木通叶绿体基因组密码子偏好性分析
Analysis of Codon Usage Bias in Chloroplast Genome of Akebia
简雪艳 1杨菊2
作者信息
- 1. 铜仁职业技术学院农学院,铜仁,554300
- 2. 贵州大学,贵州省森林资源与环境研究中心,贵阳,550025
- 折叠
摘要
木通(Akebia)是重要的经济藤本,为了解木通叶绿体基因组密码子偏好性差异,以公开的叶绿体基因组数据为研究材料,提取相关完整的CDS(Coding DNA sequence)基因序列.利用CodonW软件、EMBOSS和Seqinr R package对筛选出的CDSs进行生物信息学分析,并进行中性绘图、ENC-plot绘图和PR2-plot绘图分析和最优密码子筛选.结果表明,4种不同木通种的叶绿体基因组密码子的使用具有较强的偏好性,主要受突变和选择的影响.不同位置上的GC含量大小排序分别是GC1＞GC2＞GC3,表明叶绿体基因组密码子末位碱基偏好以A和T结尾.中性分析结果显示GC12和GC3的相关性极低且不显著.PR2-plot分析中,T碱基的使用频率＞A、G碱基的使用频率＞C;11个密码子确定为4种木通间通用的最优密码子.本研究为提高木通叶绿体基因组的外源性基因表达效率提供参考.
Abstract
Akebia is an important economic vine.In order to understand the difference in codon usage bias of Akebia chloroplast genomes,the published chloroplast genomes data was used as the research material,and the relevant complete CDS(Coding DNA sequence)sequences were extracted.Based on the selected CDSs,CodonW software,EMBOSS,and Seqinr R package performed neutral plotting,ENC-plot plotting,PR2-plot plotting analysis and optimal codon screening.The results showed that codon usage bias in the chloroplast genome of the four dif-ferent species of Akebia were mainly affected by mutation and selection.The order of GC content at different posi-tions was GC1＞GC2＞GC3,indicating that the base preference of the last codon in the chloroplast genome ends in A and T.The results of neutral analysis showed that the correlation between GC12 and GC3 were extremely low and not significant.In PR2-plot analysis,the use frequency of T bases＞A,the use frequency of G bases＞C;11 codons were determined to be the optimal codon among the 4 Akebia species.This study provides a reference for improv-ing the efficiency of exogenous gene expression of the chloroplast genome in Akebia.
关键词
木通/叶绿体基因组/密码子偏好性/最优密码子Key words
Akebia/Chloroplast genome/Codon usage bias/Optimal codon引用本文复制引用
基金项目
贵州大学实验室开放项目(SYSKF2021-082)
出版年
2024
NETL
NSTL
万方数据