‘槠叶齐’茶树线粒体基因组特征及密码子使用偏好性分析

doi:10.13305/j.cnki.jts.2026.02.005

茶叶科学 ›› 2026, Vol. 46 ›› Issue (2): 221-237.doi: 10.13305/j.cnki.jts.2026.02.005

‘槠叶齐’茶树线粒体基因组特征及密码子使用偏好性分析

陈致印^1,2,3,4, 曾文娟^1,2,3, 杨盼^1,2,3, 文聪^1,2,3, 江睿^1,2,3, 钟倩怡^1,2,3, 敬媛蓉^1,5, 朱赞江^1,5,*

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.娄底市农作物种质资源保护与利用工程技术研究中心,湖南娄底 417000

收稿日期:2025-12-19 修回日期:2026-02-17 出版日期:2026-04-15 发布日期:2026-04-22
通讯作者: ^*13707389645@139.com
作者简介:陈致印,男,副教授,主要从事茶树育种、茶与健康等方面的研究。
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）; 国家级大学生创业训练项目（202510553020X）; 湖南省大学生创新训练项目（S202510553039）

Analysis of Mitochondrial Genome Characteristics and Codon Usage Bias in Camellia sinensis cv. ‘Zhuyeqi’

CHEN Zhiyin^1,2,3,4, ZENG Wenjuan^1,2,3, YANG Pan^1,2,3, WEN Cong^1,2,3, JIANG Rui^1,2,3, ZHONG Qianyi^1,2,3, JING Yuanrong^1,5, ZHU Zanjiang^1,5,*

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, China;
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. Loudi Crop Germplasm Resources Conservation and Utilization Engineering Technology Research Center, Loudi 417000, China

Received:2025-12-19 Revised:2026-02-17 Online:2026-04-15 Published:2026-04-22

摘要/Abstract

摘要： 以‘槠叶齐’茶树为材料,采用Illumina（二代测序）与Oxford Nanopore（三代测序）相结合的策略,系统解析并高质量组装其线粒体基因组,进而通过基因注释、密码子偏好性及系统发育分析,揭示其遗传机制与进化特征。结果显示,该线粒体基因组由“1个环状+6个线性”的7个片段组成,总长911 255 bp,鸟嘌呤和胞嘧啶（Guanine-cytosine,GC）含量45.7%,其中片段1为环状结构（311 104 bp）,其余为线性。共注释77个功能基因,其中38个蛋白编码基因（Protein-coding genes,PCGs）、33个转移核糖核酸（Transfer ribonucleic acid,tRNA）、3个核糖体核糖核酸（Ribosomal ribonucleic acid,rRNA）及3个假基因,并检测到269个简单序列重复（Simple sequence repeats,SSRs）,四核苷酸重复占比最高（43.49%）,单核苷酸重复以腺嘌呤（Adenine,A）/胸腺嘧啶（Thymine,T）为主（91.18%）。长重复序列共780个,包括354个正向重复和426个回文重复。非同义替换（Nonsynonymous substitutions,Ka）/同义替换（Synonymous substitutions,Ks）分析表明,ccmB、rps10、mttB基因受到显著正选择（Ka/Ks>1）,说明其在环境适应性进化中起到关键作用。密码子偏好性分析显示,29个PCGs基因的GC₃含量（37.36%）显著低于GC₁（47.81%）和GC₂（43.01%）,ENC均值51.98,表明偏好性较弱。GC₁₂与GC₃回归分析（R²=0.004 5）揭示自然选择贡献率达88.45%,显著高于突变压力。碱基偏好表现为C₃>G₃和T₃>A₃,最优密码子以尿嘧啶（Uracil,U）/腺嘌呤结尾为主（60.87%）。系统发育分析表明‘槠叶齐’与山茶属核心分支物种聚为单系群,支持其分类地位。本研究为茶树线粒体基因组进化机制及功能基因适应性研究提供了重要依据。

关键词: 茶树, ‘槠叶齐’, 线粒体基因组, 密码子偏好性, 系统发育

Abstract: This study utilized Camellia sinensis cv. ‘Zhuyeqi’ as the research material and employed a combined strategy of Illumina ( the second-generation sequencing) and Oxford Nanopore (the third-generation sequencing) to systematically analyze and achieve a high-quality assembly of its mitochondrial genome. Furthermore, through gene annotation, codon usage bias analysis and phylogenetic analysis, this study aimed to elucidate the genetic mechanisms and evolutionary characteristics of Camellia sinensis cv. ‘Zhuyeqi’. The results indicate that the mitochondrial genome consists of seven fragments, including “one circular and six linear” structures, with a total length of 911 255 bp and a guanine-cytosine (GC) content of 45.7%. Among these fragments, fragment 1 is circular (311 104 bp), while the remaining fragments are linear. A total of 77 functional genes were annotated, including 38 protein-coding genes (PCGs), 33 transfer RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes, and 3 pseudogenes. Additionally, 269 simple sequence repeats (SSRs) were identified, with tetranucleotide repeats being the most abundant type (43.49%). Mononucleotide repeats were primarily composed of adenine (A)/thymine (T) (91.18%). A total of 780 long repeat sequences were identified, comprising 354 forward repeats and 426 palindromic repeats. The analysis of nonsynonymous substitutions (Ka) and synonymous substitutions (Ks) indicates that the ccmB、rps10 and mttB genes are under significant and positive selection (Ka/Ks>1), suggesting their crucial roles in adaptive evolution to environmental conditions. Codon usage bias analysis reveals that the GC content of the third codon position (GC₃, 37.36%) in 29 PCGs was significantly lower than that of the first (GC₁, 47.81%) and second (GC₂, 43.01%) codon positions. The mean effective number of codons (ENC) is 51.98, indicating weak codon usage bias. Regression analysis of GC₁₂ and GC₃ (R² = 0.004 5) reveals that natural selection contributed 88.45%, significantly outweighing mutational pressure. Base preference shows C₃>G₃ and T₃>A₃, with optimal codons predominantly ending in uracil (U)/adenine (A) (60.87%). Phylogenetic analysis indicates that C. sinensis cv. ‘Zhuyeqi’ forms a monophyletic group with core species of the genus Camellia, supporting its taxonomic status. This study provided critical insights into the evolutionary mechanisms of the mitochondrial genome and the adaptive functions of genes in tea plants.

Key words: tea plant, C. sinensis cv. ‘Zhuyeqi’, mitochondrial genome, codon usage bias, phylogeny

中图分类号:

S571.1
Q52

陈致印, 曾文娟, 杨盼, 文聪, 江睿, 钟倩怡, 敬媛蓉, 朱赞江. ‘槠叶齐’茶树线粒体基因组特征及密码子使用偏好性分析[J]. 茶叶科学, 2026, 46(2): 221-237. doi: 10.13305/j.cnki.jts.2026.02.005.

CHEN Zhiyin, ZENG Wenjuan, YANG Pan, WEN Cong, JIANG Rui, ZHONG Qianyi, JING Yuanrong, ZHU Zanjiang. Analysis of Mitochondrial Genome Characteristics and Codon Usage Bias in Camellia sinensis cv. ‘Zhuyeqi’[J]. Journal of Tea Science, 2026, 46(2): 221-237. doi: 10.13305/j.cnki.jts.2026.02.005.

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‘槠叶齐’茶树线粒体基因组特征及密码子使用偏好性分析

Analysis of Mitochondrial Genome Characteristics and Codon Usage Bias in Camellia sinensis cv. ‘Zhuyeqi’

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