Table_2_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，经过长期的栽培驯化，具有重要的经济、生态和药用价值。为解决因Zanthoxylum种植物形态学特征相似性所引起的分类问题，并建立可信的进化系统关系，本研究对六种Zanthoxylum叶绿体（cp）基因组（Z. piasezkii、Z. armatum、Z. motuoense、Z. oxyphyllum、Z. multijugum 和 Z. calcicola）进行了测序和注释，并将之与先前发表的Zanthoxylum种基因组信息相结合。通过生物信息学方法，对基因组特征、倒位重复（IR）区域的收缩与扩张、简单序列重复（SSR）和长重复序列的差异、物种间的Ka/Ks比值、变异热点以及14种Zanthoxylum的进化关系进行了分析。研究结果表明，Zanthoxylum的cp基因组大小介于158,071至158,963碱基对之间，包含87个编码蛋白基因、37个tRNA基因和8个rRNA基因。识别出七个突变热点，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Fagara属为Zanthoxylum的亚属，并提出了Zanthoxylum中可能存在新亚属的可能性。这些基因组的可用性将为物种鉴定、分子育种和Zanthoxylum的进化分析提供宝贵信息。