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2025 , Vol. 45 >Issue 2: 201 - 218

DOI: https://doi.org/10.13305/j.cnki.jts.2025.02.008

研究报告

‘槠叶齐’叶绿体与线粒体基因组密码子偏好性分析

  • 曾文娟 ,
  • 朱友鹏 ,
  • 陈嘉欣 ,
  • 李洪玉 ,
  • 王双辉 ,
  • 龚意辉 ,
  • 陈致印
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  • 1.湖南人文科技学院湖南省湘中特色农业资源开发利用与质量安全控制重点实验室,湖南 娄底 417000;
    2.湖南人文科技学院湖南省园艺生产与加工类创新创业教育中心,湖南 娄底 417000;
    3.湖南人文科技学院湖南省创新创业示范基地,湖南 娄底 417000;
    4.湖南人文科技学院农业与生物技术学院,湖南 娄底 417000;
    5.新化县桃花源农业开发有限公司,湖南 娄底 417000
曾文娟,女,本科在读,主要从事茶树遗传育种研究。

收稿日期: 2025-02-10

  修回日期: 2025-03-06

  网络出版日期: 2025-04-30

基金资助

湖南省自然科学基金（2023JJ50465）、湖南省科技创新计划项目（2024RC8289）、娄底市科技创新计划项目（2023RC3501）、国家级大学生创新训练项目（S202310553022）

收起

Analysis of Codon Usage Bias in Chloroplast and Mitochondrial Genomes of Camellia sinensis cv.‘Zhuyeqi’

  • ZENG Wenjuan ,
  • ZHU Youpeng ,
  • CHEN Jiaxin ,
  • LI Hongyu ,
  • WANG Shuanghui ,
  • GONG Yihui ,
  • CHEN Zhiyin
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  • 1. Key Laboratory of Characteristic Agricultural Resource Development and Quality Safety Control in Hunan Province, Hunan University of Humanities, Science and Technology, Loudi 417000, China;
    2. Innovation and Entrepreneurship Education Center for Horticultural Production and Processing in Hunan Province, Hunan University of Humanities, Science and Technology, Loudi 417000, China;
    3. Hunan University of Humanities, Science and Technology, Hunan Provincial Innovation and Entrepreneurship Demonstration Base, Loudi 417000, China;
    4. College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China;
    5. Xinhua County Taohuayuan Agricultural Development Co., Ltd., Loudi 417000, China

Received date: 2025-02-10

  Revised date: 2025-03-06

  Online published: 2025-04-30

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摘要

密码子使用偏好性作为基因表达调控与分子进化的重要驱动力,在植物细胞器基因组研究中具有特殊意义。‘槠叶齐’（Camellia sinensis cv.‘Zhuyeqi’）作为中国重要的茶树品种,其细胞器基因组密码子使用模式尚未见系统报道。本研究对‘槠叶齐’52个叶绿体编码基因和29个线粒体编码基因开展系统生物学分析。结果表明：（1）‘槠叶齐’叶绿体基因组（ENC=44.64±3.25）和线粒体基因组（ENC=51.98±3.47）均呈现弱密码子偏好性,其中叶绿体偏好性主要受自然选择驱动（GC3s与ENC相关性R2=0.482）,而线粒体受自然选择与突变压力共同作用（R2=0.312）;（2）相对同义密码子使用度（RSCU）分析揭示两个细胞器基因组均显著偏好以A/U结尾的同义密码子,其中叶绿体基因组高表达基因（rpoC2、psbA等）呈现更强的密码子偏好;（3）通过多参数筛选获得20个叶绿体最优密码子（GCA、GCU等）和23个线粒体最优密码子（GCC、AGG等）。本研究阐明了‘槠叶齐’细胞器基因组密码子使用特征及其进化驱动力,为茶树分子育种体系优化和外源基因高效表达提供了重要理论依据。

关键词： 槠叶齐; 叶绿体基因组; 线粒体基因组; 密码子使用偏好性; 最优密码子

本文引用格式

曾文娟 , 朱友鹏 , 陈嘉欣 , 李洪玉 , 王双辉 , 龚意辉 , 陈致印 . ‘槠叶齐’叶绿体与线粒体基因组密码子偏好性分析[J]. 茶叶科学, 2025 , 45(2) : 201 -218 . DOI: 10.13305/j.cnki.jts.2025.02.008

Abstract

Codon usage bias serves as an important driving force for gene expression regulation and molecular evolution, and is of particular importance in the study of plant organellar genomes. Camellia sinensis cv. ‘Zhuyeqi’, an important tea cultivar in China, has not yet received a systematic report on the codon usage patterns of its organellar genomes. This study was systematic bioinformatic analysis of the 52 chloroplast-encoded genes and 29 mitochondrial-encoded genes of ‘Zhuyeqi’. The results reveal that: (1) both the chloroplast genome (ENC=44.64±3.25) and the mitochondrial genome (ENC=51.98±3.47) exhibit weak codon usage bias, with the chloroplast bias primarily driven by natural selection (GC3s and ENC correlation R2=0.482). While the mitochondrial bias is jointly influenced by natural selection and mutational pressure (R2=0.312). (2) Relative synonymous codon usage (RSCU) analysis demonstrates that both organellar genomes significantly prefer synonymous codons ending in A/U, and the highly expressed chloroplast genes (rpoC2, psbA) exhibit stronger codon preferences. (3) a multi-parameter screening approach identified 20 optimal chloroplast codons (GCA, GCU) and 23 optimal mitochondrial codons (GCC, AGG). This study provided elucidation of the codon usage characteristics and evolutionary driving forces in the organellar genomes of Camellia sinensis cv. ‘Zhuyeqi’, offering crucial theoretical guidance for the optimization of the tea molecular breeding system and the efficient expression of exogenous genes.

Key words： Camellia sinensis cv. ‘Zhuyeqi’; chloroplast genome; mitochondrial genome; codon usage bias; optimal codons

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