Table_3_Comparative Analyses of Chloroplast Genomes From 14 Zanthoxylum Species: Identification of Variable DNA Markers and Phylogenetic Relationships Within the Genus.XLSX

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.

Zanthoxylum L. 为历史悠久的经济作物，其栽培与驯化历史悠久，具有重要的经济、生态及药用价值。为解决因 Zanthoxylum 植物形态学特征相似而引发的分类难题，并建立可靠的系统发育关系，我们对六种 Zanthoxylum 植物的叶绿体（cp）基因组（包括 Z. piasezkii、Z. armatum、Z. motuoense、Z. oxyphyllum、Z. multijugum 及 Z. calcicola）进行了测序与注释，并将这些基因组与之前发表的 Zanthoxylum 物种基因组相结合。通过生物信息学方法，我们分析了基因组特征、倒位重复（IR）区域的收缩与扩张、简单序列重复（SSRs）与长重复序列的差异、物种间 Ka/Ks 比率、突变热点以及 14 种 Zanthoxylum 物种的系统发育关系。结果显示，Zanthoxylum 的 cp 基因组大小介于 158,071 至 158,963 碱基对之间，包含 87 个蛋白质编码基因、37 个 tRNA 基因和 8 个 rRNA 基因。确定了七个突变热点作为候选 DNA 条形码序列，以区分 Zanthoxylum 物种。系统发育分析强烈支持将属 Fagara 视为 Zanthoxylum 的亚属，并提出了在 Zanthoxylum 中可能存在新亚属的可能性。这些基因组的可用性将为 Zanthoxylum 物种的鉴定、分子育种以及进化分析提供宝贵信息。