Codon usage pattern and genetic diversity in chloroplast genomes of Zanthoxylum species (Sapindales: Rutaceae)

Codon usage bias (CUB) reflects the unique characteristics of different species and can be used to analyze their evolutionary relationship, enhance the expression efficiency of target genes in heterologous systems, and further offer theoretical insights for research in molecular biology and genetic breeding. The primary objective of this study is to examine the chloroplast gene CUB in 20 Zanthoxylum species, alongside 12 species from other genera within the Rutaceae family, to offer insights for future studies on their chloroplast genomes. In Zanthoxylum plants, the chloroplast gene codons show a preference for terminating with an A/T instead of a G/C base. In the representative chloroplast genome of Zanthoxylum bungeanum, it was discovered that TTT codons are predominantly used for amino acid Phe, while TAT codons are more commonly utilized for amino acid Tyr. Moreover, natural selection strongly influenced the CUB of the chloroplast genomes in Zanthoxylum plants. Based on RSCU values, the optimal codons for these species were identified, with their similarities being highlighted. The phylogenetic tree of Zanthoxylum species was constructed and contrasted with the results of clustering analysis both based on coding sequences, supporting that Zanthoxylum and Toddalia should be considered to be merged. The Subgen. Zanthoxylum represents a substantial branch that has diverged from the Subgen. Fagara and there are significant differences in CUB between these two subgenera. Furthermore, derived from hierarchical clustering analysis utilizing RSCU values, Nicotiana sylvestris was proposed as the compatible heterologous expression receptor for the chloroplast genes of the Zanthoxylum species.