| 胡萝卜(Daucus carota var. sativa)密码子偏好性及属内质体基因组核苷酸多样性分析 |
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| 引用本文： | 康路,谢登峰,何兴金.胡萝卜(Daucus carota var. sativa)密码子偏好性及属内质体基因组核苷酸多样性分析[J].分子植物育种,2020(7):2077-2086. |
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| 作者姓名： | 康路 谢登峰 何兴金 |
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| 作者单位： | 四川大学生命科学学院 |
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| 基金项目： | 国家自然科学基金资助项目(31872647);国家科技基础条件平台教学标本子平台(2005DKA21403-JK)共同资助。 |
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| 摘 要： | 核苷酸多样性作为衡量物种遗传变异水平的重要指标,对于研究物种遗传多态性的高低、进化历史和系统位置具有重要的科学意义,密码子偏好性则跟基因表达和自然选择压力等密切相关。本研究通过计算胡萝卜属(Daucus L.) 17种植物的叶绿体基因组片段的核苷酸多样性,开发出了可用于系统学和群体遗传学等研究的叶绿体基因分子标记;并且基于Codon W和CUSP统计数据,通过相关性分析、中性绘图分析、ENC-plot分析以及PR2-plot分析,探究了胡萝卜(Daucus carota var. sativa)密码子使用偏好性。结果表明,有效密码子数(ENC)与最优密码子使用频率(FOP)、密码子适应指数(CAI)、密码子偏好指数(CBI)具有显著的相关性,胡萝卜叶绿体基因的密码子偏好性主要受到突变和自然选择的作用,其中,突变的影响更大。此外,本研究确定了5个高表达基因和18个最优密码子。这些研究结果有助于探究胡萝卜的进化历史和基因的表达,从而为品种改良和提高产量提供理论支持。
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| 关 键 词： | 胡萝卜(Daucus carota var.sativa) 叶绿体片段 核苷酸多样性 密码子偏好性 |
Codon Usage Bias Analyses of Daucus carota var. sativa and DNA Polymorphism on Chloroplast Genomes of Carrot Species |
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| Kang Lu,Xie Dengfeng,He Xingjin.Codon Usage Bias Analyses of Daucus carota var. sativa and DNA Polymorphism on Chloroplast Genomes of Carrot Species[J].Molecular Plant Breeding,2020(7):2077-2086. |
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| Authors: | Kang Lu Xie Dengfeng He Xingjin |
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| Institution: | (Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education,College of Life Sciences,Sichuan University,Chengdu,610064) |
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| Abstract: | As an important index to measure the level of genetic variation of species,nucleotide diversity is of great scientific significance for the study of genetic polymorphism,evolutionary history and phylogenetic relationship of species,while codon usage bias is closely related to gene expression and the level of translational pressure.In this study,by calculating the nucleotide diversity of plastid segments of 17 carrot species,we developed available molecular markers of cpDNA.Based on Codon W and CUSP statistics,the usage preference of Daucus carota codons was explored through correlation analysis,neutral plot analysis,ENC-plot analysis and PR2-plot analysis.The results showed that the number of effective codons(ENC)was significantly correlated with the frequency of optimal codons(FOP),codon adaptation index(CAI)and codon bias index(CBI),and codon usage bias of chloroplast genes of D.Carota var.sativa was mainly affected by both mutation and translational selection,among which mutation was dominant.Moreover,five hyper-expressed genes and 18 optimal codons were identified.These results will help to explore the evolutionary history and gene expression of carrots,thus providing theoretical support for variety breeding and yield improvement. |
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| Keywords: | Daucus carota var sativa Plastid DNA segments Nucleotide diversity Codon usage bias |
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