小果油茶与越南油茶中叶绿体基因组密码子偏好性  

Chloroplast genome codon preference in Camellia meiocarpa and Camellia vietnamensis

作　　者：张菲菲 朱艳 韩长志 Zhang Feifei;Zhu Yan;Han Changzhi(College of Forestry,Southwest Forestry,Kunming 650224,Yunnan,China;Key Laboratory of Forest Disaster Warning and Control of Yunnan Province,Kunming 650224,Yunnan,China)

机构地区：[1]西南林业大学林学院,云南昆明650224 [2]云南省森林灾害预警与控制重点实验室,云南昆明650224

出　　处：《北京林业大学学报》2025年第4期37-49,共13页Journal of Beijing Forestry University

基　　金：云南省研究生导师团队建设项目(2022100);云南省“兴滇英才支持计划”青年人才专项(YNWR-QNBJ-2020-188)。

摘　　要：【目的】研究小果油茶和越南油茶中叶绿体基因组密码子的使用模式,分析并揭示两个物种密码子使用偏好性产生的原因,明确两个物种叶绿体基因组中的最优密码子,为油茶基因组研究和良种培育提供理论依据。【方法】运用Codon W 1.4.2和在线软件CUSP、MEGA软件等,分析筛选后的小果油茶和越南油茶各52条CDS序列,获得相对同义密码子使用度(RSCU)、有效密码子数(ENC)、密码子适应指数(CAI)、GC碱基含量等参数,再进行相关性分析、中性绘图分析、ENC-plot分析和PR2-plot偏倚分析,并通过RSCU、△RSCU预测两物种高频、高表达的最优密码子。【结果】(1)小果油茶GC含量、ENC和CAI值分别为37.49%、48.561、0.158,越南油茶GC含量、ENC和CAI值分别为37.50%、48.529、0.160,小果油茶中GC_(1)(45.81%)>GC_(2)(38.00%)>GC_(3)(28.64%),越南油茶中GC_(1)(45.88%)>GC_(2)(38.02%)>GC_(3)(28.59%),两物种密码子中GC分布不均,均呈现出偏好首位的特点。(2)小果油茶和越南油茶中分别有23和11个最优密码子,其中分别有22和11个密码子以A或U结尾,表明最优密码子第3位偏好A/U。(3)小果油茶与越南油茶的ENC值分布均在35.64~61.00之间,且均值相差不大,表明两个油茶品种在密码子的使用上有一定的相似性。(4)中性绘图分析、ENC-plot分析和PR2-plot分析表明:两个油茶物种中叶绿体基因组密码子偏好性主要受到自然选择的影响。【结论】小果油茶和越南油茶叶绿体基因组密码子碱基使用偏好性不强,且偏好性主要受到自然选择的影响。小果油茶有23个最优密码子,越南油茶有11个最优密码子,研究结果为进一步探索油茶基因组和良种培育提供理论依据和数据支撑。[Objective]This paper investigates the codon usage patterns in chloroplast genomes of Camellia oleifera and C.vietnamensis,analyzes and elucidates the underlying causes of codon usage bias,identifies optimal codons in their chloroplast genomes,so as to provide theoretical foundations and data support for genomic research and breeding of oil tea species.[Method]Screened CDS sequences(52 sequences each from C.oleifera and C.vietnamensis)were analyzed using Codon W 1.4.2,CUSP,MEGA,and other online tools.Parameters including relative synonymous codon usage(RSCU),effective number of codons(ENC),codon adaptation index(CAI),and GC content were calculated.Correlation analysis,neutrality plot analysis,ENC-plot analysis,and PR2-plot bias analysis were performed.High-frequency and highly expressed optimal codons were predicted based on RSCU andΔRSCU values.[Result](1)C.oleifera exhibited GC content,ENC,and CAI values of 37.49%,48.561,and 0.158,respectively,while C.vietnamensis showed values of 37.50%,48.529,and 0.160.Both species displayed uneven GC distribution across codon positions,with GC_(1)>GC_(2)>GC_(3)(C.oleifera:GC_(1)=45.81%,GC_(2)=38.00%,GC_(3)=28.64%;C.vietnamensis:GC_(1)=45.88%,GC_(2)=38.02%,GC_(3)=28.59%),indicating a preference for GC at the first codon position.(2)C.oleifera and C.vietnamensis had 23 and 11 optimal codons,respectively,with 22 and 11 of these codons ending in A/U,suggesting a strong preference for A/U at the third codon position.(3)ENC values for both species ranged from 35.64 to 61.00,with minimal differences in mean values,reflecting similarities in codon usage patterns.(4)Neutrality plot,ENC-plot,and PR2-plot analyses revealed that natural selection predominantly influenced codon usage bias in chloroplast genomes of both species.[Conclusion]The chloroplast genomes of C.oleifera and C.vietnamensis exhibit weak codon usage bias,primarily shaped by natural selection.C.oleifera has 23 optimal codons,while C.vietnamensis has 11 optimal codons.These findings provide critical theoretical and emp

关 键 词：小果油茶 越南油茶 叶绿体基因组 密码子偏好性 最优密码子 

分 类 号：S718.43[农业科学—林学]