文心兰叶绿体基因组密码子使用的相关分析

Analysis on codon usage of chloroplast genome of Oncidium Gower Ramsey

通过对文心兰叶绿体基因组全序列密码子的研究,利用Mobyle在线软件分析了文心兰叶绿体42个基因密码子的使用模式。结果表明,文心兰叶绿体基因组密码子GC3含量为28.59%,明显低于GC1和GC2含量,说明密码子第3位富含AT。GC1与GC2极显著相关(r=0.572**),GC3与GC1(r=-0.051)和GC2(r=-0.08)均未达到显著水平。对应性分析表明第一向量轴上基因的位置坐标与该基因的表达水平(CAI)极显著负相关(r=-0.556**),与GC3和ENC的相关系数分别为0.025和0.281,均未达到显著水平;GC含量与ENC、CAI以及第一向量轴上基因位置坐标的相关系数分别为0.228、0.381*和-0.354*。将高表达优越密码子分析法和高频密码子分析法相结合,确定了17个为文心兰叶绿体基因组的最优密码子。

In the present study, the complete nucleotide sequence of the chloroplast genome of Oncidium Gower Ramsey was studied. Codon of 42 genes, which were selected from the chloroplast genome sequence of Oncidium. Gower Ramsey, was analyzed using online Mobyle software. The results showed that GC content at the third position of codons was 28.59%, which was significantly lower than that at the first and second positions. This indicated that the third position of codons was rich in A or T. The GC3 and GCI, GC2 have insignificant correlation （r=-0.051, r =-0.08, respectively）, whereas GC1 and GC2 have a significant correlation （r =0.572^＊＊）. Correspondence analysis showed that there was significant negative correlation（r=-0.556^＊） between the gene position on first axis and gene expression level with codon adaptation index （CAI） values. The correlation coefficients for first axis with GC3 and ENC were 0.025 and 0.281, respectively, and both were insignificant. From a lower positive correlation between GC content and ENC （r=0.228）, higher positive significant correlation between GC content and CAI （r=0.38^＊） and a lower significant negative correlation between GC content and gene position on first axis （-0.354^＊）, we could conclude that the GC content in coding region gave a less contribution to codon usage bias than that to gene expression level. In addition, through an analysis of both the high expression codon and high frequency codon, we defined 17 codons from 17 amino acids as the major preference codons in the chloroplast genome of Oncidium. Gower Ramsey.