摘要
为了解霸王密码子使用特征及形成原因,本研究以NCBI网站中霸王的EST数据为材料,从中选取637条高质量基因为研究对象,利用Codon W、Excel等软件分析密码子使用特征。结果表明:霸王密码子的平均ENC为51.594,平均CAI为0.179,平均GC3s为41.14%,密码子使用偏好性较弱,密码子第3位偏好使用以A/T结尾的碱基;ENC绘图分析、中性分析、偏倚分析结果说明自然选择是引起霸王密码子偏好使用的主要因素,但同时还受突变压力和其他因素的影响;偏倚分析中,大部分基因都分布在中心点的左下方,说明密码子第3位上A的使用频率小于T的使用频率,G的使用频率小于C的使用频率。以ENC值和RSCU值为参考标准,确定了28个高频密码子(RSCU>1),以A/U结尾的占82.14%;确定了27个高表达密码子(△RSCU≥0.08),最终筛选出UAU、UGU、UGA、CAU、AGC、GUG为最优密码子。本研究为霸王密码子优化以及基因工程中外源基因的改良和表达提供理论依据。
To understand the codon usage characteristics and formation reasons of Sarcozygium xanthoxylon Bunge,in this study,the transcriptome data of Sarcozygium xanthoxylon Bunge from the NCBI website are used as materials,and 637 high-quality sequences are selected as the research objects.Codon W,Excel and other software are used to analyze the characteristics of codon usage.The results showed that the average ENC of the codons of Sarcozygium xanthoxylon Bunge was 51.594,the average CAI was 0.179,and the average GCs was 41.14%,indicating that the codon usage preference is weak,and the third position of the codon prefers to use bases ending in A/T.The results of ENC mapping analysis,neutral analysis,and bias analysis indicate that the codon usage preference is mainly affected by natural selection,but it is also affected by mutation pression and other factors.In the bias analysis,most of the genes are distributed in the lower left of the center point,indicating that the use frequency of A in the third position of the codon is less than the use frequency of T,and the use frequency of G is less than the use frequency ofC.Taking ENC value and RSCU as the reference standard,28 high frequency codons(RSCU>1)were determined,82.14%of them ended with A/U,27 high expression codons(△RSCU≥0.08)were determined.Fi nally,UAU,UGU,UGA,CAU,AGC and GUG were selected as the optimal codons.This study provides a basis for codon optimization,and the improvement and expression of foreign genes in genetic engineering.
作者
吉德娟
王占林
Ji Dejuan;Wang Zhanlin(Academy of Agriculture and Forestry Sciences,Qinghai University,Xining,810016;Qinghai Plateau Forest Genetics and Breeding Laboratory,Qinghai University,Xining,810016)
出处
《分子植物育种》
CAS
北大核心
2023年第20期6705-6713,共9页
Molecular Plant Breeding
基金
青海省财政支农资金林业新技术推广项目([2020]SJTG-03)
海东河湟新区国家科技资源支撑型双创特色载体第一批特色科技项目
青海省科技厅县域创新试点县建设专项(2020-0407-NCC-0001)共同资助。
关键词
霸王
密码子偏好性
最优密码子
sSarcozygium xanthoxylon Bunge
Codon preference
Optimal codon
