‘白毫早’叶绿体与线粒体基因组密码子偏好性分析

doi:10.13305/j.cnki.jts.2025.04.005

Abstract

Abstract: Codon usage bias serves as a critical driving mechanism in gene expression regulation and molecular evolution, holding significant biological importance in the evolution of organelle genomes in plants. This study focused on the economically important tea cultivar ‘Baihaozao’ (Camellia sinensis cv. ‘Baihaozao’) and systematically analyzed the codon usage patterns and evolutionary drivers of its chloroplast (52 genes) and mitochondrial (29 genes) genomes for the first time. The results indicate: (1) the average effective codon number (ENC=44.57±4.59) of the chloroplast genome is significantly lower than that of the mitochondrial genome (ENC=51.87±5.31), with both exhibiting weak preference characteristics. Neutrality analysis reveals that the chloroplast's preference is primarily driven by natural selection (correlation between GC_3s and ENC, R² =-0.016), whereas the mitochondrial genome is regulated by a combination of natural selection and mutational pressure (R² = -0.11), which is consistent with the evolutionary constraints observed in the organelle genomes of dicotyledons. (2) RSCU analysis shows that both types of organelle genomes significantly prefer synonymous codons ending in A/U, with high-expression chloroplast genes (e.g., ndhA, rps14) exhibiting a stronger preference for A/U terminal codons. This suggests that translational selection optimizes highly expressed genes. (3) Through multivariate statistical screening, 18 optimal codons were identified for the chloroplast genome (e.g., GCA, GCU) and 18 optimal codons for the mitochondrial genome (e.g., GCA, AGA). GCA was favored in both organelle types, reflecting the adaptive convergence of functional genes across organelles. This study elucidated the heterogeneity of codon usage characteristics in the organelle genomes of ‘Baihaozao’ and their evolutionary drivers for the first time, providing a theoretical basis for the adaptive optimization of exogenous genes and the construction of cross-organelle expression regulatory networks in molecular tea breeding.

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

CLC Number:

S432.41
Q52

ZENG Wenjuan, LIU Shan, WEN Cong, ZHANG Qixiang, HUANG Jing, GONG Yihui, CHEN Zhiyin. Analysis of Codon Usage Bias in Chloroplast and Mitochondrial Genomes of Camellia sinensis cv. ‘Baihaozao’[J]. Journal of Tea Science, 2025, 45(4): 587-603.

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

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