辽细辛叶绿体基因组密码子使用偏好性分析

Analysis of Codon Usage Bias in the Chloroplast Genome of A.heterotropoides Fr.Schmidt var.mandshuricum(Maxim.)Kitag.

确定中草药辽细辛叶绿体基因组密码子使用偏好性及其成因。密码子使用特性利用CodonW 1.4.2软件和CUSP程序分析50条经筛选的CDS序列,结合中性绘图、ENC-plot和PR2-plot分析,最终确定最优密码子。结果显示,叶绿体基因组密码子不同位置碱基GC含量的总体趋势为GC_(1)(47.60%)>GC_(2)(40.25%)>GC_(3)(30.96%),ENC值与GC_(3)呈极显著正相关,RSCU值大于1的密码子数量有31个,其中30个密码子以A/U结尾,仅1个以G结尾,表明密码子第3位碱基偏好以A/U结尾;ENC值分布在38.10~58.19之间,平均值为48.77,存在较弱密码子使用偏性;进一步分析发现自然选择是影响辽细辛密码子使用偏性的主要因素;以ENC值和RSCU值为参考,共筛选出18个最优密码子,除UUG外,其余17个密码子均以A/U结尾。该结论可为辽细辛的叶绿体基因工程、系统进化、环境适应等研究提供参考依据。

To determine codon usage bias and the causes in chloroplast genome of Asarum heterotropoides Fr.Schmidt var.mandshuricum(Maxim.)Kitag..The Codon W 1.4.2 software and CUSP program were employed to analyze the codon usage characteristics of 50 CDS sequences after screening,and the optimal codon was determined by neutral plotting,ENC-plot and PR2-plot.The results showed that the general trend of GC content in different positions of the chloroplast genome codon was GC_(1)(47.60%)>GC_(2)(40.25%)>GC_(3)(30.96%),significant correlation was found between ENC and GC_(3).There were 31 codons with RSCU value greater than 1,of which 30 codons ended with A/U,and only 1 codon ended in G.It proved that the third base of codon tend to use the codons ending with A/U.The range of ENC from 38.10 to 58.19,and the average content was 48.77,which indicated that codons bias was weaker.Further analysis showed that the codon preference of chloroplast genome of A.heterotropoides Fr.Schmidt var.mandshuricum(Maxim.)Kitag.was mainly influenced by natural selection.Taking ENC value and RSCU value as reference,a total of 18 optimal codons were screened out,there are 17 codons that all ended in A/U except for UUG.The study can provided a basis for the chloroplast genetic engineering,environmental adaptation and phylogenetic of A.heterotropoides Fr.Schmidt var.mandshuricum(Maxim.)Kitag..