刺柏属4种药用植物叶绿体基因组密码子偏好性分析

目的 明确刺柏属圆柏Juniperus chinensis、垂枝香柏J.pingii、昆明柏J.gaussenii和铺地柏J.procumbens4种药用植物叶绿体基因组密码子的使用偏好性及影响其密码子偏好性的因素。方法 利用CodonW、CUSP、SPSS等软件对4种刺柏属药用植物叶绿体基因组密码子偏好性进行分析。结果4种刺柏属药用植物叶绿体基因组密码子的GC含量在35.8%～37.3%，有效密码子数（effective number of codon，ENC）值在47.10～47.79，表明其密码子偏好性较弱。中性绘图、ENC-plot、PR2-plot分析表明影响4种刺柏属药用植物叶绿体基因组密码子使用偏性的因素有选择和突变。同时利用相对同义密码子使用度（relative synonymous codon usage，RSCU）值和ENC值筛选出共65个最优密码子，其中有9个密码子为4种刺柏属植物共有的最优密码子。结论 4种刺柏属药用植物密码子偏好使用A/T结尾，其密码子使用偏性主要受到自然选择的影响。通过对4种刺柏属植物叶绿体基因组密码子的使用偏性进行分析及外类群聚类分析验证，揭示影响其密码子使用偏性的主要因素，为后续刺柏属叶绿体基因组外源蛋白表达载体的构建及优化提供理论依据。

Analysis of codon bias in the chloroplast genome of four medicinal plants of Juniperus

Objective To determine the codon usage preference of the chloroplast genome of four medicinal plants of Juniperus genus (J. chinensis, J. pingii, J. gaussenii, and J. procumbens) and the factors that affecting its codon preference.Methods CodonW, CUSP, SPSS and other software was used to analyze the codon preference of the chloroplast genome of four medicinal plants of Juniperus.Results The GC content of the chloroplast genome codons of the four medicinal plants of Juniperus was from 35.8% to 37.3%, and the effective number of codon (ENC) value was from 47.10 to 47.79, indicating that their codon preference was weak. Neutral plotting, ENC-plot, PR₂-plot analysis showed that the factors affecting the codon usage bias of the chloroplast genome of the four medicinal plants of Juniperus species were selection and mutation. At the same time, the relative synonymous codon usage (RSCU) value and ENC value were used to filter out a total of 65 optimal codons, of which nine codons are the optimal codons shared by four species of Juniperus.Conclusion The codon preference of four species of Juniperus species uses A/T ending, and its codon usage bias is mainly affected by natural selection. This study analyzes the codon usage bias of the chloroplast genome of four species of Juniperus plants and verified it by cluster analysis of the outer group cluster analysis, revealing the main factors affecting the codon usage bias of Juniperus genus, and it is the foreign protein of the subsequent Juniperus chloroplast genome. The construction and optimization of expression vectors provide a theoretical basis.