Analysis of Mitochondrial Genome Characteristics and Codon Usage Bias in Camellia sinensis cv. &#x02018;Zhuyeqi&#x02019;

CHEN Zhiyin; YANG Pan; JIANG Rui; ZHONG Qianyi; JING Yuanrong; ZHU Zanjiang; ZENG Wenjuan; WEN Cong

doi:10.13305/j.cnki.jts.2026.02.005

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Journal of Tea Science ›› 2026, Vol. 46 ›› Issue (2) : 221-237. DOI: 10.13305/j.cnki.jts.2026.02.005

Research Paper

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,*

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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

C. sinensis cv. ‘Zhuyeqi’ / codon usage bias / mitochondrial genome / phylogeny / tea plant

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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 https://doi.org/10.13305/j.cnki.jts.2026.02.005

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