Analysis of codon usage in the chloroplast genome of Broomcorn millet (Panicum miliaceum L.)

Codon usage bias (CUB) is an important evolutionary feature in a genome,which provides important information for studying organism evolution,gene function,and exogenous gene expression.The CUB and its influencing factors in the chloroplast genome of Broomcorn millet (Panicum miliaceum L.) were preliminarily analyzed in this study based on 53 length-filtered CDS sequences.Results showed that the effective number of codons (ENC) ranged from 37.14 to 61,indicating that codon bias was weak.Relative synonymous codon usage (RSCU) analysis found 32 codons with a RSCU value of more than 1,of which 28 ended with A or T,suggesting that the third codon preferred A or U.Neutrality analysis showed no significant correlation between GC₁₂ and GC₃,and the regressive slope was 0.2129,suggesting natural selection mainly contributed to the CUB.ENC-plot (ENC vs GC_3S) analysis showed that most genes followed the parabolic line of trajectory,but several genes with low ENC values below the expected curve were also observed.Furthermore,correspondence analysis of RSCU demonstrated that the first axis could explained 17.92% of variation,which was the major factor influencing codon bias.The first axis showed a significant correlation between ENC and GC_3S,whereas no significant correlation was found for CBI and GC.Finally,nine codons were identified as optimal codons.We concluded that both natural selection and mutation have impacted the formation of CUB in the Broomcorn millet chloroplast genome.