Analysis on Codon Usage Bias of Chloroplast Genome in the Ethnic medicine of Roscoea

In order to explore the preference and influencing factors of codon usage in the chloroplast genome of plants in the genus Roscoea, this study collected chloroplast genomes of three species of Roscoea, and calculated codon composition parameters using Codon W and CUSP software. Based on this data, ENC-plot, RP2-plot, neutral plot and other analyses were conducted. The results showed that the codon usage patterns in the chloroplast genomes of the three species of plants in Roscoea were mostly the same, with a preference ending in A/U. The ENC values of protein coding genes in all three species of plants were greater than 35. This indicates that the codon preference in the Roscoea is weak. The results of neutral plot, ENC-Plot and PR2-Plot analysis all show that natural selection is the main factor affecting the codon preference of Roscoea.The optimal codons for Roscoea tibetica、Roscoea humeana、Roscoea alpina were screened out at 9, 11 and 12, with a total of 6 codons, namely CUU, UCA, ACA, GCA, UAA and AGA, indicating that Roscoea is a plant belonging to the genus. The chloroplast genome is mainly affected by the combination of mutation pressure and positive selection.