人参叶绿体基因组密码子偏好性分析  

Analysis on Codon Usage Bias of Chloroplast Genome in Panax ginseng

作　　者：李阳 王杰敏 古军霞 韩晓伟 马东来 郑玉光 严玉平 孙会改 Li Yang;Wang Jiemin;Gu Junxia;Han Xiaowei;Ma Donglai;Zheng Yuguang;Yan Yuping;Sun Huigai(Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province,Hebei University of Chinese Medicine,Shijiazhuang,050200)

机构地区：[1]河北中医药大学,河北省中药炮制技术创新中心,石家庄050200

出　　处：《分子植物育种》2025年第3期926-934,共9页Molecular Plant Breeding

基　　金：河北省中医药管理局项目(2023355);河北中医学院博士科研基金项目(BSZ2019006);河北中医学院省属高校基本科研业务费专项(JCY2021011);河北中医学院优秀青年基金项目(YQ2020007);河北省科技厅重点研发项目(19276414D)共同资助。

摘　　要：为了研究人参叶绿体基因组密码子的使用偏性,本研究从NCBI下载51条人参的CDS(Coding DNA sequence),利用Python脚本、CodonW软件、EMBOSS的CUSP程序等软件计算密码子偏好性参数和核苷酸组成。结果显示:51条CDS序列的GC含量为39.84%,GC_(1)、GC_(2)、GC_(3)的GC含量分别为48.81%、39.61%和31.09%,说明人参叶绿体基因组偏向于A/T结尾的密码子;相关分析结果显示GC_(12)和GC_(3)的相关性不显著;中性绘图、奇偶偏好性和有效密码子数的综合分析表明决定人参叶绿体密码子偏性的最关键因素是自然选择,筛选出GCA、ACA、CUU、GGU、CAU等14个密码子为最优密码子,其中多数以A或U结尾。本研究为提高人参外源基因的表达水平和优化育种等研究提供一定的参考。To research the usage bias of Panax ginseng chloroplast genome,the 51 coding DNA sequences were downloaded and analyzed to the codon usage bias parameters and nucleotide composition by Python script,CodonW software,and CUSP of EMBOSS.The results showed that the GC content of 51 CDS sequences was 39.84%,and the GC content of GC_(1),GC_(2)and GC_(3)were 48.81%,39.61%and 31.09%respectively,which indicates that the base bias at the end of codons prefer A or T;the correlation analysis results revealed that the GC_(12)content was weak correlated with GC_(3).Neutrality plot analysis,ENC-plot analysis,and PR2-plot analysis presented that the CUB of Panax ginseng chloroplast genome was mainly affected by natural selection.Finally,14 codons,such as GCA,ACA,CUU,GGU and CAU were found to be the optimal codons,most of which ended with A/U.This study provides a certain reference for improving the expression level of exogenous genes in Panax ginseng and optimizing breeding.

关 键 词：人参 叶绿体基因组 密码子偏性 基因组编码序列 

分 类 号：S567.7[农业科学—中草药栽培]