Codon Usage Bias of Chloroplast Genome in Actinidia chinensis‘Hongyang’

To comprehend the preference of codons in the chloroplast genome of Actinidia chinensis‘Hongyang’, 51 coding Sequences(CDS) of A. chinensis ‘Hongyang’ were analyzed to obtain to the results of Neutrality plot, ENC−plot and PR2−plot using Codon W and online software CUSP. The results showed that the GC content varied at different positions of the codons in the chloroplast genome of A. chinensis‘Hongyang’: Namely: GC₁ > GC₂ > GC₃, indicating that the third base of codons preferred to end with A/U. The ENC value ranges from 35.70 to 56.79, indicating that codon usage bias in the chloroplast genome of A. chinensis ‘Hongyang’was generally weak. Neutrality plot, ENC plot and PR2 plot indicate that natural selection was the major factors on codon usage patterns in the chloroplast genome of A. chinensis‘Hongyang’. In addition, 17 codons were selected as the optimal codons and all of them ends with A/U.