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

ZENG Wenjuan; ZHU Youpeng; CHEN Jiaxin; LI Hongyu; WANG Shuanghui; GONG Yihui; CHEN Zhiyin

doi:10.13305/j.cnki.jts.2025.02.008

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Journal of Tea Science ›› 2025, Vol. 45 ›› Issue (2) : 201-218. DOI: 10.13305/j.cnki.jts.2025.02.008

Research Paper

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

ZENG Wenjuan^1,2,3,4, ZHU Youpeng^1,2,3,4, CHEN Jiaxin^1,2,3,4, LI Hongyu⁵, WANG Shuanghui^1,2,3,4, GONG Yihui^1,2,3,4, CHEN Zhiyin^1,2,3,4,*

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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 / codon usage bias / mitochondrial genome / optimal codons

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ZENG Wenjuan, ZHU Youpeng, CHEN Jiaxin, LI Hongyu, WANG Shuanghui, GONG Yihui, CHEN Zhiyin. Analysis of Codon Usage Bias in Chloroplast and Mitochondrial Genomes of Camellia sinensis cv.‘Zhuyeqi’[J]. Journal of Tea Science. 2025, 45(2): 201-218 https://doi.org/10.13305/j.cnki.jts.2025.02.008

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