Abstract
In this study, the codon usage patterns of the chloroplast genome of Rhododendron farrerae were analyzed to provide genetic information for the conservation and innovation of Rhododendron germplasm resources. Codon usage and preferences of 54 protein coding sequences (CDS) from R. farrerae were analyzed using software such as Codon, R package, and EMBOSS. The results showed that the average GC content of the 54 CDS in the chloroplast genome of R. farrerae was 38.10%, with GC1 (46.11%), GC2 (39.68%), and GC3 (28.51%) representing the GC contents at different positions, indicating that the third base of codons in the chloroplast genome of R. farrerae is predominantly composed of A and T. ENC-plot, PR2-plot, and neutral plotting analysis revealed that natural selection pressure was the most significant factor influencing the synonymous codon usage preference in the chloroplast genome of R. farrerae, leading to the identification of 16 optimal codons. This study provides genetic information for the chloroplast genome of R. farrerae and serves as a reference for genetic improvement and germplasm innovation.