Open Access

ARTICLE

Codon Usage Bias in the Chloroplast Genome of the Traditional Chinese Medicinal Plant Corydalis yanhusuo

Bo Li^*, Yuying Liang, Muqing He, Xiuhe Fan, Honghong Jiao

Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi University of Chinese Medicine, Xianyang, China

* Corresponding Author: Bo Li. Email:

Phyton-International Journal of Experimental Botany 2026, 95(3), 9 https://doi.org/10.32604/phyton.2026.076367

Received 19 November 2025; Accepted 04 February 2026; Issue published 31 March 2026

Abstract

This study aims to clarify the codon usage bias and influencing factors of protein-coding genes in the chloroplast genome of the medicinal plant Corydalis yanhusuo. The chloroplast genome sequence of C. yanhusuo was obtained by resequencing, approximately 50 protein-coding genes were screened, and the nucleotide composition and codon usage patterns were calculated and analyzed using CodonW 1.4.2 and EMBOSS software. The results showed that the total guanine and cytosine (GC) content of codons in the chloroplast genome of C. yanhusuo was 40.06%, and the GC contents at the third, second, and first codon positions (GC₃, GC₂, and GC₁) were 32.12%, 40.21%, and 47.84%, respectively, indicating that codons in the chloroplast genome of C. yanhusuo preferentially used adenine (A) or uracil (U). The effective number of codons (ENC) ranged from 42.87 to 61.00, with an average value of 50.54, indicating weak codon usage bias. A significant positive correlation existed between the GC content at the third codon position (GC₃) and ENC, showing that codon bias was mainly affected by the third base. Neutral plot, ENC-plot, and PR2-plot analyses showed that the codon bias of the chloroplast genome of C. yanhusuo was mainly influenced by natural selection. Sixteen optimal codons—UUA, AUU, GUU, GUA, UCU, AGU, CCU, ACU, GCU, CAA, AAA, GAU, UGU, CGU, CGA, and GGU—were finally determined based on the relative synonymous codon usage analysis of high-frequency and highly expressed codons, all of which preferentially ended with A/U. Overall, this study reveals the codon usage bias of the chloroplast genome of C. yanhusuo and its influencing factors, and provides a theoretical basis for chloroplast genetic engineering and phylogenetic research.

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Keywords

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