛LEPR基因中均有使用,两种类型水牛偏好使用的密码子有28个,其中使用偏好性较强的密码子为AGA(RSCU≥2),表明河流型水牛和沼泽型水牛LEPR基因密码子使用特征相似。水牛及参考物种LEPR基因均偏好使用以A/U结尾的密码子,但水牛与其他参考物种间偏好使用密码子的种类和数目有差异。密码子使用偏好聚类分析表明,河流型水牛与沼泽型水牛亲缘关系最近,先聚为一类,然后与家牛、野牦牛和野牛聚为一类,再与绵羊、山羊、小鼠和人等物种聚为一类。在密码子使用频率上,河流型水牛LEPR基因与酵母密码子偏好性差异小于与大肠杆菌和小鼠密码子偏好性差异,从而揭示酵母更适合作为水牛LEPR基因的外源表达系统。

The experiment was aimed to study the synonymous codon usage features of leptin receptor （LEPR） gene in buffalos, the codon usage differences and evolutionary relationships between buffalo and other reference species. The coding region of LEPR gene from 27 river buffalo and 41 swamp buffalo were sequencing,and Bos taurus,Bos mutus,Bos bison,Ovis aries,Capra hircus,Mus musculus and Homo sapiens were chosen as reference species from NCBI database. The results showed that all synonymous codons were used in the LEPR gene of river buffalo and swamp buffalo. Two kinds of buffalo had 28 biased usage codons. Among them,strongly biased codon was AGA （RSCU≥2）,which indicated that codon usage features were similar in LEPR gene of two types of buffalo. Furthermore,buffalo and the species compared in this study were bias toward the synonymous codons with A/U at the third codon position in LEPR gene.However,the types and numbers of bias usage codons were different between buffalo and the species compared. Clustering analysis showed that the relationship between river buffalo and swamp buffalo was the closest,and they gathered into one group firstly,then they gathered with Bos taurus,Bos mutus and Bos bison,and further gathered in turn with Ovis aries,Capra hircus,Mus musculus and Homo sapiens.The frequency differences of synonymous codon usage between buffalo LEPR gene and yeast genome were less than that between buffalo and E.coli,Mus musculus genome,suggesting that yeast might be more suitable as an external expression system for buffalo LEPR gene.