Abstract
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.
Highlights
Zanthoxylum L. belongs to the Rutoideae subfamily of the Rutaceae family
Our results have laid the foundation for future studies on the molecular identification of Zanthoxylum species
The 14 Zanthoxylum cp genomes contain 87 proteincoding genes (79 unigenes were protein-coding), 37 tRNA genes, and 8 rRNA genes, which is similar to Citrus (Carbonellcaballero et al, 2015)
Summary
Zanthoxylum L. belongs to the Rutoideae subfamily of the Rutaceae family. Zanthoxylum is widely distributed in tropical and subtropical regions and consists of approximately 250 species (Huang, 1997). Owing to its important economic and medicinal value, Zanthoxylum has a long history of cultivation and domestication in Asia. The Chinese pharmacopeia (2015 Edition) records that the Chloroplast Genomes From Zanthoxylum Species dried and mature peel of Zanthoxylum schinifolium Sieb. The pericarp of Z. armatum, Z. bungeanum, and other Zanthoxylum species has a strong fragrance and is one of the traditional Chinese “eight major condiments.”. Owing to its economic potential, Zanthoxylum has been planted to restore farmland to forests and has high ecological value for soil and fertilizer preservation (Hu et al, 2012) The pericarp of Z. armatum, Z. bungeanum, and other Zanthoxylum species has a strong fragrance and is one of the traditional Chinese “eight major condiments.” In addition, owing to its economic potential, Zanthoxylum has been planted to restore farmland to forests and has high ecological value for soil and fertilizer preservation (Hu et al, 2012)
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