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Journal of Tea Science ›› 2025, Vol. 45 ›› Issue (2): 201-218.

• Research Paper • Previous Articles     Next Articles

Analysis of Codon Usage Bias in Chloroplast and Mitochondrial Genomes of Camellia sinensis cv.‘Zhuyeqi’

ZENG Wenjuan1,2,3,4, ZHU Youpeng1,2,3,4, CHEN Jiaxin1,2,3,4, LI Hongyu5, WANG Shuanghui1,2,3,4, GONG Yihui1,2,3,4, CHEN Zhiyin1,2,3,4,*   

  1. 1. Key Laboratory of Characteristic Agricultural Resource Development and Quality Safety Control in Hunan Province, Hunan University of Humanities, Science and Technology, Loudi 417000, China;
    2. Innovation and Entrepreneurship Education Center for Horticultural Production and Processing in Hunan Province, Hunan University of Humanities, Science and Technology, Loudi 417000, China;
    3. Hunan University of Humanities, Science and Technology, Hunan Provincial Innovation and Entrepreneurship Demonstration Base, Loudi 417000, China;
    4. College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China;
    5. Xinhua County Taohuayuan Agricultural Development Co., Ltd., Loudi 417000, China
  • Received:2025-02-10 Revised:2025-03-06 Online:2025-04-15 Published:2025-04-30

Abstract: Codon usage bias serves as an important driving force for gene expression regulation and molecular evolution, and is of particular importance in the study of plant organellar genomes. Camellia sinensis cv. ‘Zhuyeqi’, an important tea cultivar in China, has not yet received a systematic report on the codon usage patterns of its organellar genomes. This study was systematic bioinformatic analysis of the 52 chloroplast-encoded genes and 29 mitochondrial-encoded genes of ‘Zhuyeqi’. The results reveal that: (1) both the chloroplast genome (ENC=44.64±3.25) and the mitochondrial genome (ENC=51.98±3.47) exhibit weak codon usage bias, with the chloroplast bias primarily driven by natural selection (GC3s and ENC correlation R2=0.482). While the mitochondrial bias is jointly influenced by natural selection and mutational pressure (R2=0.312). (2) Relative synonymous codon usage (RSCU) analysis demonstrates that both organellar genomes significantly prefer synonymous codons ending in A/U, and the highly expressed chloroplast genes (rpoC2, psbA) exhibit stronger codon preferences. (3) a multi-parameter screening approach identified 20 optimal chloroplast codons (GCA, GCU) and 23 optimal mitochondrial codons (GCC, AGG). This study provided elucidation of the codon usage characteristics and evolutionary driving forces in the organellar genomes of Camellia sinensis cv. ‘Zhuyeqi’, offering crucial theoretical guidance for the optimization of the tea molecular breeding system and the efficient expression of exogenous genes.

Key words: Camellia sinensis cv. ‘Zhuyeqi’, chloroplast genome, mitochondrial genome, codon usage bias, optimal codons

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