Chloroplast genome codon preference in Camellia meiocarpa and Camellia vietnamensis

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 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.