茶树&#x02018;大面白&#x02019;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

doi:10.13305/j.cnki.jts.2025.01.006

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茶叶科学 ›› 2025, Vol. 45 ›› Issue (1) : 61-78. DOI: 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^1,2, 张牧彤¹, 徐子林¹, 欧阳茜¹, 王美暄¹, 李文婷¹

作者信息 +

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

YIN Minghua^1,2, ZHANG Mutong¹, XU Zilin¹, OUYANG Qian¹, WANG Meixuan¹, LI Wenting¹

Author information +

文章历史 +

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。

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.

导出引用

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

YIN Minghua, ZHANG Mutong, XU Zilin, OUYANG Qian, WANG Meixuan, LI Wenting. Analysis of the Structural Characteristics and Codon Usage Biase of the Mitochondrial Genome in Tea Cultivar ‘Damianbai’[J]. Journal of Tea Science. 2025, 45(1): 61-78 https://doi.org/10.13305/j.cnki.jts.2025.01.006

中图分类号： S571.1 Q52

参考文献

[1] 彭丽媛, 曾鸿哲, 万丽玮, 等. EGCG对非肥胖型糖尿病大鼠肾损伤的改善作用及调节机制研究[J]. 茶叶科学, 2023, 43(6): 784-794.
Peng L Y, Zeng H Z, Wan L W, et al.The investigation of the ameliorate effect and mechanism of EGCG on non-obese GK rat with diabetic kidney damage[J]. Journal of Tea Science, 2023, 43(6): 784-794.
[2] 郭青, 谢明威, 蔡淑娴, 等. 安化黑茶的调节免疫作用[J]. 中国茶叶, 2023, 45(12): 1-13.
Guo Q, Xie M W, Cai S X, et al.The immunomodulatory effect of Anhua dark tea[J]. China Tea, 2023, 45(12): 1-13.
[3] 王鹏杰, 杨江帆, 张兴坦, 等. 茶树基因组与测序技术的研究进展[J]. 茶叶科学, 2021, 41(6): 743-752.
Wang P J, Yang J F, Zhang X T, et al.Research advance of tea plant genome and sequencing technologies[J]. Journal of Tea Science, 2021, 41(6): 743-752.
[4] 朱艳宇, 于文涛, 高水练, 等. 福建安溪茶树种质资源遗传多样性与铁观音衍生品种遗传关系[J]. 浙江农业学报, 2024, 36(7): 1591-1601.
Zhu Y Y, Yu W T, Gao S L, et al.The diversity of tea germplasm resources and genetic relationship of ‘Tieguanyin’-derived varieties in Anxi, Fujian, China[J]. Acta Agriculturae Zhejiangensis, 2024, 36(7): 1591-1601.
[5] 尹明华, 张嘉欣, 乐芸, 等. 茶树大面白叶绿体基因组特征、密码子偏好性及其系统发育分析[J]. 茶叶科学, 2024, 44(3): 411-430.
Yin M H, Zhang J X, Le Y, et al.Genomic characteristics, codon preference, and phylogenetic analysis of chloroplasts of Camellia sinensis cv. ‘Damianbai’[J]. Journal of Tea Science, 2024, 44(3): 411-430.
[6] 王士圻. 茶树良种—大面白的选育及其鉴定报告[J]. 茶业通报, 1981(5): 40-45.
Wang S Q.Breeding and identification report of tea tree variety: Damianbai[J]. Journal of Tea Business, 1981(5): 40-45
[7] 唐征, 昂海燕, 裴徐梨, 等. 青花菜线粒体基因组组装与序列特征分析[J]. 西北农业学报, 2024, 33(6): 1074-1082.
Tang Z, Ang H Y, Pei X L, et al.Mitochondrial genome assembly and sequence characterization in Broccoli[J]. Acta Agriculturae Boreali-occidentalis Sinica, 2024, 33(6): 1074-1082.
[8] 苏相年, 杨选文, 侯婷, 等. 油棕线粒体比较基因组学和系统发育关系分析[J]. 基因组学与应用生物学, 2024, 43(8): 1340-1352.
Su X N, Yang X W, Hou T, et al.Comparative genomic and phylogenetic analyses of mitochondrial genome in oil palm[J]. Genomics and Applied Biology, 2024, 43(8): 1340-1352.
[9] 王茹, 罗永坚, 邱道寿. 二倍体紫苏线粒体基因组特征及其系统发育分析[J]. 亚热带农业研究, 2024, 20(2): 83-92.
Wang R, Luo Y J, Qiu D S.Mitochondrial genomic characterization and phylogenetic analysis of Perilla citriodora (Lamiaceae)[J]. Subtropical Agriculture Research, 2024, 20(2): 83-92.
[10] 贾雪, 蔡回彩, 于澜, 等. 紫花苜蓿不育系与保持系线粒体全基因组比较分析[J]. 草地学报, 2024, 23(9): 2737-2748.
Jia X, Cai H C, Yu L, et al.Comparison of mitochondrial genome between sterile line and maintainer line of Medicago sativa L.[J]. Acta Agrestia Sinica, 2024, 23(9): 2737-2748.
[11] 陈欣雨, 朱守玟, 江转转. 李属植物线粒体基因组特征与系统发育分析[J]. 福建农林大学学报(自然科学版), 2024, 53(4): 491-500.
