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Zanthoxylum  L. is an economic crop with a long history of cultivation and domestication and has important economic, ecological, and medicinal value. To solve the classification problems caused by the similar morphological characteristics of  Zanthoxylum  and establish a credible phylogenetic relationship, we sequenced and annotated six  Zanthoxylum  chloroplast (cp) genomes ( Z. piasezkii, Z. armatum, Z. motuoense, Z. oxyphyllum, Z. multijugum , and  Z. calcicola ) and combined them with previously published genomes for the  Zanthoxylum  species. We used bioinformatics methods to analyze the genomic characteristics, contraction, and expansion of inverted repeat (IR) regions; differences in simple sequence repeats (SSRs) and long repeat sequences; species pairwise Ka/Ks ratios; divergence hotspots; and phylogenetic relationships of the 14  Zanthoxylum  species. The results revealed that cp genomes of  Zanthoxylum  range in size from 158,071 to 158,963 bp and contain 87 protein-coding, 37 tRNA, and 8 rRNA genes. Seven mutational hotspots were identified as candidate DNA barcode sequences to distinguish  Zanthoxylum  species. The phylogenetic analysis strongly supported the genus  Fagara  as a subgenus of  Zanthoxylum  and proposed the possibility of a new subgenus in  Zanthoxylum.  The availability of these genomes will provide valuable information for identifying species, molecular breeding, and evolutionary analysis of  Zanthoxylum.

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Comparative Analyses of Chloroplast Genomes From 14 Zanthoxylum Species: Identification of Variable DNA Markers and Phylogenetic Relationships Within the Genus