AUTHOR=Zhao Kaihui , Li Lianqiang , Quan Hong , Yang Junbo , Zhang Zhirong , Liao Zhihua , Lan Xiaozhong 

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

JOURNAL=Frontiers in Plant Science

VOLUME=11

YEAR=2021

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2020.605793

DOI=10.3389/fpls.2020.605793

ISSN=1664-462X

ABSTRACT=<p><italic>Zanthoxylum</italic> 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 <italic>Zanthoxylum</italic> and establish a credible phylogenetic relationship, we sequenced and annotated six <italic>Zanthoxylum</italic> chloroplast (cp) genomes (<italic>Z. piasezkii, Z. armatum, Z. motuoense, Z. oxyphyllum, Z. multijugum</italic>, and <italic>Z. calcicola</italic>) and combined them with previously published genomes for the <italic>Zanthoxylum</italic> 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 <italic>Zanthoxylum</italic> species. The results revealed that cp genomes of <italic>Zanthoxylum</italic> 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 <italic>Zanthoxylum</italic> species. The phylogenetic analysis strongly supported the genus <italic>Fagara</italic> as a subgenus of <italic>Zanthoxylum</italic> and proposed the possibility of a new subgenus in <italic>Zanthoxylum.</italic> The availability of these genomes will provide valuable information for identifying species, molecular breeding, and evolutionary analysis of <italic>Zanthoxylum.</italic></p>