翅果油树叶绿体基因组密码子偏好性分析  

Analysis on Codon Usage Bias in Chloroplast Genome of Elaeagnus mollis

作　　者：郭媛婷 张敏 杨玉洁 胡晓艳 杜淑辉[1] GUO Yuanting;ZHANG Min;YANG Yujie;HU Xiaoyan;DU Shuhui(College of Forestry,Shanxi Agricultural University,Taigu 030801,China)

机构地区：[1]山西农业大学林学院,山西太谷030801

出　　处：《山西农业科学》2023年第3期233-240,共8页Journal of Shanxi Agricultural Sciences

基　　金：科技部科技基础资源调查专项子课题(2019FY100802_04);山西省基础研究计划(自由探索类)(20210302124175);山西农业大学科技创新基金项目(2016YJ14)。

摘　　要：为明确翅果油树叶绿体基因组密码子使用偏好性,从Gen Bank数据库下载翅果油树叶绿体基因组序列,筛选出合适长度的序列并进行密码子使用偏好及其影响因素分析;使用Codon W软件分析序列得出A_(3)、T_(3)、C_(3)、G_(3)、GC_(3)、有效密码子数(ENC)、相对同义密码子使用度(RSCU)等重要参数,并进行相关指数分析、中性绘图分析、ENC-plot绘图分析、PR2-plot分析及最优密码子的确定。结果表明,翅果油树叶绿体基因组密码子不同位点上GC含量分布差异较大,其大小表现为GC_(1)(41.08%)>GC_(2)(38.17%)>GC_(3)(36.55%);ENC平均值为50.95,表明密码子使用偏好性较弱;密码子偏好使用A或U结尾,最终选出的20个最优密码子也均以A或U结尾。中性绘图和ENC-plot绘图分析发现,翅果油树叶绿体基因组密码子内部碱基组成之间不具有显著相关性,选择压力远胜于突变压力;PR2-plot绘图分析表明,在突变压力之外翅果油树叶绿体基因组密码子使用还受到了强烈外界压力的影响,自然选择是影响翅果油树叶绿体基因组密码子使用模式的最主要因素。In order to clarify codon usage bias in chloroplast genome of Elaeagnus mollis,in this study,the whole chloroplast genome sequence of E.mollis was downloaded from Gen Bank database,the gene sequence of appropriate length was screened,and codon usage bias and its influencing factors were analyzed.Then Codon W software was used to analyze the sequence and obtain the important parameters including A_(3),T_(3),C_(3),G_(3),GC_(3),effective number of codon(ENC),relative synonymous codon usage(RSCU).Correlation index analysis,neutral plot analysis,ENc-plot analysis,PR2-plot analysis,and determination of optimal codons were carried out.The results showed that GC content at different locations of codons in the chloroplast genome of E.mollis was different:GC_(1)(41.08%)>GC_(2)(38.17%)>GC_(3)(36.55%).The average ENC value was 50.95,indicating the codon usage bias was weak.Adenine and Uracil were used more frequently in the ends of codons and the finally selected 20 optimal codons had the ends with A or U.Neutral plot analysis and ENc-plot analysis showed that there was no significant correlation within the composition of codons in the chloroplast genome of E.mollis,and the selection pressure was much higher than the mutation pressure.Analysis of PR2-plot revealed that the codon usage in the chloroplast genome of E.mollis was also strongly affected by external stress in addition to mutation pressure.It was concluded that natural selection was the most important factor influencing codon usage pattern in the chloroplast genome of E.mollis.

关 键 词：翅果油树 叶绿体基因组 密码子使用偏性 最优密码子 

分 类 号：S565.9[农业科学—作物学]