| 7种睡莲属植物叶绿体基因组密码子偏好性分析 |
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| 引用本文： | 毛立彦,黄秋伟,龙凌云,檀小辉,谢红辉,唐毓玮,丁丽琼.7种睡莲属植物叶绿体基因组密码子偏好性分析[J].西北林学院学报,2022,37(2):98-107. |
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| 作者姓名： | 毛立彦 黄秋伟 龙凌云 檀小辉 谢红辉 唐毓玮 丁丽琼 |
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| 作者单位： | （广西壮族自治区农业科学院 亚热带作物研究所，广西 南宁 530001） |
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| 摘 要： | 以7种睡莲属植物叶绿体基因组为研究对象，分析其叶绿体基因组的密码子使用偏好性，探讨影响其密码子偏好性形成的主要因素。结果表明，7种睡莲叶绿体密码子使用偏好性相似，基因组序列富含A/T碱基，密码子第3位碱基以A/T结尾为主；有效密码子数（ENc）分别为40.14~61.00、40.14~61.00、40.55~57.61、39.77~57.61、39.55~57.30、39.56~61.00和40.10~61.00，均明显大于35，表明其密码子使用偏好性较弱。ENc-plot、PR2-plot和中性绘图分析表明，它们的叶绿体密码子偏好性形成受自然选择、碱基突变等多种因素共同影响，其中自然选择起主导作用。通过同义密码子RSCU值分析，发现以A/T结尾的高频密码子27个，以G/C结尾的低频密码子26个，进一步依据密码子RSCU和△RSCU值，最终确定出4个最优密码子。此外，基于7种睡莲叶绿体基因组密码子使用偏好特征RSCU值、CDS序列及其全基因组序列分别构建系统进化树，分析发现3种方法构建的物种间进化关系相似，均划分为2大分支，其中Nymphaea alba var.rubra、Nymphaea alba、Nymphaea ampla、Nymphaea capensis、Nymphaea jamesoniana和Nymphaea lotus划归第1分支，Nymphaea mexicana单独形成第2分支。研究结果进一步支持了物种内遗传关系与密码子使用偏好性之间存在一定关系。
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| 关 键 词： | 睡莲 叶绿体基因组 密码子偏好性 最优密码子 |
Comparative Analysis of Codon Usage Bias in Chloroplast Genomes of Seven Nymphaea Species |
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| MAO Li-yan,HUANG Qiu-wei,LONG Ling-yun,TAN Xiao-hui,XIE Hong-hui,TANG Yu-wei,DING Li-qiong. Comparative Analysis of Codon Usage Bias in Chloroplast Genomes of Seven Nymphaea Species[J].Journal of Northwest Forestry University,2022,37(2):98-107. |
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| Authors: | MAO Li-yan HUANG Qiu-wei LONG Ling-yun TAN Xiao-hui XIE Hong-hui TANG Yu-wei DING Li-qiong |
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| Institution: | (Guangxi Subtropical Crops Research Institute,Nanning 530001,Guangxi,China) |
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| Abstract: | In this study,the codon usage bias and sources of variance in chloroplast genomes of seven different Nymphaea species were systematically analyzed to explore the main factors influencing codon preference.The results showed that the chloroplast genomes of seven Nymphaea species harbored similar codon usage bias,showing that A/T base was rich in chloroplast genome,and the codons in the 3rd position were mainly terminated by A/T.The ranges of effective number of codons (ENc) were 40.14-61.00,40.14-61.00,40.55-57.61,39.77-57.61,39.55-57.30,39.56-61.00 and 40.10-61.00 for seven Nymphaea species,respectively.The ENc values were more than 35 in all genes,which indicated that the codon usage bias was weak in theses seven species.According to the results of neutrality plot,ENc-plot,and PR2-plot analysis,the codon usage bias in these choroplast genomes were influenced by many factors,such as natural selection,mutation bias and so on,and the natural selection dominated in these factors.Through relative synonymous codon usage (RSCU) analysis,27 high frequency codons preferred to end with A/T,and 26 low frequency codons inclined to end with G/C in the seven species were detected.Finally,according to the codon RSCU and △RSCU values,4 optimal codons were screened out.Furthermore,the phylogenetic tree from seven Nymphaea choloplasts was constructed by using codon preference RSCU values,CDS sequence and whole genome sequence,respectively.The results demonstrated that the evolutionary relationships among species constructed by the three methods were similar,and they were classified into two clusters:cluster Ⅰ,N.alba var.rubra,N.alba,N.ampla,N.capensis,N.jamesoniana and N.lotus,and cluster Ⅱ,N.mexicana,which further supported that there was a certain relationship between the genetic relationships within species and codon usage bias. |
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| Keywords: | NymphaeaNymphaea chloroplast genome codon usage bia optimal codon |
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