3种榕属叶绿体基因组密码子偏好性分析

Codon Usage Bias in Chloroplast Genomes of Three Ficus Species

为更好了解黄葛榕、榕树和异叶榕叶绿体基因组密码子的使用模式,利用Codon W、CUSP、EXCEL等软件对其叶绿体编码基因的密码子使用偏好性进行系统分析。结果表明,3种榕属植物的第3位碱基以A/T为主且GC3的含量远低于GC1和GC2;并且大部分的ENC值都在40以上,说明3种榕属植物的密码子偏好性较弱;中性绘图、ENC-plot和PR2-plot绘图分析表明,3种榕属植物的密码子偏好性不仅受选择的影响,还受突变等多重因素的影响;此外,还确定了3种榕属植物的最优密码子,且都以A/U结尾。该研究结果可为榕属植物叶绿体基因组后续的外源基因改良奠定基础。

To better understand the codon usage patterns of the chloroplast genome in Ficus virens,F.microcarpa and F.heteromorpha,the codon usage preferences were systematically analyzed by Codon W,CUSP and EXCEL software.The results showed that the third base of the three Ficus species was dominated by A/T and the content of GC3 was much lower than those of GC1 and GC2.Most of the ENC values were above 40,indicating weak codon bias in the three Ficus species.The results of neutrality plot,ENC-plot and PR2-bias plot showed that the codon bias of the three Ficus species was influenced not only by selection but also by multiple factors such as mutations.In addition,optimal codons were identified for the three Ficus species,most of which ended in A/U,and 11 of which were the same optimal codons for the three Ficus species.In addition,the optimal codons for each of the three Ficus species were identified,all of them ending in A/U.This results could form the basis for subsequent exogenous gene improvement in the chloroplast genome of Ficus species.