茶叶科学2026，Vol.46Issue(2)：221-237,17.
'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'
摘要
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.关键词
茶树/'槠叶齐'/线粒体基因组/密码子偏好性/系统发育Key words
tea plant/C.sinensis cv.'Zhuyeqi'/mitochondrial genome/codon usage bias/phylogeny分类
农业科技引用本文复制引用
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):221-237,17.基金项目
湖南省自然科学基金(2023JJ50465) （2023JJ50465）
湖南省科技创新计划项目(2024RC8289) （2024RC8289）
国家级大学生创业训练项目(202510553020X) （202510553020X）
湖南省大学生创新训练项目(S202510553039) （S202510553039）
