罂粟基因组密码子使用模式和偏好性分析  

Analysis of Codon Usage Pattern and Bias in Genomes of of Codon Usage Pattern and Bias in Genomes of Papaver somniferum L.

作　　者：凌立贞 王琴 杨桃 张书东 Ling Lizhen;Wang Qin;Yang Tao;Zhang Shudong(Key Laboratory of Liupanshui City for Study and Utilization of Ethnic Medicinal Plant Resourcesof Western Guizhou Province,School of biological science and technology,Liupanshui Normal University,Liupanshui 553004,China)

机构地区：[1]贵州省特色农业种质资源开发与利用特色重点实验室,六盘水师范学院生物科学与技术学院,贵州六盘水553004

出　　处：《六盘水师范学院学报》2024年第6期58-68,共11页Journal of Liupanshui Normal University

基　　金：六盘水市科技计划项目“六盘水市生物多样性保护和利用科技创新人才团队”(52020〔2022〕PT-20)。

摘　　要：为了揭示罂粟全基因组密码子使用的偏好性特征及其影响因素,以罂粟的全基因组蛋白质编码序列为研究对象,采用CodonW软件以及在线工具CUSP系统分析获得的68828条蛋白质编码序列。研究结果显示:罂粟编码基因中的密码子平均GC含量为41.52%,第三位碱基的GC3s含量为33.61%。进一步分析表明密码子第三位置上四种碱基的使用程度依次为T>A>G>C,其基因密码子的有效密码子数(ENC)平均值为50.60。这些研究结果显示,罂粟基因偏好使用末尾以A或T的密码子,但这种使用的偏好性较弱。中性图、PR2-plot和ENC-plot的分析结果显示:除了自然选择外,突变和基因表达水平等因素也对使用罂粟基因组密码子产生了影响。通过分析同义密码子相对使用度(RSCU)值最终确定出22个最优密码子,主要以A和T结尾。研究结果为罂粟有效成分的基因表达系统选择及其基因工程提供了理论依据。The study aimed to investigate the codon usage preference characteristics and influencing factors in the whole ge-nome ofpoppy(Papaver somniferum L.).The research focused on analyzing the 68,828 protein coding sequences(CDS)of poppy us-ing CodonW and the online software CUSP.Results revealed that the average GC content of the codons in the poppy encoding gene was 41.52%,with the GC3s content of the third base at 33.61%.Further analysis indicated a preference for four bases at the third position of the codon in the order of T>A>G>C,with an average ENC(Effective Number of Codons)of 50.60.This suggests a ten-dency for poppy genes to use codons ending in A or T,albeit weakly.Neutral plot,PR2-plot,and ENC-plot analysis demonstrated that natural selection can influence codon usage preference in the poppy genome and mutations and gene expression levels as well.Based on the Relative Synonymous Codon Usage(RSCU)values,22 optimal codons were identified,predominantly ending in A and T.These findings offer a theoretical foundation for selecting gene expression systems for bioactive ingredients in poppy and its genetic engineering.

关 键 词：罂粟 基因组 密码子偏好性 

分 类 号：R282.12[医药卫生—中药学]