5种冰草叶绿体基因组密码子偏好性分析  

Analysis of the Codon Usage Bias in the Chloroplast Genome of Five Agropyron Species

作　　者：韩慧杰 邱锐 刘叶飞 周昕越 高翠萍 赵彦 Han Huijie;Qiu Rui;Liu Yefei;Zhou Xinyue;Gao Cuiping;Zhao Yan(College of Grassland,Resources and Environment,Inner Mongolia Agricultural University,Hohhot,010018)

机构地区：[1]内蒙古农业大学草原与资源环境学院,呼和浩特010018

出　　处：《分子植物育种》2023年第18期6010-6018,共9页Molecular Plant Breeding

基　　金：内蒙古自治区关键技术攻关计划项目(2019GG352,2020GG0176);“科技兴蒙”重点专项项目(2020-科技兴蒙-草种业技术创新中心-2)共同资助。

摘　　要：本研究从5种冰草叶绿体基因组中各筛选出52条蛋白编码序列,利用CodonW、SPSS、EXCEL等软件对其进行密码子偏好性使用模式分析。结果显示,在RSCU分析结果中,共有31个高频密码子,有28个是以A/U结尾,密码子偏好性在冰草叶绿体基因组中的表现较弱。中性分析结果显示,自然选择在冰草叶绿体基因组密码子偏好性发挥作用;在有效密码子数的结果中,偏好性多受突变影响;PR2-plot分析结果,大部分基因由选择调控。此外筛选出8个高频高表达的最优密码子,分别为CGA、UUG、UCA、GAU、UUU、UCC、GGA、ACA。冰草叶绿体基因组密码子偏好性种间差异不显著,且根据中性分析、ENC-plot、PR2-plot分析密码子偏好性可能受多种因素共同作用。最优密码子的选择,为冰草叶绿体基因组工程中外源性基因表达效率的提高奠定基础。We selected 52 protein coding sequence from each Agropyron chloroplast genome and analyzed codon usage bias patterns of these 5 Agropyron species chloroplast genome by CodonW,SPSS,and EXCEL.The results display that in the results of RSCU,there are 31 high frequency codons,and 28 of them are end of A/U,therefore the Agropyron chloroplast genome codon bias is weak.The neutrality plot shows that the natural selection plays a role in codon bias of the Agropyron chloroplast genome.However,ENC-plot shows the codon preference was more affectedbythe mutation.About PR2-plot showsa large ofgene iscontrolled byselection ofnature.In addition,the CGA,UUG,UCA,GAU,UUU,UCC,GGA,ACA wereselected asoptimal codon.The difference ofcodon usage pattern of Agropyron chloroplast genome are not significantly,as the results of neutrality plot,ENC-plot,PR2-plot shows that codon usage may be affected by natural selection,and the optimal codons will lay the foundation for the improvement of the expression efficiency of the genes in the Agropyron chloroplast genome project.

关 键 词：冰草属 叶绿体基因组 密码子 密码子偏好性 

分 类 号：S543.9[农业科学—作物学]