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Zanthoxylum stenophyllum Hemsl., a type species for the genus Zanthoxylum (Rutaceae), is a traditional medicinal plant. We studied the complete chloroplast genome of this species using BGISEQ-500 platform. The chloroplast genome was 158,314 bp in size with a GC content of 38.45%. The genome contained two short inverted repeat (IRa and IRb) regions of 27,052 bp, a large single-copy region (LSC, 86,029 bp) and a small single-copy region (SSC, 18,181 bp). The annotated complete chloroplast genome contains 133 distinct genes, including 88 protein-coding genes, 37 transfer RNAs (tRNAs), and 8 ribosomal RNAs (rRNAs). Phylogenetic analysis indicated that Z. stenophyllum is clustered with Z. schiniflium and Z. pinnatum in the same branch with 100% bootstrap support. This complete chloroplast genome provides valuable genomic information for the molecular phylogeny and sustainable utilization of Zanthoxylum.

Zanthoxylum undulatifolium is an excellent economic tree species with important medical value. This study reports the first complete chloroplast genome sequence of Z. undulatifolium. Its whole chloroplast genome is 158,400 bp in length, including a large single-copy (LSC) region of 85,898 bp, a small single-copy (SSC) region of 17,610 bp, and two inverted repeat (IR) regions of 27,446 bp. The chloroplast genome contains a total of 132 genes, comprising 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the chloroplast genome is 38.46%, with the corresponding values in the LSC, SSC, and IR regions are 36.87%, 33.51%, and 42.55%, respectively. Phylogenetic analysis revealed the sister relationship between Z. undulatifolium and Z. bungeanum.

Zanthoxylum bungeanum var. pubescensis is a variety species of Z. bungeanum Maxim. that is characterized with small leaf plants and possess high resistant to cold stress among the genus Zanthoxylum. In the current study, the complete chloroplast genome sequences of two different leaf shapes were assembled. One type of leaflets is thin paper, and the color on both sides is obviously different after drying, and the fruit stalk is slender and elongated; the other type of leaflets are the thick paper, the leaf surface and fruit stalk are glabrous, the fruit stalk is thicker, and the lateral veins are recessed on the leaf surface and appear to be cracked. Their circular DNA lengths were all 158,565 bp. Both genomes were made up of a large single-copy (LSC), a small single-copy (SSC), and two inverted repeat (IRs) regions. Each genome encoded 132 genes, including 87 protein-coding, 37 tRNA, and 8 rRNA genes. Phylogenetic analysis indicated that both species were closely related to the congeneric Z. bungeanum.