豇豆叶绿体基因组密码子使用偏好性分析  

Analysis of Codon Usage Bias in the Cowpea Chloroplast Genome

作　　者：仇学文 李丹 甘玉迪 杨有新[1] 程柳洋 徐梦怡 吴才君[1] QIU Xuewen;LI Dan;GAN Yudi;YANG Youxin;CHENG Liuyang;XU Mengyi;WU Caijun(College of Agriculture,Jiangxi Agricultural University,Nanchang,Jiangxi 330000)

机构地区：[1]江西农业大学农学院,江西南昌330000

出　　处：《核农学报》2023年第6期1118-1129,共12页Journal of Nuclear Agricultural Sciences

基　　金：江西省现代农业产业技术体系建设专项资金资助(赣财农指[2022]7号)。

摘　　要：为了探究豇豆(Vigna unguiculata)叶绿体基因组密码子的使用模式,本研究从NCBI下载完整的豇豆叶绿体基因组序列,并对其进行结构分析。利用CodonW和CUSP对筛选获得的50条可编码蛋白序列(CDS)进行分析,获得GC1、GC2、GC3、RSCU、CAI、CBI、Fop、ENc、RFSC等重要参数,并进行中性绘图、PR2-plot绘图、ENc-plot绘图以及对应分析、最优密码子分析和其他物种对比分析。结果发现,豇豆叶绿体基因密码子更偏向以A或U(T)结尾,G和C在密码子各位置中的占比较低,平均值为36.31%;有效密码子数(ENc)的平均值为44.903,密码子偏好性较弱;GC1与GC2、GC3间均有相关性,表明碱基突变对密码子选择也有影响。从中性绘图、PR2-plot绘图、ENc-plot绘图结果可以看出,豇豆叶绿体密码子使用偏好性同时受到了碱基突变与自然选择的影响。本研究最终筛选出20个最优密码子,并将豇豆叶绿体基因组密码子使用频率与其他物种进行比较,发现豇豆与番茄在密码子使用频率上存在较高的相似度。本研究结果为提高豇豆叶绿体外源基因的表达效率提供了参考依据。To investigate the pattern of chloroplast codon usage in cowpea(Vigna unguiculata),the complete cowpea genome sequence was downloaded from NCBI and structurally analysed in this study.The sequences were screened to obtain 50 protein-coding sequences(CDS),which were analysed by CodonW and CUSP to obtain important parameters such as GC1,GC2,GC3,RSCU,CAI,CBI,Fop,ENc,RFSC,and further analysed by neutral plot analysis,PR2-plot analysis,ENc-plot analysis,correspondence analysis,optimal codon analysis and comparative analysis of other species.The results showed that cowpea chloroplast gene codons preferred to end at A or U(T),and G and C were lower in all positions of codons,with a mean value of 36.31%.The mean value of the effective codon number ENc was 44.903,with weak codon preference;there was correlation between GC1 and GC2 and GC3,indicating that base mutations also had an effect on codon selection.From the neutral plot,PR2-plot and ENc-plot,it is clear that cowpea chloroplast codon usage bias is influenced by both base mutations and natural selection.In this study,totally 20 optimal codons were successfully screened.Compared with other species,cowpea and tomato have high similarity in codon usage frequency.This study provides a reference for improving the efficiency of cowpea chloroplasts genes as an exogenous gene expression.

关 键 词：豇豆 叶绿体 基因组 密码子 使用偏好性 

分 类 号：S643.4[农业科学—蔬菜学]