Analysis and comparison of chloroplast genome codon usage patterns in five accessions of Toxicodendron vernicifluum

The chloroplast (cp.) is the photosynthetic organelle of plants and algae, responsible for acquiring essential energy. It possesses relatively independent genetic material, a highly conserved structure, a small genome size, and low mutation and recombination rates. Consequently, the chloroplast genome plays a crucial role in elucidating the origin, evolution, and phylogenetic relationships of species. Toxicodendron vernicifluum, belonging to the family Anacardiaceae, is an important special economic forest distributed in Yunnan, Sichuan and Guizhou provinces of China. Codon preference is a universal phenomenon in the genomes of prokaryotes and eukaryotes. The formation of codon preference is mainly influenced by the natural selection and mutation pressure. Studying the codon preference of plant chloroplast genome is helpful to determine the optimal codon design and vector design in chloroplast genetic engineering.

Analysis of the codon utilization patterns in the chloroplast genomes of five T. vernicifluum accessions revealed a high degree of similarity among them. All five accessions exhibited similar base compositions, with high A/T content and low G/C content and a preference for A/T-ending codons. 6 optimal codons were identified in each chloroplast genome of the five T. vernicifluum accessions, and all end with A/T. According to the ENc-plot, PR2-plot and neutrality-plot, the formation of codon preference T. vernicifluum was affected by multiple factors, and natural selection was the dominant factor. Arabidopsis thaliana, Populus trichocarpa and Saccharomyces cerevisiae have potential value as the heterologous expression host for five accessions of T. vernicifluum genes.

This study highlights the remarkable similarity in codon usage patterns among the five accessions of T. vernicifluum chloroplast genomes, driven by natural selection. Understanding the gene expression characteristics of T. vernicifluum and elucidating the laws governing its genetic evolution are facilitated by investigating the codon preferences in these accessions. Our results provide an important theoretical basis for evolutionary analysis and transgenic research of chloroplast genes.