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

In this study, we successfully obtained the complete chloroplast genome sequence of Rhodiola dumulosa (Franch.) S. H. Fu using second-generation sequencing technology. We then analyzed the codon usage patterns and evolutionary driving factors of its 52 protein-coding sequences (CDS). The results showed that the average values of adequate codon numbers (ENC) values of the 52 CDS were 42.86, and the bias was middle level; Twenty-nine 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;Correlation analysis showed significant positive correlation between ENC,GC₃ and Nc, Nc,ENC and GC₃, GC₁,GCall and GC₂, 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.