Analysis of Codon Usage Bias in the Chloroplast Genome of Bletilla and its Related Species

To acquire a more comprehensive understanding of the genetic traits of of Bletilla plants, an analysis was conducted on the codon usage patterns and primary influencing factors of 4 species belonging to the genus. The neutrality plot, ENC-plot, and PR2-plot analysis of chloroplast genome codons in 4 Bletilla plants of B. striata, B. formosana, B. sinensis, B. ochracea were conducted based on CUSP, Codon W 1.4.2 and EMBOSS software. The study revealed that 4 optimal codons shared by these four species all exhibit the characteristic that the third base is A/U, and the effective number of codons(ENC) of all protein-coding genes exceeds the threshold of 35. This phenomenon reflects a relatively weak trend in codon preference in Bletilla plants. Furthermore, through parity preference(PR2-Plot) analysis, the study observed that the distribution of genes in 4 regions is not balanced; and effective codon number analysis(ENC-Plot) showed that most genes are located below the standard curve. Furthermore, in the neutral plot analysis, all genes were significantly shifted upward from the diagonal. This series of analyzes collectively shows that codon usage bias is affected by both mutation and natural selection, but natural selection plays a more critical role in this process and has a more significant impact on codon preference.