Analysis of codon preference in chloroplast genomes of four Zygophyllum species

[Objective] Codon usage bias of four Zygophyllum chloroplast genomes, and their main patterns and causes were analyzed for better understanding of the codon optimization, preference mechanism, and genetic evolution relationship of Zygophyllum . [Methods] The parity preference (PR2-plot) analysis, effective number of codons (NEC-plot), neutrality plot, and RSCU cluster analysis of 40 genes from four Zygophyllum species were carried out using CodonW, EMBOSS, and other softwares in this study. [Results] The codon usage patterns in the plastomes of four Zygophyllum species were similar, the GC content of codon was followed by GC1> GC2> GC3, the average ENC values were more than 35, and the CAI was 0.17, indicating that gene expression of the chloroplast genome of Zygophyllum species was low and codon preference was weak. The results of neutral mapping analysis, ENC-plot selection, and PR2- plot analysis showed that the codon usage pattern was predominantly affected by natural selection. RSCU cluster analysis showed that Z. fabago, Z. obliquum , Z. xanthoxylum , and Z. kaschgaricum had 19, 13, 14, and 14 optimal codons, respectively. By constructing the high and low gene expression library of the target genes, four optimal genes were selected that were ending with A/U. [Conclusion] Codon bases of the chloroplast genome from four Zygophyllum species are mostly ended with A/U. The preference is weak and the main influencing factor is natural selection. Four optimal codons, including CGA, GAA, UAU and UUA, are identified in this study.