艾纳香叶绿体基因组密码子使用偏性分析  

Codon Usage Bias of Chloroplast Genome in Blumea balsamifera

作　　者：赵月梅 徐其碧 杨贵清 尹鑫 徐林 ZHAO Yuemei;XU Qibi;YANG Guiqing;YIN Xin;XU Lin(School of Biological Sciences,Guizhou Education University,Guiyang Guizhou 550018,P.R.China)

机构地区：[1]贵州师范学院生物科学学院,贵州贵阳550018

出　　处：《西部林业科学》2023年第3期55-62,77,共9页Journal of West China Forestry Science

基　　金：国家自然科学基金项目(31900273);贵州师范学院博士科研启动项目(2022BS015);大学生创新创业训练计划项目(S202114223051)。

摘　　要：为了明确艾纳香叶绿体基因组密码子的使用偏性,以53条蛋白质编码序列为研究对象,利用Codon W 1.4.2和在线软件CUSP等对其密码子进行中性绘图、ENC-plot和PR2-plot分析。结果显示:(1)艾纳香叶绿体基因组密码子不同位置GC碱基含量为GC 1(45.20%)>GC 2(38.51%)>GC_(3)(29.20%),说明密码子末位碱基偏好以A/U结尾。(2)有效密码子数(ENC)取值范围是37.03~58.20,表明密码子偏性较弱。(3)相对同义密码子(RSCU)>1的密码子有30个,其中以A、U结尾的有29个。(4)GC_(3)和GC_(12)相关性不显著;ENC-plot中大部分基因分布于期望曲线周围和下方,ENC比值分布在-0.05~0.05区间的基因有34%;PR2-plot分析中,T的使用频率高于A,G的使用频率高于C;上述分析均表明密码子偏性主要受自然选择的影响。(5)筛选出16个密码子为最优密码子,多以A或U结尾。研究结果对指导艾纳香叶绿体基因进行遗传转化、提高外源基因的表达效率、系统进化分析等方面具有一定的意义。To comprehend the codon usage pattern of chloroplast(cp)genome and its shaping factors in Blumea balsamifer,53 coding sequences(CDS)of B.balsamifera were used to analyze its cp codon bias using CodonW1.4.2 and online software CUSP in this study.The result show that(1)the GC content at different locations of the codons in the chloroplast genome of B.balsamifera were GC 1(45.20%)>GC 2(38.51%)>GC_(3)(29.20%),indicating that the codon terminal base preferred to end with A/U.(2)The value range of the effective codon number(ENC)was 37.03-58.20 which indicating a weak codon bias in B.balsamifera.(3)There were 30 codons with the Relative synonymous codon(RSCU)value>1,of which 29 codons ending with A and U;(4)There was no significant correlation between GC_(3) and GC_(12);Most of the genes in ENC-plot were distributed around and below the expectation curve,and there were 34%genes distributed between-0.05-0.05;In PR2-plot analysis,the usage frequency of T was higher than that of A,and G was higher than C.The above results all indicated that codon bias was mainly affected by selection.(5)16 codons were selected as the optimal codons,most of which ended with A or U.The results provide important significance in genetic transformation,improving the expression of exogenous gene and systematic evolution in Asteraceae species.

关 键 词：艾纳香 叶绿体基因组 最优密码子 密码子偏性 

分 类 号：S567.239[农业科学—中草药栽培]