Analysis of synonymous codon usage bias in the chloroplast genome of five Caragana

The genus Caragana, known for its adaptability and high forage value, is commonly planted to rehabilitate barren land and prevent desertification. Several Caragana species are also used for medicinal purposes. Analysis of synonymous codon usage bias and their primary influencing factors in chloroplast genomes aims to provide insights into molecular research and germplasm innovation for Caragana plants. The GC content of the five Caragana species ranged from 36.00% to 37.10%, showing a preference for codons ending in A/U, although the codon bias was weak. The screening identified nine to twelve optimal codons, but their frequency of use was low. Correlation analysis, neutrality plots, ENC plots and PR2 plots of the parameters identified two potential groups among the five species: Caragana arborescens and Caragana jubata, and Caragana turkestanica, Caragana opulens and Caragana tibetica. These groups showed a high level of intragroup similarity in the parameter analyses. In the RSCU cluster tree analysis, Caragana turkestanica and Caragana arborescens grouped together, while Caragana tibetica, Caragana jubata and Caragana opulens formed a separate clade in the CDS sequence and complete sequence phylogenetic tree analysis. The codon usage bias in the chloroplast genomes of the five Caragana species showed high similarity, suggesting that natural selection has a greater influence on codon bias than mutation. Furthermore, the identified optimal codons provide valuable insights for germplasm improvement of Caragana plants.