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

• DOI: 10.1186/s12870-025-06351-x
• Publication Date: 2025-03-13T03:03:38Z
• Authors: XinJuan Li; LiE Liu; QianDan Ren; Tian Zhang; Na Hu; Jing Sun; Wu Zhou
• Keywords: Caragana

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