苋菜AtGAI基因密码子偏好性与进化分析

Codon bias and evolution analysis of AtGAI in Amaranthus tricolor L.

关键词:  苋菜  AtGAI基因  密码子偏好性  进化分析  遗传转化受体

Key words:  Amaranthus tricolor L  AtGAI gene  codon usage bias  evolution analysis  genetic transformation receptors

摘要:

为明确苋菜AtGAI基因密码子的使用特性，采用CodonW、SPSS软件及EMBOSS在线程序分析苋菜AtGAI基因密码子的偏好性，通过中性绘图、ENc绘图和偏倚分析GAI基因密码子偏好性形成的可能原因。结果表明：1）苋菜AtGAI基因的有效密码子数（ENc）、密码子适应指数（CAI）和GC含量分别为50.75、0.195和41.91%，表明其密码子偏好性较弱，偏好使用A/T结尾的密码子；2）CDS序列及RSCU聚类分析表明，苋菜AtGAI基因与双子叶植物中石竹目含甜菜色素的植物偏好性最相近；3）密码子碱基成分和相关性分析发现，GAI基因的密码子偏好性主要受碱基突变的影响；4）密码子使用频率比较分析发现，酵母真核表达系统更适合苋菜AtGAI异源表达，模式植物拟南芥、烟草、番茄和甜菜均可做为苋菜AtGAI基因的遗传转化受体，其中甜菜是其最理想的遗传转化受体。突变压力是GAI基因密码子偏好性形成的主要因素，苋菜AtGAI基因外源表达和遗传转化时需要根据宿主基因偏好性进行密码子优化和改造。

Abstract:

To understand the codon bias of AtGAI in Amaranthus tricolor L.,AtGAI gene codon bias was analyzed by CodonW,SPSS and EMBOSS online program.Neutral drawing,ENc plots and parity rule 2 plot were subsequently used for the exploration of possible factors that affect the formation of the bias.The optimal receptor system was explored by comparing the frequency of the AtGAI gene and the pattern biocodon usage.The results showed that:1) The ENc,CAI,and GC content of AtGAI were respectively 50.75,0.195,and 41.91%,indicating that the codon bias level of AtGAI in A.tricolor L.was low and biased toward the synonymous codons with A or T.2) The CDS sequence and RSCU cluster analysis showed that the preference of AtGAI gene was the closest to that of caryophyllales containing betalain in dicotyledonous plants.3) The codon base composition and correlation analysis showed that the codon bias of GAI gene was mainly affected by the base mutation.4) The codon usage frequency comparison and analysis showed that the yeast eukaryotic expression system was more suitable for heterologous expression of AtGAI gene.The model plants Arabidopsis thaliana,tobacco,tomato and beet can be used as genetic transformation receptors for AtGAI gene,but beet is the most ideal genetic transformation receptor.This study indicated that mutational stress was the main factor in the formation of GAI gene codon bias.It is necessary to optimize and modify AtGAI codon according to the codon bias of the host genome for heterologous expression and genetic transformation analysis.