菝葜叶绿体基因组的组装分析与分子标记研究＊

目的 采用高通量测序数据和新组装手段对药用植物菝葜的叶绿体基因组进行精细组装,并以此为基础厘清其分类地位,开发分子鉴定标记。方法 利用两种测序手段重新测定并精细组装菝葜叶绿体基因组;重建菝葜近缘物种在时间尺度下的系统发育关系;分析菝葜叶绿体基因组一级结构并检测编码区选择压力;筛选并验证具备种群特异性的SSR引物。结果 混合组装结果显示菝葜叶绿体基因组全长157959 bp,内含编码基因86个。菝葜族与油点草族和百合族互为姐妹群;其内部约26.5Mya开始出现分化。在accD、rbcL及rpl20基因中存正选择信号。247个SSR位点中的3个具备作为菝葜分子鉴定标记的潜力。结论 利用短读长和长读长共同组装菝葜叶绿体基因组的结果更佳。已探明的3个SSR位点能为筛选分子标记提供数据支撑。

Assembly and Molecular Markers of Smilax China Chloroplast Genome

Objective To clarify the taxonomic status and establish promise molecular markers of Smilax china, a traditional Chinese medicinal plant, we reassembled its chloroplast (cp) genome based on both short-reads and long-reads sequencing data via latest methods.Methods The isolated genomic DNA of S. china were sequenced by Illumina and Nanopore pipelines; then the cp genome was reference-based assembled via Canu and Unicycler software respectively. The time-scale phylogenetic tree of S. china together with related species was reconstructed on the dataset of the updated cp genome sequence. We also analyzed the primary structure of S. china cp genome and the selection pressure among its harbored coding sequences. Moreover, the selected SSR-sites from different regions in cp genome were tested using designed primers.Results Our results indicated that the S. china cp genome was 157959bp in length and harbored 87 coding genes. Our phylogenetic analysis supported Smilaceae as sister to Tricyrteae and Lilieae, and the differentiation started at about 26.5Mya inside Smilaceae. The positive selection signal was detected in accD, rbcL and rpl20. Three among total 247 SSR loci had potential as molecular markers.Conclusion The reassembled S. china cp genome via both short-reads and long-reads outperformed the reference cp genome and other approaches in current research. The proven 247 SSR sites can provide data support for establishing novo molecular markers.