摘要
为确定中药藿香叶绿体基因组密码子的使用模式及其成因,本研究利用Codon W 1.4.2和在线软件CUSP对藿香叶绿体基因组中的53条基因编码序列密码进行中性绘图、ENC-plot和PR2-plot分析。结果表明:RSCU>1的密码子有29个,其中有28个以A/U结尾,说明叶绿体基因组的同义密码子中偏好以A/U结尾。藿香叶绿体基因组密码子的GC含量GC_(1)(46.95%)>GC_(2)(39.39%)>GC_(3)(28.98%),ENC值平均值大于45,其中大于45的有40个,说明藿香叶绿体基因组存在较弱的偏性。通过中性绘图分析、ENC-plot分析以及PR2-plot分析发现,藿香叶绿体基因组密码子的偏好性受到选择作用的影响为主要因素。通过构建目标基因的高低基因表达库,最终确定19个最优密码子:UUU、UUA、UUG、AUU、GUA、UCU、AGU、CCU、ACU、GCU、UAU、CAU、AAU、AAA、GAU、GAA、UGU、CGA、GGU。本研究为通过外源基因密码子改造后以藿香叶绿体为载体进行异源表达及种源鉴定提供了科学根据。
To determine the codon usage pattern of chloroplast genome of Agastache rugosa,a total of 53 selected protein-coding sequences were analyzed using Codon W 1.4.2 and CUSP software,and the codons were analyzed by neutral plotting,ENC-plot and PR2-plot.The results showed that there were 29 codons with RSCU>1,and 28of them ended with A/U,indicating that synonymous codons in chloroplast genome tend to end with A/U.The GC content of codon in chloroplast genome of A.rugosa was GC_(1)(46.95%)>GC_(2)(39.39%)>GC_(3)(28.98%),and there were 40 with ENC value greater than 45,which indicates that there was weak bias in chloroplast genome of A.rugosa.PR2-plot analysis showed that the number of genes located at the left-bottom of PR2-plot ichnography was the largest.Neutral mapping analysis,ENC-plot analysis and PR2-plot analysis demonstrated that the codon preference of chloroplast genome of A.rugosa was mainly influenced by natural selection.Through the constructed high and low gene expression libraries,15 optimal codons were finally determined,which were UUU,UUA,UUG,AUU,GUA,UCU,AGU,CCU,ACU,GCU,UAU,CAU,AAU,AAA,GAU,GAA,UGU,CGA,GGU.The present study took some basis for the determination of chloroplast genome and genetic diversity analysis of A.rugosa.
作者
梁湘兰
覃逸明
孙晓波
郭松
Liang Xianglan;Qin Yiming;Sun Xiaobo;Guo Song(College of Food and Biochemical Engineering,Guangxi Science&Technology Normal University,Laibin,546199)
出处
《分子植物育种》
CAS
北大核心
2023年第3期809-818,共10页
Molecular Plant Breeding
基金
广西科技师范学院高层次人才启动经费(GXKS2020GKY009)
广西科技师范学院特色瑶药资源研究与开发校级重点实验室经费(KJ5CSH000005)共同资助
广西高校中青年教师科研基础能力提升项目(2021KY0862)。
