菠萝叶绿体基因组密码子偏好性分析

叶绿体基因组密码子偏好性影响基因的表达效率,对于叶绿体基因工程应用及物种遗传改良具有重要的科学意义.为了明确菠萝叶绿体基因组密码子偏好性的使用特征及主要影响因素,本研究以菠萝叶绿体基因组为研究对象,利用生物信息学软件分析其密码子的使用模式和偏好性.密码子偏好性相关参数分析显示:(1)菠萝叶绿体基因密码子的GC含量平均值...

Analysis of Codon Usage Bias in the Chloroplast Genome of Ananas comosus

The codon usage bias of chloroplast genome affects the genes expression efficiency, which provides important information for chloroplast genetic engineering and species genetic improvement. To determine the codon usage characteristic of the chloroplast genome and its main influencing factors in pineapple (Ananas comosus), the codon usage pattern and its preference of pineapple chloroplast genome were analyzed using bioinformatics softwares. The average GC content of codons of pineapple chloroplast genes was 38.31%, the average GC content of codons from the first position to the third position was 46.78%, 39.61% and 28.53%, respectively, and the average GC contents at the first and second positions of codons were significantly higher than that at the third position. The value range of effective number of codons (ENC) was 38.48—61.00, and its average value was 47.21, indicating weak codon bias. GC1 was significantly correlated with GC2, GC_all was significantly positively correlated with GC1, GC2 and GC3, and GC3 was not significantly correlated with GC1 and GC2. ENC was not significantly correlated with GC1, but significantly and extremely significantly correlated with GC2 and GC3, respectively. Codon number (N) was only significantly correlated with GC3, which indicating that the base composition of the third position in the three positions of the codon mainly affects codon number. RSCU analysis showed that among the 29 codons with RSCU>1, 12 codons ended with A, 16 codons ended with U, and 1 codon ended with G. Neutrality plot analysis showed that there was not significant correlation between GC12 and GC3, and the correlation coefficient and regression coefficient was 0.065 and 0.085, respectively. ENC-plot analysis showed most genes were distributed near the standard curve, and most ENC ratios were distributed in the interval of -0.05—0.05. PR2-plot analysis showed that all genes were unevenly distributed in the four regions of the PR2 plan, and the use frequency of pyrimidine T/C at the third position of codon was higher than that of purine A/G. Bias analysis of Neutrality plot, ENC-plot and PR2-plot suggested that natural selection and mutation as the main factors affect the codon usage bias of pineapple chloroplast genome. Analysis of optimal codons and RSCU showed that most of the 29 codons with RSCU>1 and the 18 optimal codons ended with A or U. The results provide scientific basis for codon optimization of exogenous genes and improvement of their expression efficiency.