Analysis of Codon Usage Patterns in 41 Aconitum species

Abstract

Abstract Background The Ranunculaceae family comprises an essential group of genus known as Aconitum. Globally, 350 Aconitum species are found, and about 170 species are found in China. Aconitum species have several pharmacological effects and are also frequently used to treat joint pain, cold abdominal pain, and other diseases. Codon usage bias (CUB) analysis is an effective method for studying evolutionary relationships and phylogenetics. On the basis of protein-coding sequences (PCGs), 41 Aconitum species were selected for performing CUB analysis. Results The results revealed that the presence of GC content was less than 50% at different positions in Aconitum species. The distribution of GC content was also irregular and showed a trend of GC1 > GC2 > GC3, indicating that Aconitum species were biased towards A/T bases. Relative synonymous codon usage (RSCU) heat map analysis found the presence of conservative codons with silght differences in the genus. The effective number of codons (ENC)-Plot and the parity rule 2 (PR2)-bias plot analysis found natural selection as the main factor affecting the variation in codon usage. Consequently, various optimal codons were screened out, and A/T bases were preferred as the last codon. In addition, the results of Maximum Likelihood (ML) based on PCGs among 41 Aconitum species were consistent with the results of complete chloroplast (cp) genome data, inferring that the mutation analysis of PCGs is an efficient method to show phylogeny between species at the genus level. Conclusions The CUB analysis in 41 Aconitum species was majorly impacted by natural selection. The present study highlights the CUB patterns of Aconitum species in order to establish sources for future research on the genetic modifications and phylogeny.