Comparative Chloroplast Genomes and Phylogenetic Analyses of Zanthoxylum L. Provide Insights into Species Delimitation and Phylogenetic Relationships

Abstract

Abstract Background: Zanthoxylum L. (Rutaceae), including a large number of economically, ecologically and medicinally important species, is widely distributed all over the world. However, there are few studies about its chloroplast genome information to date. Results: Our results showed that the chloroplast genomes have a typical quadripartite structure with one large single copy, one small single copy, and two inverted repeat regions. The size of the genomes ranged from 157,231 bp to 158,728 bp in length, and 132 genes were identified in four species, which including 87 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNAs, while contained 133 genes (88 protein-coding genes) in Z. piasezkii chloroplast genome. The IR-SC boundary regions exhibited great variation among these five chloroplast genomes. Conclusions: Our findings suggest that the rpl22 gene was truncated in Z. piasezkii, which was was different from other Zanthoxylum species and could be used as a marker for accurate identify Z. piasezkii. Our plastid tree indicates the possibility that the earlier intrageneric classifications, especially subgenus, need to be further refined. These findings will provide insights into the genetic diversity, evolutionary history, and species identification of Zanthoxylum.