29种桃金娘目物种psbA基因密码子偏好及聚类分析

Codon Preference and Cluster Analysis of psbA Gene in 29 Species of Myrtales Species

为探究桃金娘目(Myrtales)物种psbA基因密码子使用偏好性,本研究从NCBI数据库获取29个桃金娘目物种的psb A基因的编码区序列,运用CodonW、EMBOSS和DAMBE软件获得基因碱基组成和密码子使用偏性的相关参数。29种桃金娘目物种psbA基因的ENC范围在39.532~43.104,CAI均值是0.310,GC含量均小于50%。psbA基因密码子中有25个偏好性较强的密码子;ENC-plot、中性绘图分析、奇偶偏差分析显示,密码子偏好主要受自然选择的影响。基于RSCU值和CDS序列的聚类中,桃金娘科的11个物种存在差异。桃金娘目物种psbA基因编码区在选择碱基时倾向于AT,对A/T结尾的密码子使用偏好更强。密码子整体偏好性不强,基因表达量不高。自然选择是影响桃金娘目物种psbA基因密码子偏好性的主要因素。烟草是进行基因功能验证的较合适受体,大肠杆菌适宜作异源表达载体。

Explore the factors affecting codon preference in 29 Myrtales species,and to screen suitable receptors for heterologous expression and genetic transformation of psbA genes.The coding region sequences of psbA genes of 29 Myrtales species were obtained from NCBI database,and the related parameters of gene base composition and codon usage bias were obtained by using CodonW,EMBOSS and DAMBE software.The ENC range of psbA gene in 29 species of Myrtales ranged from 39.532 to 43.104,the CAI mean was 0.310,and the GC content was less than 50%.There were 25 codons with strong preference in psbA gene.ENC-plot,neutral plot analysis and parity bias analysis show that codon preference is mainly influenced by natural selection.Clusters based on RSCU values and CDS sequences showed differences among 11 species of Myrtales family.In Myrtales species,the coding region of psbA gene tended to be AT when selecting bases,and the codon AT the end of A/T was preferred.The overall codon bias is not strong,and the gene expression is not high.Natural selection is the main factor that affects codon preference of psbA gene in Myrtales species.Solanum lycopersicum is a suitable receptor for gene function verification,and Escherichia coli is a suitable heterologous expression vector.