Analysis of Codon Usage Bias in Chloroplast Genome of Capsicum annuum cv'Xiangla NO.14'
HE Daoshan
YANG Xiaoqiang
QIN Yalin
HE Haiyan
XIE Wei
LUO Zhiguo
LI Peng
Abstract：In order to confirm the codon usage pattern of chloroplast genome of Capsicum annuum cv'Xiangla NO.14',the 52 protein coding genes of the chloroplast genome of'Xiangla N0.14'were selected as materials in this work,and base composition and codon usage bias of'Xiangla N0.14'were detected using Codon Wl.4.2.The main factors affecting codon preference were analyzed by neutral plot,PR2-plot and ENC-plot,and the optimal codon was further determined.The results indicated that the average ratio of GCall in the'Xiangla NO.14'chloroplast genome was 38.70％,with GC1(47.29％)＞GC2(39.74％)＞GC3(29.05％).The ENC value varied from 34.10 to 54.31,with an average of 46.69.There were 29 codons with RSCU＞1 and ended with A or U,which revealed that the third base of the codon preferred to end with A/U.ENC was significantly correlated with GC3,but not with GCall,GC1 and GC2.The graphical analysis showed that codon usage bias was affected by natural selection and mutation in the'Xiangla NO.14'chloroplast genome.A total of 19 optimal codons such as GCA,GCU,AGA were screened out,and ten codons ended with A,and nine codons ended with U.The third base of codon preferred to use A/U ending.The findings obtained in this work provided a theoretical basis for the development of chloroplast genetic engineering of Capsicum in Solanaceae.
Keywords：Capsicum annuum cv'Xiangla NO.14'chloroplast genomecodon usage biasoptimal codons
Publication Date：2025-01-19
Online Publishing Date：2026-08-28(First online date of this platform, not the publication date of the document)
Pages：9( 47-54,79 )