Analysis of chloroplast genome codon preference in <i>Camellia meiocarpa</i> and <i>Camellia vietnamensis</i>

Zhang Feifei; Zhu Yan; Han Changzhi

doi:10.12171/j.1000-1522.20240200

Journal of Beijing Forestry University > 2025 > Corrected proof > DOI: 10.12171/j.1000-1522.20240200

Zhang Feifei, Zhu Yan, Han Changzhi. Analysis of chloroplast genome codon preference in Camellia meiocarpa and Camellia vietnamensis[J]. Journal of Beijing Forestry University. DOI: 10.12171/j.1000-1522.20240200

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Analysis of chloroplast genome codon preference in Camellia meiocarpa and Camellia vietnamensis

Zhang Feifei^1,,
Zhu Yan¹,
Han Changzhi^{1, 2, ,}

1.
College of Forestry, Southwest Forestry, Kunming 650224, Yunnan, China
2.
Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Kunming 650224, Yunnan, China

More Information

Received Date: June 18, 2024
Revised Date: September 08, 2024
Accepted Date: March 18, 2025
Available Online: March 27, 2025

Graphical Abstract

Abstract

Abstract

Objective
This paper investigates the codon usage patterns in chloroplast genomes of Camellia oleifera and C. vietnamensis, analyzes and elucidates the underlying causes of codon usage bias, identifies optimal codons in their chloroplast genomes, so as to provide theoretical foundations and data support for genomic research and breeding of oil tea species.
Method
Screened CDS sequences (52 sequences each from C. oleifera and C. vietnamensis) were analyzed using Codon W 1.4.2, CUSP, MEGA, and other online tools. Parameters including relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), and GC content were calculated. Correlation analysis, neutrality plot analysis, ENC-plot analysis, and PR2-plot bias analysis were performed. High-frequency and highly expressed optimal codons were predicted based on RSCU and ΔRSCU values.
Result
(1) C. oleifera exhibited GC content, ENC, and CAI values of 37.49%, 48.561, and 0.158, respectively, while C. vietnamensis showed values of 37.50%, 48.529, and 0.160. Both species displayed uneven GC distribution across codon positions, with GC₁ > GC₂ > GC₃(C. oleifera: GC₁ = 45.81%, GC₂ = 38.00%, GC₃ = 28.64%; C. vietnamensis: GC₁ = 45.88%, GC₂ = 38.02%, GC₃ = 28.59%), indicating a preference for GC at the first codon position. (2) C. oleifera and C. vietnamensis had 23 and 11 optimal codons, respectively, with 22 and 11 of these codons ending in A/U, suggesting a strong preference for A/U at the third codon position.(3) ENC values for both species ranged from 35.64 to 61.00, with minimal differences in mean values, reflecting similarities in codon usage patterns. (4) Neutrality plot, ENC-plot, and PR2-plot analyses revealed that natural selection predominantly influenced codon usage bias in the chloroplast genomes of both species.
Conclusion
The chloroplast genomes of C. oleifera and C. vietnamensis exhibit weak codon usage bias, primarily shaped by natural selection. C. oleifera has 23 optimal codons, while C. vietnamensis has 11 optimal codons. These findings provide critical theoretical and empirical insights for advancing oil tea genomic studies and breeding programs.
- Camellia meiocarpa,
- Camellia vietnamensis,
- chloroplast genome,
- codon preference,
- optimal codon

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References (43)

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Analysis of chloroplast genome codon preference in Camellia meiocarpa and Camellia vietnamensis