Analysis of Codon Usage Bias in the Chloroplast Genome of Cymbopogon Citratus
MU Zhencai
WU Jiaqi
LI Junpeng
XIAO Qiang
Abstract：To analyze the codon usage bias of the chloroplast genome of Cymbopogon citratus(DC.)Stapf and its evolutionary driving factors,the codon patterns were systematically analyzed,providing a basis for subsequent research on the functions of the genome and the development of germplasm resources.The complete sequence of the chloroplast genome of Cymbopogon citratus was obtained from the national center for biotechnology information(NCBI)database,and 50 protein-coding sequences(CDS)were screened.Combined with methods such as effective number of codons plot(ENC-plot),parity rule 2 plot(PR2-plot),and neutrality plot,the codon usage bias and influencing factors were explored.The overall guanine and cytosine(GC)content of the chloroplast genome of Cymbopogon citratus was 38.70%,and the average GC content at the third base position(GC3)was 29.60%,both of which were lower than those of other species in the same family.The average value of the codon adaptation index(CAI)was 0.17,and the average value of the effective number of codons(ENC)was 48.62,indicating that the codon usage bias was weak.The 30 frequently used codons were screened out,among which 26 were highly expressed codons.Furthermore,12 optimal codons with both high frequency and high expression density were determined,such as leucine and alanine.This study indicated that natural selection was the main driving force for the formation of the codon usage bias of the chloroplast genome of Cymbopogon citratus.
Keywords：Cymbopogon citratuschloroplast genomecodon usage biasprotein-coding sequencecodon adaptation indexeffective number of codonsnatural selection
Publication Date：2025-09-20
Online Publishing Date：2025-09-24(First online date of this platform, not the publication date of the document)
Pages：7( 327-333 )