茶叶科学 >

2025 , Vol. 45 >Issue 1: 61 - 78

DOI: https://doi.org/10.13305/j.cnki.jts.2025.01.006

研究报告

茶树‘大面白’线粒体基因组结构特征及其密码子偏好性分析

  • 尹明华 ,
  • 张牧彤 ,
  • 徐子林 ,
  • 欧阳茜 ,
  • 王美暄 ,
  • 李文婷
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  • 1.上饶师范学院生命科学学院,江西 上饶 334001;
    2.上饶市药食同源植物资源保护与利用重点实验室,江西 上饶 334001
尹明华,女,教授,主要从事植物生物技术方面的研究,yinminghua04@163.com

收稿日期: 2024-10-28

  修回日期: 2024-11-19

  网络出版日期: 2025-03-03

基金资助

国家自然科学基金项目（31960079、31860084、32060092）、2024年省级大学生创新创业训练计划项目（2024-PX-25）

收起

Analysis of the Structural Characteristics and Codon Usage Biase of the Mitochondrial Genome in Tea Cultivar ‘Damianbai’

  • YIN Minghua ,
  • ZHANG Mutong ,
  • XU Zilin ,
  • OUYANG Qian ,
  • WANG Meixuan ,
  • LI Wenting
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  • 1. College of Life Sciences, Shangrao Normal University, Shangrao 334001, China;
    2. Key Laboratory of Protection and Utilization of Medicinal and Edible Plant Resources in Shangrao, Shangrao 334001, China

Received date: 2024-10-28

  Revised date: 2024-11-19

  Online published: 2025-03-03

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摘要

茶树‘大面白’（Camellia sinensis cv. ‘Damianbai’）是上饶市广信区自主培育的国家级品种,其线粒体基因组结构特征及密码子偏好性尚不清楚。以‘大面白’为试验材料,采用高通量测序技术对其线粒体全基因组进行测序、组装、注释,采用生物信息学软件对其线粒体基因组的结构特征和密码子偏好性进行分析。结果表明,‘大面白’线粒体基因组全长886 354 bp,结构为完整单环状分子,GC含量为45.76%;共注释到78个功能基因,包括41个蛋白质编码基因,33个tRNA基因,4个rRNA基因;共检测到59个SSR（主要为A/T单核苷酸重复）和100个Long repeat（主要为正向重复和回文重复）。‘大面白’线粒体基因组密码子偏好性较弱,密码子偏好以A/U结尾,密码子使用偏好性主要受自然选择的影响,受内部突变压力的影响小;‘大面白’线粒体基因组的最优密码子为14个（AAU、GAU、CAU、UUU、AUU、GCU、GGA、ACU、GUU、CGA、UUA、UUG、UCA、UCU）。11个近缘物种的线粒体基因组在基因区与‘大面白’线粒体基因组具有高度同源性;‘大面白’线粒体基因组与‘凌云白毫’（ON782577）线粒体基因组的共线性最高,两者的基因排列顺序基本一致;‘大面白’线粒体基因组与其叶绿体基因组之间具有62个高度同源性的基因片段;‘大面白’与‘凌云白毫’单独聚成一小分支,两者亲缘关系较近。本研究分析了‘大面白’线粒体基因组序列特征及系统发育进化关系,为加强‘大面白’种质鉴定及其资源多样性的开发利用提供了参考依据。

关键词： ‘大面白’; 结构特征; 密码子偏好性; 线粒体基因组

本文引用格式

尹明华 , 张牧彤 , 徐子林 , 欧阳茜 , 王美暄 , 李文婷 . 茶树‘大面白’线粒体基因组结构特征及其密码子偏好性分析[J]. 茶叶科学, 2025 , 45(1) : 61 -78 . DOI: 10.13305/j.cnki.jts.2025.01.006

Abstract

Camellia sinensis cv. ‘Damianbai’ is a national cultivar in Guangxin District, Shangrao. Its mitochondrial genome structure and codon preference are still unclear. Using ‘Damianbai’ as the experimental material, high-throughput sequencing technology was used to sequence, assemble, and annotate the entire mitochondrial genome of ‘Damianbai’. Bioinformatics software was used to analyze the structural characteristics and codon preferences of its mitochondrial genome. The results show that the mitochondrial genome of ‘Damianbai’ was 886 354 bp in length, with a complete single circular molecule structure and a GC content of 45.76%. A total of 78 functional genes were annotated in the mitochondrial genome of ‘Damianbai’, including 41 protein-coding genes, 33 tRNA genes and 4 rRNA genes. A total of 59 SSRs (mainly A/T single nucleotide repeats) and 100 Long repeats (mainly positive and palindromic repeats) were detected in the mitochondrial genome of ‘Damianbai’. The codon bias of the mitochondrial genome in ‘Damianbai’ is relatively weak, with a preference for codons ending in A or U. The codon usage bias of the mitochondrial genome of ‘Damianbai’ is mainly influenced by natural selection, and is less affected by internal mutation pressure. The optimal codons for the mitochondrial genome of ‘Damianbai’ are 14 (AAU, GAU, CAU, UUU, AUU, GCU, GGA, ACU, GUU, CGA, UUA, UUG, UCA, UCU). The mitochondrial genomes of 11 closely related species exhibit high homology with the mitochondrial genome of ‘Damianbai’ in the gene region. The mitochondrial genomes of ‘Damianbai’ and ‘Lingyunbaihao’ (ON782577) have the highest collinearity, and their gene arrangement orders are basically the same. There are 62 highly homologous gene fragments between the mitochondrial genome and chloroplast genome of ‘Damianbai’. ‘Damianbai’ and ‘Lingyunbaihao’ belong to a small branch separately, indicating they are closely related. This study analyzed the mitochondrial genome sequence characteristics and phylogenetic relationships of ‘Damianbai’, providing a reference for strengthening the identification of ‘Damianbai’ germplasm and the development and utilization of its resource diversity.

Key words： Camellia sinensis cv. ‘Damianbai’; codon usage biase; mitochondrial genome; structural features

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