杜仲基因密码子使用模式分析

Analysis of codon usage pattern of Eucommia ulmoides

关键词:  杜仲基因, 密码子, 偏好性, 使用模式, 代表性物种

Key words:  Eucommia ulmoides gene, codon, preference, usage pattern, representative species

摘要:

为了解杜仲基因密码子使用模式,该文以杜仲基因组密码子为研究对象,运用CodonW软件对杜仲的320个蛋白编码基因进行同义密码子相对使用频率(RSCU)分析、ENC-GC3s关联分析编码基因的密码子ENC值、PR2-plot偏倚分析编码基因的密码子碱基使用频率,并运用CUSP软件与Codon Usage Database软件对杜仲基因密码子的GC含量、使用频率与代表性物种烟草、拟南芥、大肠杆菌和酿酒酵母的密码子GC含量和使用频率进行比较。结果表明:杜仲基因密码子的RSCU>1的密码子有30个,其中18个以G/C结尾、12个以A/U结尾,说明杜仲基因密码子偏好以G/C结尾,且偏好性较强; 有效密码子数(ENC)范围为30～60,该范围内的密码子距离标准曲线较远,其ENC值小,偏好性较强; PR2-plot偏倚分析碱基使用频率显示,G>C、U>A; 杜仲与代表性物种的GC含量分析显示,杜仲的GC12、GC3以及平均GC含量均高于代表性物种; 杜仲与代表性物种的密码子使用频率分析显示,杜仲与烟草、酿酒酵母的密码子偏好较为接近,杜仲与拟南芥、大肠杆菌的密码子偏好差距较大。杜仲是我国特有的珍贵中药材,对其进行密码子使用模式分析,并研究其密码子偏好规律,为杜仲植物基因工程中外源基因的改良及表达提供了理论基础。

Abstract:

To comprehend the codon usage pattern of genes in Eucommia ulmoides, taking the E. ulmoides genome codons as the research object, the 320 coding DNA sequences was analyzed to obtain the results of relative synonymous codon usage(RSCU), ENC-GC3s analysis of codon ENC values of coding genes and PR2-plot bias analysis of the codon base usage frequency of the coding genes. By using CUSP and Codon Usage Database software to compare the GC contents and codon occurrence frequency of E. ulmoides with those of Arabidopsis thaliana, Nicotiana tabacum, Escherichia coli and Saccharomyces cerevisiae. The results were as follows: The number of RSCU value greater than 1 had 30 codons, including 18 genes with ending G/C and 12 genes ending with A/U, and these suggested that the codons preferred ends with G/C, and had a strong bias; The number of effective codons(ENC)ranges from 30 to 60, and the codons within this range were far away from the standard curve and their ENC values were smaller and had a higher preference; PR2-plot analysis showed that G>C,U>A, in the base usage frequency; Analysis of GC contents of Eucommia ulmoides and representative species showed that the E. ulmoides GC12, GC3 and average GC contents were higher than those of representative species; The analysis of the codon usage frequency of E. ulmoides and representative species showed that the codon preferences of E. ulmoides and Nicotiana tabacum, Saccharomyces cerevisiae were close, and the codon preferences of Eucommia ulmoides, Arabidopsis thaliana and Escherichia coli were quite different. Eucommia ulmoides is a precious Chinese medicinal material unique in China. Analysis of the codon usage pattern and studies of its codon preference will provide a theoretical basis for the improvement and expression of foreign genes in E. ulmoides plant genetic engineering.