云南蓝果树叶绿体基因组密码子偏好性分析

以云南蓝果树叶绿体基因组为研究对象，采用Codon W 1.4.2等软件，通过分析云南蓝果树叶绿体基因组52个基因密码子的偏好性，探究影响密码子使用偏性形成的主要因素。结果表明:1) Codon W和CUSP软件分析显示密码子第3位碱基GC含量为28.40%，ENC值>45的基因有39个，说明密码子偏好以AT结尾，且存在较弱偏性。2)中性绘图分析显示，GC₁₂与GC₃的相关系数为0.161 2，相关性不显著，说明密码子第1、第2位与第3位碱基组成存在显著差异。3) ENC绘图结合ENC比值频率表显示，大部分基因距离标准曲线较远，说明密码子偏好性主要受选择的影响。4) PR2-plot分析显示密码子第3位碱基使用频率方面，T>A，G>C，说明密码子偏好性受多重因素影响。5) 确定UUG、UCA、GCU、AAU、GAU和GGA为最优密码子。综上所述，云南蓝果树叶绿体基因组密码子的使用主要受选择的影响，受其他如突变等因素的影响较弱。

Codon Usage Bias Analysis of Chloroplast Genome in Nyssa yunnanensis

The chloroplast genome of Nyssa yunnanensis was taken as the research object,the codon usage bias of 52 genes from the chloroplast genome of N.yunnanensis was analyzed by the software Codon W 1.4.2,and the main factors affecting the formation of codon usage bias was explored.The results showed as follows 1) According to the analysis results of the software Codon W and CUSP,the GC content of the 3^rd base composition of the codons was 28.40%,there were 39 genes when ENC value was greater than 45,therefore,these phenomena illustrated that the codons preferred to end with AT,and had a weaker bias.2) Neutrality analysis revealed the correlation coefficient of GC₁₂ and GC₃ was 0.161 2,these had no significant correlation,which declared that the 1^st two base composition and the 3^rd of the codons existed significant variation.3) The combination of ENC plot with ENC ration table indicated that most genes were far from the standard curve,which suggested that the codon usage bias was principally affected by selection pressure.4) PR2-plot analysis revealed that the 3^rd codon base composition in the frequency of utilization,T>A and G>C,which stated the codon usage bias was affected by multi-factors.5) The optimal codons were determined as UUG,UCA,GCU,AAU,GAU and GGA.It was summarized that the codon usage bias of the genes from the chloroplast genome of N.yunnanensis was mainly affected by selection pressure,other factors,such as mutation presented little effect.