皂角基因密码子偏好性分析OA

Codon usage bias in organisms has a considerable impact on the heterologous expression of genes.To investigate the codon usage bias characteristics of Gleditsia sinensis genes,a systematic analysis of the codon usage patterns of 40,181 protein-coding genes was conducted using the Gleditsia sinensis genome as material,with the aid of the cubar package in RStudio software.The analysis pri-marily included the calculation of relative synonymous codon usage(RSCU),evaluation of codon us-age bias based on the ENC-GC3 relationship,and bias analysis of base usage frequency at each codon position through PR2-plot plotting.The results showed that Gleditsia sinensis preferentially used co-dons ending with A/U,totaling 26 codons,such as UUU,CUU,and UCA;only three codons end-ing with C/G were preferred,namely UUG,AAG,and GUG.The effective number of codons(ENC)ranged from 30 to 60,with relatively low ENC values indicating strong codon usage bias.PR2-plot bias analysis of base usage frequency showed that G＞C and U＞A.The codon usage bias of Gleditsia sinensis differed to varying degrees from that of other representative species.The GC12,GC3,and average GC contents of Eucommia ulmoides were lower than those of the representative species.Comparison of codon usage bias between Gleditsia sinensis and Nicotiana tabacum,Arabi-dopsis thaliana,Escherichia coli,and Saccharomyces cerevisiae showed that Gleditsia sinensis and Nicotiana tabacum were relatively close in codon usage bias,with all ratios falling within the range of 0.5-2.0,whereas slight differences were observed with Arabidopsis thaliana,Escherichia coli,and Saccharomyces cerevisiae,with 4,16,and 6 ratios falling outside the 0.5-2.0 range,respectively.