Analysis of Codon Usage Bias in the chloroplast genome of Helianthus annuus J-01

In order to determine the usage of the codon against Helianthus annuus chloroplast genome, this study used Codon W 1.4.2 and online software CUSP to perform neutral mapping, ENC-plot and PR2-plot analysis on the coding sequence codes of 51 genes in the H. annuus J-01 chloroplast genome. The results showed the GC content of H. annuus J-01 chloroplast genome codons was GC 1 (47.14%) > GC 2 (39.44%) > GC 3 (28.42%), indicating that the preference for synonymous codons in the chloroplast genome ends with A/U. The average ENC value is greater than 45, of which 37 are greater than 45. It shows that the H. annuus J-01 chloroplast genome has a weak bias. Through neutral plot analysis, ENC-plot analysis and PR2-plot analysis, it is found that the preference of H. annuus J-01 chloroplast genome codons is affected by selection as the main factor. The 12 optimal codons in the H. annuus J-01 chloroplast genome were finally determined: CUU, AUA, UAU, UAG, CAU, AAA, CCA, ACU, GCU, GAU, AGU, GGA.