摘要
为了探究迎春樱桃叶绿体基因组的密码子偏好性,本研究使用CodonW 1.4.4软件对该物种59条蛋白质编码序列的密码子使用特征进行分析,结果表明迎春樱桃的第3位的GC含量为28.72%,且RSCU>1的30个密码子中,有29个密码子以A/U碱基结尾,证明叶绿体基因组偏好使用A/U结尾的密码子;有效密码子数值范围介于35.10~61.00,平均值为46.75,证明密码子的偏好性较弱。中性绘图分析、ENC-plot分析以及PR2-plot偏倚分析结果都证明自然选择是密码子偏好性的重要影响因素。以有效密码子数及RSCU值为标准,最终筛选出9个最优密码子,且均以A/U结尾。基于CDS序列构建的系统进化树和基于RSCU值构建的聚类谱系图结果较吻合,表明密码子偏好性和系统发育关系有一定相关性。本研究为叶绿体基因组的密码子偏好性以及系统进化的相关研究提供了依据。
To detect the codon bias of chloroplast genomes in Prunus discoidea, the CodonW 1.4.4 software were employed to analyze the codon usage characteristics of the 59 protein-coding sequences. The results showed that the average GC content in the 3rd position was 28.72%. There were 29 codons with a RSCU>1, in which29 codons ended with A/U. It proved that the protein-coding genes in the chloroplast genome tend to use the codons ending with A/U. The range of effective codon number from 35.14 to 61.00, and the average content was46.75, which indicated that codons bias was weaker. The results of neutral plot analysis, ENC-plot analysis,and PR2-plot bias analysis all proved that selection was an important factor affecting codon bias. With ENC value and RSCU as the standard, 9 codons were ended with A/U. The phylogenetic tree based on CDS sequence and the cluster genealogy diagram based on RSCU value indicated that codon preference was correlated with phylogenetic relationship to some extent. This study has implications on codon bias of chloroplast genome and phylogenetic evolution.
作者
叶琦
宋炎峰
李蒙
伊贤贵
王绍军
王贤荣
Ye Qi;Song Yanfeng;Li Meng;Yi Xiangui;Wang shaojun;Wang Xianrong(Co-Innovetion Center for Sustainble Forestry in Southem Chin,Nanjing Forestry University,Nanjing,210037;Cllge of Biology and the Envi-ronmen,Nanjing Forestry University,Nanjing,210037;Meishan Shengshi Landscaping Co,Ltd,Meishan,620010)
出处
《分子植物育种》
CAS
北大核心
2022年第14期4576-4585,共10页
Molecular Plant Breeding
基金
四川省应用基础研究项目(2019YJ0715)
江苏省产学研合作项目(BY2018067)共同资助。