Chen X Y, Zhu S W, Jiang Z Z.Structural characterization and phylogenetic resolution analysis of mitochondrial genomes of Prunus plants[J]. Journal of Fujian Agriculture and Forestry University (Natural Science Edition), 2024, 53(4): 491-500.
[12] 李龙, 余波, 刘敏. 梵净山山茶属2种植物根系真菌群落结构[J]. 东北林业大学学报, 2024, 52(7): 96-102.
Li L, Yu B, Liu M.Community structure of root-associated fungi in two species of Camellia on Fanjing Mountain[J]. Journal of Northeast Forestry University, 2024, 52(7): 96-102.
[13] 单文书, 牛婷婷, 陈伟立, 等. 山茶属植物病毒病害的研究进展[J]. 中国植保导刊, 2024, 44(5): 22-29.
Shan W S, Niu T T, Chen W L, et al.Research progress on virus diseases of Camellia plants[J]. China Plant Protection, 2024, 44(5): 22-29.
[14] 颜超, 肖旭, 冉朝辉, 等. 山茶属瘤果茶组10种植物的花粉和叶表皮微形态研究[J]. 广西植物, 2024, 44(9): 1795-1806.
Yan C, Xiao X, Ran C H, et al.Pollen morphology and leaf epidermal micromorphology of 10 species of sect. Tuberculata (Camellia L.)[J]. Guihaia, 2024, 44(9): 1795-1806.
[15] 邝雪琨, 郑倩, 孔庆博, 等. 山茶属植物系统发育及分类研究进展[J]. 园艺学报, 2024, 51(1): 53-66.
Kuang X K, Zheng Q, Kong Q B, et al.Research progress on phylogeny and classification of Camellia[J]. Acta Horticulturae Sinica, 2024, 51(1): 53-66.
[16] 李丰钰, 黄平, 郑勇奇, 等. 基于SSR标记的山茶属位点组合品种鉴别能力分析评价[J]. 林业科学, 2023, 59(8): 74-84.
Li F Y, Huang P, Zheng Y Q, et al.Analysis and evaluation of variety discrimination power among genus Camelliawith loci combinations selected by using SSR markers[J]. Scientia Silvae Sinicae, 2023, 59(8): 74-84.
[17] 胡悦, 刘兵兵. 心叶毛蕊茶叶绿体基因组特征及系统发育分析[J]. 植物资源与环境学报, 2024, 33(3): 1-13.
Hu Y, Liu B B.Analyses on chloroplast genome characteristics and phylogeny of Camellia cordifolia[J]. Journal of Plant Resources and Environment, 2024, 33(3): 1-13.
[18] Li J, Tang H, Luo H, et al.Complete mitochondrial genome assembly and comparison of Camellia sinensis var. Assamica cv. Duntsa[J]. Frontiers in Plant Science, 2023, 14: 1117002. doi: 10.3389/fpls.2023.1117002.
[19] Zhang F, Li W, Gao C W, et al.Deciphering tea tree chloroplast and mitochondrial genomes of Camellia sinensis var. assamica [J]. Nature Publishing Group, 2019, 6: 209. doi: 10.1038/s41597-019-0201-8.
[20] Liu H X, Qin L, Chen Y L, et al.The complete mitochondrial genome of Camellia nitidissima (Theaceae)[J]. Mitochondrial DNA Part B, 2023, 8(5): 565-569.
[21] Doyle J J.A rapid DNA isolation procedure for small quantities of fresh leaf tissue[J]. Phytochemical Bulletin, 1987, 19(1): 11-15.
[22] Li H.Minimap2: pairwise alignment for nucleotide sequences[J]. Bioinformatics, 2018, 34(18): 3094-3100.
[23] Langmead B, Salzberg S L.Fast gapped-read alignment with bowtie 2[J]. Nature Methods, 2012, 9(4): 357-359.
[24] Wick R R, Judd L M, Gorrie C L, et al.Unicycler: resolving bacterial genome assemblies from short and long sequencing reads[J]. Plos Computational Biology, 2017, 13(6): e1005595. doi: 10.1371/journal.pcbi.1005595.
[25] Tillich M, Lehwark P, Pellizzer T, et al.GeSeq-versatile and accurate annotation of organelle genomes[J]. Nucleic Acids Research, 2017, 45(W1): W6-W11.
[26] Kearse M, Moir R, Wilson A, et al.Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data[J]. Bioinformatics, 2012, 28(12): 1647-1649.
[27] Lohse M, Drechsel O, Bock R.OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes[J]. Current Genetics, 2007, 52(5/6): 267-274.
[28] Thiel T, Michalek W, Varshney R, et al.Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)[J]. Theoretical & Applied Genetics, 2003, 106(3): 411-422.
