黄檗叶绿体基因组密码子偏好性分析  

Analysis of codon usage bias in chloroplast genome of Phellodendron amurense

作　　者：卢梦月 周梦梦 杨俊 吴振宇 王博文 邹玉 杨洪升[1] LU Mengyue;ZHOU Mengmeng;YANG Jun;WU Zhenyu;WANG Bowen;ZOU Yu;YANG Hongsheng(College of Biology and Agriculture,Jiamusi University,Jiamusi 154007,China)

机构地区：[1]佳木斯大学生物与农业学院,黑龙江佳木斯154007

出　　处：《安徽农学通报》2025年第8期75-78,共4页Anhui Agricultural Science Bulletin

基　　金：佳木斯大学大学生创新创业计划训练项目(S202410222085);佳木斯大学国家自然科学基金培育项目(JMSUGP-ZR^(2)023-010)。

摘　　要：为探究黄檗叶绿体基因组中密码子的使用偏好及其主要影响因素,采用该乔木叶绿体基因组编码区序列(CDS)筛选,排除长度小于300bp、含终止密码子及重复序列的片段,最终保留52条有效序列;通过Codon W和CUSP软件计算这些序列的GC含量和有效密码子数(ENC),进一步通过密码子偏好参数的相关性分析探究密码子使用偏好性的影响因素。结果表明,黄檗叶绿体基因组密码子的平均GC含量为39.34%,其中密码子三个碱基的GC含量依次为:GC_(3)(30.32%)<GC_(2)(40.07%)<GC_(1)(47.63%)。密码子偏好参数相关性分析结果显示,密码子的第三位碱基偏好碱基A和U,ENC平均值为49.13,表明密码子使用偏好程度较弱,自然选择压力是影响密码子使用偏好的主要因素。共筛选出10种优化密码子,这些密码子对碱基A和U类型具有显著偏好。本研究为黄檗叶绿体基因工程及密码子优化工作奠定了数据基础。To explore the codon usage bias and its major influencing factors in the chloroplast genome of Phellodendron amurense,the coding sequences(CDS)of the chloroplast genome of P.amurense were utilized.Fragments shorter than 300 bp,containing stop codons,or repetitive sequences were excluded,ultimately retaining 52 valid sequences.The GC content and effective number of codons(ENC)of these sequences were calculated using Codon W and CUSP software,and the influencing factors of codon preference were further discussed by correlation analysis of codon preference parameters.The findings indicated that the average GC content within the chloroplast genome of P.amurense was 39.34%,with the GC content at the three positions ranked as follows:GC_(3)(30.32%)<GC_(2)(40.07%)<GC_(1)(47.63%).The codon preference parameter correlation analysis revealed a preference for A and U as the third base of the codon,with an average ENC value of 49.13,indicating a weak codon usage bias.Natural selection pressure was identified as the primary factor affecting codon usage bias.Ten optimized codons were identified,which showed a significant preference for the A and U types.This research lays a data foundation and provides a reference for gene engineering and the optimization of codons in the chloroplast genome of P.amurense.

关 键 词：黄檗 叶绿体基因组 密码子偏好性 最优密码子 

分 类 号：Q943.2[生物学—植物学] S792.31[农业科学—林木遗传育种]