Table_4_Comparative Analyses of Chloroplast Genomes From 14 Zanthoxylum Species: Identification of Variable DNA Markers and Phylogenetic Relationships Within the Genus.XLS

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.

刺茱萸属（Zanthoxylum L.）作为一种历史悠久的经济作物，经历了长期的栽培与驯化，其具有重要的经济、生态和药用价值。为解决刺茱萸与形态学特征相似性导致的分类问题，并建立可信的进化系统关系，我们对六种刺茱萸叶绿体基因组（Z. piasezkii, Z. armatum, Z. motuoense, Z. oxyphyllum, Z. multijugum, Z. calcicola）进行了测序与注释，并将其与先前发表的刺茱萸属物种基因组相结合。通过生物信息学方法，我们分析了基因组特性、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种刺茱萸的进化关系。结果表明，刺茱萸的叶绿体基因组大小介于158,071至158,963碱基对之间，包含87个编码蛋白基因、37个转运RNA基因和8个核糖体RNA基因。我们确定了七个突变热点作为候选DNA条形码序列，以区分刺茱萸属物种。系统发育分析强烈支持将属Fagara视为刺茱萸属的亚属，并提出了在刺茱萸属中可能存在新亚属的可能性。这些基因组的可用性将为刺茱萸属物种鉴定、分子育种和进化分析提供宝贵信息。