[29] Stefan K, Choudhuri J V, Enno O, et al.REPuter: the manifold applications of repeat analysis on a genomic scale[J]. Nucleic Acids Research, 2001, 29(22): 4633-4642.
[30] Sharp P M, Li W H.Codon usage in regulatory genes in Escherichia coli does not reflect selection for ‘rare’ codons[J]. Nucleic Acids Research, 1986, 14(19): 7737-7749.
[31] Wright F.The ‘effective number of codons’ used in a gene[J]. Gene, 1990, 87(1): 23-29.
[32] Sueoka N.Directional mutation pressure and neutral molecular evolution[J]. PNAS, 1988, 85(8): 2653-2657.
[33] Sueoka N.Near homogeneity of PR2-bias fingerprints in the human genome and their implications in phylogenetic analyses[J]. Journal of Molecular Evolution, 2001, 53(4/5): 469-476.
[34] Harris R S.Improved pairwise Alignmnet of genomic DNA [D]. Pennsylvania: The Pennsylvania State University, 2007: 17-25.
[35] 张东, 李文祥, 高芳銮, 等. PhyloSuite在多基因系统发育分析中的应用[J]. Bio-protocol, 2021: e1010661. doi: 10.21769/BioProtoc.1010661.
Zhang D, Li W X, Gao F L, et al.Application of phylosuite to phylogenetic analysis using concatenated sequences[J]. Bio-protocol, 2021: e1010661. doi: 10.21769/BioProtoc. 1010661.
[36] Darling A C E, Mau B, Blattner F R, et al. Mauve: multiple alignment of conserved genomic sequence with rearrangements[J]. Genome Research, 2004, 14(7): 1394-1403.
[37] Gogarten J P, Townsend J P.Horizontal gene transfer, genome innovation and evolution[J]. Nature Reviews Microbiology, 2005, 3(9): 679-87.
[38] Helena T, Manuela K.Methods for assembling complex mitochondrial genomes in land plants[J]. Journal of Experimental Botany, 2024, 75(17): 5169-5174.
[39] Arimura S, Nakazato I.Genome editing of plant mitochondrial and chloroplast genomes[J]. Plant and Cell Physiology, 2024, 65(4): 477-483.
[40] 郭亮亮. 桑属植物叶绿体和线粒体基因组学和进化分析[D]. 镇江: 江苏科技大学, 2022.
Guo L L.Chloroplast and mitochondrial genomics and evolutionary analysis of mulberry plants [D]. Zhenjiang: Jiangsu University of Science and Technology, 2022.
[41] Wang H J, Wu Z G, Li T, et al.Highly active repeat-mediated recombination in the mitogenome of the aquatic grass Hygroryza aristata[J]. BMC Plant Biology, 2024, 24(1): 644. doi: 10.1186/s12870-024-05331-x.
[42] Zhang J W, Liu G M, Wei J H.Assembly and comparative analysis of the first complete mitochondrial genome of Setaria italica[J]. Planta, 2024, 260(1): 23. doi: 10.1007/s00425-024-04386-2.
[43] Zhang J, Huang H Z, Qu C Q, et al.Comprehensive analysis of chloroplast genome of Albizia julibrissin Durazz. (Leguminosae sp.)[J]. Planta, 2022, 255(1): 26. doi: 10.1007/s00425-021-03812-z.
[44] Duminil J, Besnard G.Utility of the mitochondrial genome in plant taxonomic studies[J]. Molecular Plant Taxonomy, 2021, 2222: 107-118.
[45] Sanchez-Puerta M V, Edera A, Gandini C L, et al. Genome-scale transfer of mitochondrial DNA from legume hosts to the holoparasite Lophophytum mirabile (Balanophoraceae)[J]. Molecular Phylogenetics Evolution, 2019, 132: 243-250.
[46] 田相军. 水稻线粒体基因组—序列多态性和基因组进化, 以及线粒体、叶绿体和细胞核基因组间的基因迁移[D]. 杭州: 浙江大学, 2006.
Tian X J.Rice mitochondrial genomes: sequence variations and genome evolutions, and gene transfers among mitochondrial, plastid and nuclear genomes[J]. Hangzhou: Zhejiang University, 2006.
[47] 陈柏宇, 李翔, 田燕, 等. 宁夏枸杞与茄科其他植物线粒体基因组的比较与系统进化分析[J]. 基因组学与应用生物学, 2024, 43(1): 45-62.
Chen B Y, Li X, Tian Y, et al.Comparison and phylogenetic analysis of mitochondrial genome among Lycium barbarum and other solanaceae plants[J]. Genomics and Applied Biology, 2024, 43(1): 45-62.