珊瑚菜叶绿体基因组密码子使用偏性分析  

Analysis on codon usage bias of chloroplast genome of Glehnia littoralis

作　　者：孙月琪 李密密[2] 周义峰[2] SUN Yueqi;LI Mimi;ZHOU Yifeng(College of Forestry and Grassland,College of Soil and Water Conservation,Nanjing Forestry University,Nanjing 210037,China;Jiangsu Key Laboratory for the Research and Utilization of Plant Resources,Institute of Botany,Jiangsu Province and Chinese Academy of Sciences(Nanjing Botanical Garden Mem.Sun Yat-Sen),Nanjing 210014,China)

机构地区：[1]南京林业大学林草学院、水土保持学院,江苏南京210037 [2]江苏省中国科学院植物研究所(南京中山植物园)江苏省植物资源研究与利用重点实验室,江苏南京210014

出　　处：《植物资源与环境学报》2023年第6期1-10,共10页Journal of Plant Resources and Environment

基　　金：国家自然科学基金项目(31600169)。

摘　　要：为探究珊瑚菜(Glehnia littoralis F.Schmidt ex Miq.)叶绿体基因组密码子使用偏性及其影响因子,本研究基于珊瑚菜叶绿体基因组测序数据筛选到51个蛋白质编码基因,并对其密码子使用模式进行分析。结果显示:珊瑚菜叶绿体基因组密码子总GC含量(G_(Call))为38.8%,密码子第3位碱基的GC含量(GC3)最低,仅为29.2%,3个位置碱基的GC含量均小于50%,表明珊瑚菜叶绿体基因组密码子偏好使用A或U。珊瑚菜叶绿体基因组有效密码子数(ENC)为34.6~54.5,密码子适应指数(CAI)为0.100~0.270,密码子偏好指数(CBI)为-0.190~0.226,最优密码子使用频率(FOP)为0.276~0.550,表明珊瑚菜叶绿体基因组密码子使用偏性较弱;相关性分析结果表明珊瑚菜叶绿体基因组密码子第3位碱基的组成对基因表达有很大影响。中性绘图分析、PR2-plot分析、ENC-plot分析和对应性分析结果表明珊瑚菜叶绿体基因组密码子使用偏性受自然选择和突变的共同影响,以自然选择为主;基于相对同义密码子使用度(RSCU)和高、低表达组的RSCU差值(ΔRSCU)共获得16个最优密码子,且大部分以A或U结尾。综合分析结果表明:珊瑚菜叶绿体基因组密码子使用偏性较弱,且主要受自然选择的影响。To explore the codon usage bias and its affecting factors of chloroplast genome of Glehnia littoralis F.Schmidt ex Miq.,51 protein-coding genes were screened out based on the chloroplast genome sequencing data of G.littoralis in this study,and the codon usage pattern was analyzed.The results show that the total GC content(G_(Call))of codons in chloroplast genome of G.littoralis is 38.8%,the GC content of the third base of codon(GC 3)is the lowest,which is only 29.2%,and the GC contents of base at three positions are all less than 50%,indicating a preference for the use of A or U as codons in chloroplast genome of G.littoralis.The effective number of codon(ENC)in chloroplast genome of G.littoralis is 34.6-54.5,the codon adaptation index(CAI)is 0.100-0.270,the codon bias index(CBI)is-0.190-0.226,and the frequency of optimal codon(FOP)is 0.276-0.550,indicating the codon usage bias in chloroplast genome of G.littoralis is relatively week;the correlation analysis result shows that the composition of the third base of codon in chloroplast genome of G.littoralis has a great impact on gene expression.The results of neutral mapping analysis,PR2-plot analysis,ENC-plot analysis,and correspondence analysis show that the codon usage bias of chloroplast genome of G.littoralis is co-affected by natural selection and mutation,and natural selection plays the dominant role.A total of 16 optimal codons are obtained based on the relative synonymous codon usage(RSCU)and the RSCU difference(ΔRSCU)between high and low expression groups,and most of them are ended with A or U.The comprehensive analysis results show that the codon usage bias of chloroplast genome of G.littoralis is relatively weak,and is mainly affected by natural selection.

关 键 词：珊瑚菜 叶绿体基因组 密码子使用偏性 最优密码子 

分 类 号：Q943.2[生物学—植物学] Q949.763.3