摘要
密码子的偏好性由突变、自然选择进化而来,研究叶绿体基因组密码子偏性可进一步明确基因表达效率,对理解物种的系统发育和分子进化具有重要的参考价值。本研究利用Codon W和CUSP软件分析了裸果木植物叶绿体基因组中50个候选基因的密码子使用偏好模式及其形成原因。研究结果显示裸果木叶绿体基因组的密码子碱基组成表现为GC_(1)>GC_(2)>GC_(3),表明密码子偏爱以A和T结尾;G和C在密码子各位置中的占比较低,平均值为37.98%;有效密码子数(ENC)的平均值为47.55,表明密码子的偏好性较弱;中性绘图、ENC-plot、PR2-plot显示裸果木叶绿体基因组密码子使用偏好主要受突变和自然选择共同影响。另外,联合使用高频密码子和高表达密码子的方法共筛选出裸果木叶绿体基因组中均是由A和U结尾的最优密码子共14个。本研究深入探讨了裸果木叶绿体基因组的最优密码子及成因,可为旱生植物叶绿体基因组的应用与研究提供理论参考。
Codon usage bias were evolved from mutation,natural selection,studying condon usage bias of chloroplast genome could further clarify the efficiency of gene expression,which had important reference value for understanding the phylogeny and molecular evolution relationships of species.To explore the formation reasons and characteristics of codon usage bias,Codon W and CUSP were used to analysis the detailed indexes of codon usage bias with 50 candidate genes in the chloroplast(cp)genome of Gymnocarpos przewalskii.The results showed that the contents of base pairs were GC_1>GC_2>GC_3,indicating the cpDNA codon prefered to end with A and T;the proportion of G and C in each codon was relatively low,with an average of 37.98%;the average number of effective codon(ENC)was 47.55,and the codon has a weak bias.Besides,the results of neutrality plot analysis,ENC-plot analysis and PR2-plot analysis,showed that the codon usage preference of cp genome was mainly influenced by mutation and natural selection.Besides,the combination of high frequency codons and high expression codons has selected 14 optimal codons whose endings were both A and U.This study delves into the optimal codons and causes of the chloroplast genome of G.przewalskii,providing theoretical reference for the application and research of chloroplast genomes in arid trees.
作者
陈晓丹
冯玉玺
郭海洋
贾立强
魏作富
张林静
Chen Xiaodan;Feng Yuxi;Guo Haiyang;Jia Liqiang;Wei Zuofu;Zhang Linjing(College of Life Sciences,Shanxi Normal University,Taiyuan,030092)
出处
《分子植物育种》
CAS
北大核心
2023年第23期7715-7724,共10页
Molecular Plant Breeding
基金
山西省基础研究计划项目(202203021212400
20210302123328)
山西省高等学校科技创新项目(2022L257)
国家自然科学基金面上项目(42071067)共同资助。
关键词
裸果木
叶绿体基因组
密码子偏好性
最优密码子
Gymnocarpos przewalskit
Chloroplast genome
Codon preference
Optimal codon
