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

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 and establish a credible phylogenetic relationship, we sequenced and annotated six chloroplast (cp) genomes ( , and ) and combined them with previously published genomes for the 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 species. The results revealed that cp genomes of 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 species. The phylogenetic analysis strongly supported the genus as a subgenus of and proposed the possibility of a new subgenus in The availability of these genomes will provide valuable information for identifying species, molecular breeding, and evolutionary analysis of