‘白毫早’叶绿体与线粒体基因组密码子偏好性分析

茶叶科学 ›› 2025, Vol. 45 ›› Issue (4): 587-603.

‘白毫早’叶绿体与线粒体基因组密码子偏好性分析

曾文娟^1,2,3,4, 刘珊^1,2,3,4, 文聪^1,2,3,4, 张其湘^1,2,3,4, 黄静⁵, 龚意辉^1,2,3,4, 陈致印^1,2,3,4,*

1.湖南人文科技学院农业与生物技术学院,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;
5.湖南省农业科学院茶叶研究所,湖南长沙 410125

收稿日期:2025-01-07 修回日期:2025-04-16 出版日期:2025-08-15 发布日期:2025-08-15
通讯作者: *772612626@qq.com
作者简介:曾文娟,女,本科在读,主要从事茶树遗传育种、茶叶精深加工方面的研究。
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）

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

ZENG Wenjuan^1,2,3,4, LIU Shan^1,2,3,4, WEN Cong^1,2,3,4, ZHANG Qixiang^1,2,3,4, HUANG Jing⁵, GONG Yihui^1,2,3,4, CHEN Zhiyin^1,2,3,4,*

1. College of Agriculture and Biotechnology, 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;
4. Key Laboratory of Characteristic Agricultural Resource Development and Quality Safety Control in Hunan Province, Hunan University of Humanities, Science and Technology, Loudi 417000, China;
5. Tea Research Institute of Hunan Academy of Agricultural Sciences, Changsha 410125, China

Received:2025-01-07 Revised:2025-04-16 Online:2025-08-15 Published:2025-08-15

摘要/Abstract

摘要： 密码子使用偏好性作为基因表达调控与分子进化的关键驱动机制,在植物细胞器基因组演化中具有重要生物学意义。以茶树品种‘白毫早’（Camellia sinensis cv. ‘Baihaozao’）为对象,系统解析其叶绿体（52个基因）与线粒体（29个基因）基因组的密码子使用模式及进化驱动力。结果表明：（1）叶绿体基因组平均有效密码子数（ENC=44.57±4.59）显著低于线粒体基因组（ENC=51.87±5.31）,两者均呈现弱偏好性特征。中性分析揭示,叶绿体偏好性主要由自然选择主导（GC_3s与ENC相关性R²=0.016）,而线粒体则受自然选择与突变压力协同调控（R²=0.11）,与双子叶植物细胞器基因组的进化约束差异规律一致。（2）相对同义密码子使用度（Relative synonymous codon usage,RSCU）分析表明,两类细胞器基因组均显著偏好以A/U结尾的同义密码子,其中叶绿体高表达基因（如ndhA、rps14）表现出更强的A/U末端偏好性,暗示翻译选择对高表达基因的优化作用。（3）通过多变量统计筛选,确定18个叶绿体最优密码子（GCA、GCU等）及18个线粒体最优密码子（GCA、AGA等）,其中GCA在两类细胞器中均被优选,显示跨细胞器功能基因的适应性趋同。本研究阐明了‘白毫早’细胞器基因组密码子使用特征的异质性及其进化驱动力,为茶树分子育种中外源基因的适配性优化及跨细胞器表达调控网络的构建提供了理论依据。

关键词: 白毫早, 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

Abstract: Codon usage bias serves as a critical driving mechanism in gene expression regulation and molecular evolution, holding significant biological importance in the evolution of organelle genomes in plants. This study focused on the economically important tea cultivar ‘Baihaozao’ (Camellia sinensis cv. ‘Baihaozao’) and systematically analyzed the codon usage patterns and evolutionary drivers of its chloroplast (52 genes) and mitochondrial (29 genes) genomes for the first time. The results indicate: (1) the average effective codon number (ENC=44.57±4.59) of the chloroplast genome is significantly lower than that of the mitochondrial genome (ENC=51.87±5.31), with both exhibiting weak preference characteristics. Neutrality analysis reveals that the chloroplast's preference is primarily driven by natural selection (correlation between GC_3s and ENC, R² =-0.016), whereas the mitochondrial genome is regulated by a combination of natural selection and mutational pressure (R² = -0.11), which is consistent with the evolutionary constraints observed in the organelle genomes of dicotyledons. (2) RSCU analysis shows that both types of organelle genomes significantly prefer synonymous codons ending in A/U, with high-expression chloroplast genes (e.g., ndhA, rps14) exhibiting a stronger preference for A/U terminal codons. This suggests that translational selection optimizes highly expressed genes. (3) Through multivariate statistical screening, 18 optimal codons were identified for the chloroplast genome (e.g., GCA, GCU) and 18 optimal codons for the mitochondrial genome (e.g., GCA, AGA). GCA was favored in both organelle types, reflecting the adaptive convergence of functional genes across organelles. This study elucidated the heterogeneity of codon usage characteristics in the organelle genomes of ‘Baihaozao’ and their evolutionary drivers for the first time, providing a theoretical basis for the adaptive optimization of exogenous genes and the construction of cross-organelle expression regulatory networks in molecular tea breeding.

Key words: Camellia sinensis cv. ‘Baihaozao’, chloroplast genome, mitochondrial genome, codon usage bias, optimal codon

中图分类号:

S432.41
Q52

曾文娟, 刘珊, 文聪, 张其湘, 黄静, 龚意辉, 陈致印. ‘白毫早’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(4): 587-603.

ZENG Wenjuan, LIU Shan, WEN Cong, ZHANG Qixiang, HUANG Jing, GONG Yihui, CHEN Zhiyin. Analysis of Codon Usage Bias in Chloroplast and Mitochondrial Genomes of Camellia sinensis cv. ‘Baihaozao’[J]. Journal of Tea Science, 2025, 45(4): 587-603.

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