Analysis of Codon Preference in Chloroplast Genome of Extremely Small Population Plant Gleditsia japonica var. velutina

doi:10.13438/j.cnki.jdzk.2025.06.007

Abstract

Abstract: In this study,Codon W,CUSP and R software were used to analyze the codon preference of Gleditsia japonica var. velutina chloroplast genome.Codon characteristic analysis revealed that the codons of chloroplast genes in Gleditsia japonica preferred to end with A or U,and the codon preference was relatively weak,with the effective codon number (ENC) ranging from 35.83 to 52.01.The correlation analysis among the parameters of the codon shows that the base composition of the first two positions of the codon is similar,but there is a significant difference from that of the third position.Analysis of relative synonymous codon usage revealed that the synonymous codons of chloroplast genes in Gleditsia japonica preferred to end with A or U.PR2-Plot analysis shows that the third base of the synonymous codon prefers to end with U or G (especially U).Optimal codon analysis shows that there are a total of 20 optimal codons,namely GCU,AGA,CGA,AAU,UGU,CAA,GAA,GGU,CAU,AUA,AUU,UUA,AAA,UUU,CCU,AGU,ACU,UAU,GUA and GUU.Neutral evolutionary analysis revealed that natural selection and mutational stress jointly shaped the codon preference of chloroplast genes in Gleditsia japonica.The analysis of ENC-Plot and ENC ratio showed that the influence of natural selection on codon preference was greater than that of mutational pressure.This indicates that natural selection is the main driving force for the formation of codon of chloroplast genes in Gleditsia japonica.

Key words: :extremely small population, Gleditsia japonica var. velutina, chloroplast genome, codon preference

YU Xiao, SUN Tian, GAO Chen. Analysis of Codon Preference in Chloroplast Genome of Extremely Small Population Plant Gleditsia japonica var. velutina[J]. Journal of Jishou University(Natural Sciences Edition), 2025, 46(6): 47-56.

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