Analysis of codon usage bias in Ziziphi Spinosae Semen based on transcriptome data

Abstract

The characteristics of codon usage and the influencing factors of the transcriptomic coding sequence in Ziziphi Spinosae Semen were investigated. The optimal codon was determined by analyzing 5,045 CDS samples using the Perl program and Codon W 1.4.2 software. The average content of GC, GC1, GC2 and GC3 of CDS ranged from 38.53–48.82%. The ENC-plot, bias, and neutral analyses showed that the codon preference is affected by mutation under selection. A total of 28 optimal codons were obtained, including UCC, UGC, UCG, etc. These were identified by the gene high expression screening codon methods, most of which end with C and G, and only CGU ends with U. Selection pressure has a great impact on the codon usage preference in Ziziphi Spinosae Semen CDS, and the mutation pressure also has some effects. The results of this study will provide a theoretical basis for the carrier selection for saponins and flavonoid synthesis and the evolution and contribution to the increased production of this medicinal plant species.