Codon Usage Bias and Evolutionary Drivers in the Chloroplast Genome of Rhodiola dumulosa

The study successfully obtained the complete chloroplast genome sequence of Rhodiola dumulosa using second-generation sequencing technology, analyzed the codon usage patterns and evolutionary driving factors of its 52 protein-coding sequences (CDS), thereby elucidating the main factors influencing codon usage bias in this species. The results showed that the overall GC content of the chloroplast genome is 38%. The average values of adequate codon numbers (ENC) values of the 52 CDS were 42.86, and the bias was middle level; 29 of the codons with RSCU > 1, 28 were all ending with A/U, indicating that it is more biased towards the use of codons ending with A/U; ENC exhibited a highly significant positive correlation with GC₃ and Nc; Nc displayed a significant positive correlation with ENC and GC₃; GC₁ was highly significantly positively correlated with GCall and GC₂; GC₃ showed a significant positive correlation with Nc; GCall was highly significantly positively correlated with GC₁, GC₂, and GC₃, indicates that it has some effect on codon usage bias; through neutral drawing ENC-plot, PR₂-plot, Equivalent bias analysis found that the codon preference of the chloroplast genome of R. dumulosa was influenced by both mutation and selection, and this influence may be related to the function of the corresponding genes; after filtering, 18 optimal codons and 17 of which end with A/U.