冬凤兰叶绿体基因组密码子使用偏好性分析

Analysis of Codon Bias of Chloroplast Genome of Cymbidium dayanum

为明确冬凤兰叶绿体基因组密码子的使用模式及其影响因素,利用CodonW、CUSP、CHIP等软件对得到的43条序列进行分析。结果表明:冬凤兰叶绿体基因组密码子GC3平均值为27.78%,ENC平均值为47.59,偏好性较弱;GC3碱基组成较GC1、GC2存在显著差异,且3位碱基使用T>A,G>C;结合30个高频密码子和22个高表达密码子,确定GCA、CGU、CGA、AAU、UGU、CAA、GGU、CAU、AUU、UUA、AAA、UUU、CCU、GAA、UCU、UCA、ACU、UAU、GUA等19个密码子为最优密码子。综合分析表明,冬凤兰叶绿体基因组偏好A/U结尾密码,主要受自然选择的影响,同时也受其他如突变和碱基组成等因素的影响,这对应用叶绿体基因工程对其进行性状改良和外源基因表达等具有指导意义。

In order to ascertain the codon usage pattern of Cymbidium dayanum chloroplast genome and its influencing factors, 43 sequences which were selected from the chloroplast genome sequence of Cymbidium dayanum were analyzed using CodonW, CUSP, CHIP and other software. The results showed that the GC3average value of Cymbidium dayanum chloroplast genome was 27.78%, and the average number of ENC was 47.59, and the preference was weak. The base composition of GC3was significantly different than that of GC1and GC2, and the frequency of use of the 3rdbase was T>A and G>C. Combine 30 high frequency codons and 22 high expression codons to determine GCA, CGU, CGA, AAU, UGU, CAA, GGU, CAU, AUU, UUA, AAA, UUU, CCU, GAA, UCU, UCA,ACU, UAU, GUA, etc. 19 codons as optimal codons. Comprehensive analysis shows that chloroplast genome of Cymbidium dayanum prefers A/U ending codes, which is mainly affected by natural selection, but also by other factors such as mutations and base composition, and it has guiding significance in the application of chloroplast genetic engineering to its traits improvement and external source gene expression.