双软件多参数联合对草鱼同义密码子偏性的分析  

Analysis of Synonymous Codon Biasin Grass Carp(Ctenopharyngodon idella)Via combined Multipara Metersusing Double Soft Wares

作　　者：肖波[1] 迟晓艳[1] 屈慧鸽[1] 张莉[1] 王晓洁[1] 

机构地区：[1]鲁东大学生命科学学院,山东烟台264025

出　　处：《中国农学通报》2014年第17期39-45,共7页Chinese Agricultural Science Bulletin

基　　金：山东省烟台市科技发展计划项目"草鱼呼肠孤病毒DNA疫苗的制备及其免疫学效应研究"(2011066);鲁东大学引进人才基金"草鱼呼肠孤病毒表达库的构建及其免疫学效应研究"(LY20083307)

摘　　要：密码子偏性分析数据有助于被用来构建高效表达载体,提高外源基因在宿主体内的表达效率。为了解草鱼密码子使用情况,以便在草鱼中高效表达外源目标蛋白来预防草鱼疾病的发生,应用Codon W及CAIcal软件分析了草鱼(Ctenopharyngodon idella)基因组中的208个蛋白质的编码序列。通过分别计算密码子中各个位置的GC含量、密码子适应指数(CAI)、有效密码子数(ENc)、密码子偏爱指数(CBI)、同义密码子的使用频率、最优密码子使用频率(FOP)等,分析了草鱼的密码子使用偏性,确定了草鱼的最优密码子。结果显示,草鱼密码子第2位的GC含量明显低于第1、3位,第3位表现出对以G或C碱基结尾的密码子偏向使用;所确定的23个最优密码子中,除终止密码子是以碱基A结尾外,有18个以碱基G或C结尾,4个以碱基U结尾。所分析结果既可用于分析草鱼基因的组成结构,了解草鱼的分子进化状态,又可以通过所获的结果来指导对外源基因进行分子改造,提高外源基因在草鱼中的表达效率。Abstract： The data of codon bias facilitate to construct expression vector for improving the efficiency of the expression of foreign genes in host. In order to understand the grass carp codon usage, and further to efficiently express the target protein in the grass carp to prevent the grass carp disease, the Coding DNA Sequences （CDS） of 208 proteins in the genome of grass carp （Ctenopharyngodon idella） were analyzed using the software of Codon W and CAIcal. The synonymous codon bias in Ctenopharyngodon idella was analyzed by calculating the content of G/C at three positions of codons, the Codon Adaptation Index（CAI）, the Effective Number of Codon（ ENC）, the Absolute Frequency of Synonymous Codon Usage（AFSCU）, the Relative Synonymous Codon Usage （RSCU）, the Codon Bias Indices （CBIs） and the Frequency of Optimal Codons（FOP）, respectively. The optimal codons were also determined. The results showed that the content of G or C at the position of second codons was significantly lower than that at the first and third positions, and genes prefer to the codons with C or G at the third position. In addition, 23 codons were determined as the optimal codons. Apart from the stop codon, which was terminated in A, there were 18 codons terminated in G or C, four codons terminated in U. The results provide evidences for many fields, such as analyzing the composition of grass carp gene structure, understanding the grass carp molecular evolution condition, guiding the molecular modification of exogenous gene to increase the expression efficiency in grass carp, and so on.

关 键 词：草鱼 同义密码子 密码子偏爱性 最优密码子 

分 类 号：Q527[生物学—生物化学]