[1]曾文娟,刘珊珊,张其湘,等.茶树品种白毫早线粒体基因组结构特征、进化选择模式和密码子偏好性分析[J].江苏农业学报,2025,(08):1616-1627.[doi:doi:10.3969/j.issn.1000-4440.2025.08.018]
　ZENG Wenjuan,LIU Shanshan,ZAHNG Qixiang,et al.Analysis of mitochondrial genome structural characteristics, evolutionary selection patterns and codon bias of Camellia sinensis cv. Baihaozao[J].,2025,(08):1616-1627.[doi:doi:10.3969/j.issn.1000-4440.2025.08.018]
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茶树品种白毫早线粒体基因组结构特征、进化选择模式和密码子偏好性分析()

江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2025年08期
页码:
1616-1627
栏目:
园艺
出版日期:
2025-08-31

文章信息/Info

Title:
Analysis of mitochondrial genome structural characteristics, evolutionary selection patterns and codon bias of Camellia sinensis cv. Baihaozao
作者:
曾文娟; 刘珊珊; 张其湘; 陈致印; 杨岚琪; 邹坤
(湖南人文科技学院农业与生物技术学院/湖南省园艺生产与加工类创新创业教育中心/湖南省创新创业示范基地/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)
Author(s):
ZENG Wenjuan; LIU Shanshan; ZAHNG Qixiang; CHEN Zhiyin; YANG Lanqi; ZOU Kun
(College of Agriculture and Biotechnology， Hunan University of Humanities, Science and Technology/Innovation and Entrepreneurship Education Center for Horticultural Production and Processing in Hunan Province/ Hunan Provincial Innovation and Entrepreneurship Demonstration Base/Key Laboratory of Development, Utilization, Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan Province, Loudi 417000, China)
关键词:
茶树; 线粒体基因组; 结构特征; 密码子偏好性
Keywords:
Camellia sinensis; mitochondrial genome; structural characteristics; codon usage bias
分类号:
S571.1
DOI:
doi:10.3969/j.issn.1000-4440.2025.08.018
文献标志码:
A
摘要:
本研究首次系统解析了茶树品种白毫早(Camellia sinensis cv. Baihaozao)线粒体基因组的结构特征与进化规律。通过高通量测序得到总长为909 843 bp的11个线性片段(GC含量45.54%),注释到63个功能基因,包括36个蛋白质编码基因(PCG)、24个转运RNA编码基因、3个核糖体RNA编码基因和2个假基因(Pseudogene)。ATP合酶编码基因atp1、atp8、atp9，泛醌细胞色素c还原酶编码基因cob，细胞色素c氧化酶编码基因cox1、cox2、cox3，还原型烟酰胺腺嘌呤二核苷酸（NADH）脱氢酶编码基因nad3、nad4、nad4L、nad5、nad9，核糖体蛋白编码基因rpl2、rpl5、rpl16、rps3、rps12、rps13、rps19的Ka/Ks值均低于1.00,表明这些涉及能量代谢核心功能的基因因强烈的纯化选择而呈现高度保守性。而ccmB(细胞色素c还原酶编码基因)、mttB(膜转运蛋白编码基因)和sdh4(琥珀酸脱氢酶编码基因)的Ka/Ks值分别为1.16±0.16、1.78±0.42和1.24±0.31,均高于1.00,表明这些基因可能受到正选择的驱动或者处于松弛选择的压力下。在线粒体基因组密码子使用偏性形成过程中,自然选择的作用(87%)显著高于突变压力的作用(13%)。基于同义密码子相对使用度（RSCU）＞1.00和△RSCU≥0.08的标准,共筛选到18个密码子,其中88.89%密码子以U/A结尾。茶树品种白毫早与槠叶齐(C. sinensis cv. Zhuyeqi)形成高支持率的单系分支(bootstrap支持率＞90%),并且白毫早与多个茶树栽培变种(C. sinensis var. sinensis、C. sinensis var. pubilimba、C. sinensis var. assamica等)聚为一支,与博白大果油茶(Camellia gigantocarpa)、油茶(Camellia oleifera)、浙江红山茶(Camellia chekiangoleosa)等野生近缘种形成姐妹群,表明山茶属(Camellia)栽培变种与野生近缘种间存在线粒体基因组的显著分化。本研究系统分析了茶树线粒体基因组的进化特征,为茶树种质资源鉴定和遗传改良提供了分子依据。
Abstract:
This study is the first to systematically analyze the structural characteristics and evolutionary laws of the mitochondrial genome of the tea plant cultivar Camellia sinensis cv. Baihaozao. Through high-throughput sequencing, 11 linear fragments with a total length of 909 843 bp (with a GC content of 45.54%) were obtained, and 63 functional genes were annotated, including 36 protein-coding genes (PCGs), 24 transfer RNA-coding genes, three ribosomal RNA-coding genes, and two pseudogenes. The Ka/Ks values of ATP synthase-encoding genes (atp1, atp8, atp9), ubiquinol-cytochrome c reductase-encoding gene (cob), cytochrome c oxidase-encoding genes (cox1, cox2, cox3), nicotinamide adenine dinucleotide (NADH) dehydrogenase-encoding genes (nad3, nad4, nad4L, nad5, nad9), and ribosomal protein-encoding genes (rpl2, rpl5, rpl16, rps3, rps12, rps13, rps19) were all below 1.00, indicating that the genes involved in core energy metabolism functions were highly conserved due to strong purifying selection. In contrast, the Ka/Ks values of ccmB (cytochrome c reductase-encoding gene), mttB (membrane transport protein-encoding gene), and sdh4 (succinate dehydrogenase-encoding gene) were 1.16±0.16, 1.78±0.42, and 1.24±0.31, respectively, all were above 1.00, suggesting that these genes might be driven by positive selection or under relaxed selection pressure. In the process of forming codon usage bias in the mitochondrial genome, the effect of natural selection (87%) was significantly higher than that of mutation pressure (13%). Based on the criteria of relative synonymous codon usage (RSCU)＞1.00 and △RSCU≥0.08, a total of 18 codons were screened, among which 88.89% ended with U/A. The tea plant cultivar Baihaozao and C. sinensis cv. Zhuyeqi formed a monophyletic clade with high support (bootstrap support＞90%), and Baihaozao clustered with multiple cultivated varieties of C. sinensis (such as C. sinensis var. sinensis, C. sinensis var. pubilimba, C. sinensis var. assamica, etc.), forming a sister group with wild relatives such as Camellia gigantocarpa, Camellia oleifera, and Camellia chekiangoleosa. This indicated significant differentiation in mitochondrial genomes between cultivated varieties and wild relatives within the genus Camellia. This study systematically analyzed the evolutionary characteristics of the tea plant mitochondrial genome, providing a molecular basis for germplasm resource identification and genetic improvement.

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备注/Memo

备注/Memo:
收稿日期：2025-05-20基金项目：湖南省自然科学基金项目(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)；湖南人文科技学院研究生科研创新项目（ZSCX2025Y46）作者简介：曾文娟(2004-),女,湖南邵阳人,本科,主要从事茶学研究，(E-mail)2103562420@qq.com。刘珊珊为共同第一作者。通讯作者：陈致印，(E-mail)772612626@qq.com；邹坤,(E-mail)394644373@qq.com
更新日期/Last Update: 2025-09-23