2024年5月22日 星期三
24份忍冬属材料叶绿体基因组密码子使用偏好性分析
Analysis on codon usage bias of chloroplast genomes of 24 Lonicera materials
2023年 第32卷 第3期 页码[12-23]    下载全文[2MB]  
摘要

使用CodonW1.4.2和SPSS 22.0等软件对24份忍冬属(Lonicera Linn.)材料叶绿体基因组进行密码子偏好性分析,并基于叶绿体基因组序列构建了系统发育树。结果显示:24份忍冬属材料叶绿体基因组中1 314个蛋白质编码基因的GC含量为38.7%,密码子第3碱基位置的GC含量(GC3)最低,仅为31.4%,表明其密码子偏好以A或U结尾;根据基因功能将1 314个基因分为5类,每类显示出特定的密码子特征;24份忍冬属材料叶绿体基因组的有效密码子数(ENC)为50.2,表明密码子使用偏好性较低。密码子适应指数(CAI)、密码子偏好指数(CBI)和最优密码子使用频率(FOP)与GC3值、总GC含量(GCall)和同义密码子第3碱基位置的GC含量(GC3s)呈显著或极显著相关,说明密码子第3碱基位置的碱基组成对基因表达有很大影响。中性绘图、PR2-plot和ENC-plot以及对应性分析结果表明影响密码子使用模式的因子并不单一,自然选择起主要作用,突变压力起次要作用。基于相对同义密码子使用度(RSCU)和高、低表达组的RSCU差值(ΔRSCU),共鉴定出29个高频密码子和18个最优密码子,且大部分以A或U结尾。系统发育分析结果显示:24份忍冬属材料聚为一支,各物种间的进化相似且亲缘关系较近。综合分析结果表明:忍冬属植物叶绿体基因组密码子使用偏好性低且富含A或U,受到自然选择和突变压力的双重影响,其中自然选择占主导地位。

Abstract

The codon usage bias of chloroplast genomes of 24 Lonicera Linn. materials were analyzed by using softwares including CodonW1.4.2 and SPSS 22.0, and a phylogenetic tree was constructed based on the chloroplast genome sequences. The results show that the GC content of 1 314 protein-coding genes in chloroplast genomes of 24 Lonicera materials is 38.7%, and the GC content at the third base position of codon (GC3) is the lowest, which is only 31.4%, indicating that their codons  prefer to end with A or U; 1 314 genes are divided into 5 categories based on gene function, and each category shows specific codon characteristics; the effective number of codon (ENC) of chloroplast genomes of 24 Lonicera materials is 50.2, indicating that the codon usage bias is relatively low. The codon adaptation index (CAI), codon bias index (CBI), and frequency of optimal codon (FOP) show significant or extremely significant correlations with GC3 value, total GC content (GCall), and GC content at the third base position of synonymous codon (GC3s), indicating that the base composition of the third base position of codon has a great influence on gene expression. The neutral mapping, PR2-plot, ENC-plot, and correspondence analysis results show that the factors affecting codon usage pattern are not single, and natural selection plays a dominant role, while mutation pressure plays a secondary role. Based on relative synonymous codon usage (RSCU) and RSCU difference between high and low expression groups (ΔRSCU), 29 high frequency codons and 18 optimal codons are identified in total, and most of them end with A or U. The phylogenetic analysis result shows that 24 Lonicera materials can be clustered into one branch, and the evolution among each species is similar and their genetic relationships are relatively close. The comprehensive analysis result shows that the codon usage bias of chloroplast genomes of 24 Lonicera materials is low and they are rich in A or U, and they are under dual influences of natural selection and mutation pressure, in which natural selection plays a major role.

关键词忍冬属; 叶绿体基因组; 密码子使用偏好性; 自然选择; 突变压力
Key wordsLonicera Linn.; chloroplast genome; codon usage bias; natural selection; mutation pressure
作者王杰敏1,2,3, 马东来1,2,3, 韩晓伟1,2,3, 严玉平1,2,3, 郑玉光1,2,3, 孙会改1,2,3
所在单位1. 河北中医学院, 河北 石家庄 050200; 2. 河北省中药炮制技术创新中心, 河北 石家庄 050200;3. 河北省中药资源利用与质量评价国际联合研究中心, 河北 石家庄 050200
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基金项目河北省中医药管理局科研计划项目(2023355); 河北省二期现代农业产业技术体系创新团队项目(HBCT2018060205); 河北中医学院科研能力提升项目(KTY2019077; KTZ2019006)