短短芽孢杆菌GZDF3全基因组密码子偏好性分析

Analysis of Codon Bias in Whole Genome of Brevibacillus brevis GZDF3

为了解短短芽孢杆菌GZDF3全基因组密码子的使用特性,采用Codon W 1.4.2软件和Mobyle portal在线软件分析菌株GZDF3全基因组密码子偏好性,分析该菌的相对同义密码子使用度(relative synonymous codon usage,RSCU)、密码子适应指数(codon adaption index,CAI)、有效密码子数(effective number of codon,Nc)、同义密码子第3位中G/C含量(GC3s)和高表达优越密码子。结果表明,短短芽孢杆菌GZDF3密码子第2位密码子的GC含量明显低于第1位和第3位,为37.56%,第1位和第3位的GC含量差异较小,分别为55.50%和51.13%;基因组大部分Nc值介于30~60,说明密码子偏好性普遍偏弱;RSCU值大于1的密码子共有27个,其中以A或T结尾的14个,占51.9%,并确定了27个最优密码子,为外源基因表达提供理论基础。

To understand the operating characteristics of whole genome codon of Brevibacillus brevis GZDF3, in this study, bais analysis of strain GZDF3 was performed by using bioinformatics software Codon W 1.4.2 and Mobyle portal online program, parsing the bacteria’s relative synonymous codon usage（RSCU）, codon adaption index（CAI） and effective number of codon（Nc）, the GC content of the third codon position（GC3 s） and superior high expression of codon. The results showed that the GC content of the second codon position was about 37.56%,significantly lower than the first and the third, which were respectively about 55.50% and 51.13%, slightly differed.Nc value of gemone were mostly between 30 and 60, which meant that codon bais generally was weak. Relative synonymous codon usage（RSCU） revealed 27 optimal codons（RSCU value〉1）, of which 14（51.9%） ended with A or T, providing theoretical basis for exogenous gene expression.