Analysis of Codon Usage Bias in the Chloroplast Genome of Koelreuteria bipinnata

In order to elucidate the codon usage pattern of the chloroplast genome of Koelreuteria bipinnata, we select 52 protein coding sequences as the research object. The GC, RSCU and ENC parameters of codons were obtained, and the neutral plot, PR2−plot and optimal codon analysis were performed using the Codon W 1.4.2 software, and online CUSP program. The results showed that the GC content at different locations of the codon is GC₁(47.27%) > GC₂ (39.49%) > GC₃(29.84%). There were 29 codons with a relative synonymous codon usage RSCU > 1, in which 28 ending with A/U, indicating that the codon preference ends with A/U. The effective codon number(ENC) of the chloroplast gene ranged from 36 to 61, suggesting that the codon usage bias is weak. There is a significant correlation between ENC and GC₃, indicating that the base composition at the third codon position affects codon usage bias. Neutral analysis showed that there was no significant correlation between GC₃ and GC₁₂(r = 0.198, P > 0.05), and the regression coefficient was 0.2652, indicating that selection had an important effect on codon usage bias. ENC−plot analysis and PR2−plot analysis showed that codon bias is also influenced by other factors. In conclusion, the codon bias in chloroplast genomes of K. bipinnata was weak, and the selection was the main influencing factor, while it was also impacted by other factors. Combined with the high expression codon and high frequency codon, we determine 12 optimal codon, including CUU, GUU, AGU, GCA, CAA, CAU, AAA, GAU, CGU, CGA, GGU and GGA.