川芎转录组密码子使用偏好性分析

Preference Analysis of Codon Usage of Ligusticum chuanxiong Transcriptome

为了解川芎(Ligusticum chuanxiong Hort.)阿魏酸生物合成相关基因的密码子使用偏好性特点,为运用基因工程技术实现阿魏酸的异源生物合成提供理论依据,对川芎转录组中共50 108条Unigenes使用Codon W、Cusp和Chips进行在线分析。结果表明,总GC含量为41.4%,有效密码子占总数的16.17%,最优密码子偏好以A/U结尾,表明川芎转录组Unigenes密码子偏好程度整体水平不高。比较分析了川芎转录组中阿魏酸生物合成相关基因(PAL、C4H、C3H与COMT)与不同模式生物的稀有密码子,表明与大肠杆菌基因组密码子使用频率差值较大的有4个,与酵母、烟草和拟南芥基因组差值较大的均有3个,这预示着川芎阿魏酸生物合成相关基因在酵母、烟草和拟南芥中的表达效率较高。

In order to understand the codon usage preference of genes involved in the biosynthesis of ferulic acid in Ligusticum chuanxiong Hort.,and thereby providing a theoretical basis for the application of genetic engineering technology to achieve heterologous biosynthesis of ferulic acid,50 108 unigenes of L. chuanxiong transcriptome were analyzed on-line using Codon W,Cusp and Chips at first. As a result,the total GC content was 41.4%,valid codons was 16.17% and the optimal codon preferred A/U as end. Furthermore,the rare codons of PAL,C4 H,C3H and COMT were compared with those of candidate expressed hosts,including E. coli,yeast,tobacco and Arabidopsis thaliana. As a result,4 codons were found between E.coli and L. chuanxiong,and 3 codons were found among yeast,tobacco and Arabidopsis thaliana. It suggests high expressional ratio of PAL,C4 H,C3H and COMT might take place in yeast,tobacco and Arabidopsis thaliana.