樟树叶绿体基因组密码子偏好性分析

Codon usage bias analysis of chloroplast genome of camphora tree(Cinnamomum camphora)

为分析樟树(Cinnamomum camphora)叶绿体基因组密码子偏好性使用模式,该研究利用CodonW、EMBOSS、R语言等软件和程序,对53条樟树叶绿体基因组密码子使用模式及偏好性进行了系统分析。结果表明:樟树叶绿体基因的有效密码子数(ENC)在36.82～59.30之间,表明密码子的偏好性较弱。相对同义密码子使用度(RSCU)分析发现RSCU>1的密码子有32个,其中28个以A、U结尾,表明第3位密码子偏好使用A和U碱基。中性绘图分析发现GC3与GC12的相关性不显著,回归曲线斜率为0.049,说明密码子偏好性主要受到自然选择的影响。ENC-plot分析发现大部分基因落在曲线的下方,同样表明选择是影响密码子偏好性的主要因素。该研究发现共有9个密码子(UUU、CUU、UCA、ACA、UAU、AAU、GAU、UGA、GGA)被鉴定为樟树叶绿体基因组的最优密码子。

In order to analyze the codon usage patterns of the chloroplast genome of camphora tree,53 CDS(coding DNA sequences)were selected from the chloroplast genome of camphora tree and the codon usage pattern and bias were analyzed by CodonW,EMBOSS,R language and other softwares.The results showed that the effective codon number(ENC)of the chloroplast gene ranged from 36.82 to 59.30,indicating that bias of codons was weak.There were 32 codons with relative codon usage greater than 1,of which 28 were rich in A and U,indicating that the 3rd position of codon prefers A and U genetic bases.Neutral analysis found that the correlation between GC 3 and GC 12 was not significant,and the slope of the regression curve was 0.049,suggesting that codon bias was mainly affected by natural selection,while the ENC-plot analysis found that most genes fell below and around the curve.It was shown that the mutation also affected the formation of codon bias.Eventually,nine codons(UUU,CUU,UCA,ACA,UAU,AAU,GAU,UGA,GGA)were identified as the optimal codons for the chloroplast genome of camphora tree.