DataSheet_5_Assembly and Annotation of a Draft Genome of the Medicinal Plant Polygonum cuspidatum.xlsx

Polygonum cuspidatum (Japanese knotweed, also known as Huzhang in Chinese), a plant that produces bioactive components such as stilbenes and quinones, has long been recognized as important in traditional Chinese herbal medicine. To better understand the biological features of this plant and to gain genetic insight into the biosynthesis of its natural products, we assembled a draft genome of P. cuspidatum using Illumina sequencing technology. The draft genome is ca. 2.56 Gb long, with 71.54% of the genome annotated as transposable elements. Integrated gene prediction suggested that the P. cuspidatum genome encodes 55,075 functional genes, including 6,776 gene families that are conserved in the five eudicot species examined and 2,386 that are unique to P. cuspidatum. Among the functional genes identified, 4,753 are predicted to encode transcription factors. We traced the gene duplication history of P. cuspidatum and determined that it has undergone two whole-genome duplication events about 65 and 6.6 million years ago. Roots are considered the primary medicinal tissue, and transcriptome analysis identified 2,173 genes that were expressed at higher levels in roots compared to aboveground tissues. Detailed phylogenetic analysis demonstrated expansion of the gene family encoding stilbene synthase and chalcone synthase enzymes in the phenylpropanoid metabolic pathway, which is associated with the biosynthesis of resveratrol, a pharmacologically important stilbene. Analysis of the draft genome identified 7 abscisic acid and water deficit stress-induced protein-coding genes and 14 cysteine-rich transmembrane module genes predicted to be involved in stress responses. The draft de novo genome assembly produced in this study represents a valuable resource for the molecular characterization of medicinal compounds in P. cuspidatum, the improvement of this important medicinal plant, and the exploration of its abiotic stress resistance.

虎杖（Polygonum cuspidatum，俗称日本虎杖，中文又名虎杖（Huzhang））可产生芪类（stilbenes）与醌类（quinones）等生物活性成分，长期以来在传统中草药领域具有重要应用价值。为深入解析该植物的生物学特性，并阐明其天然产物生物合成的遗传机制，本研究采用Illumina测序技术组装了虎杖的草图基因组（draft genome）。该草图基因组大小约为2.56 Gb，其中71.54%的序列被注释为转座元件（transposable elements）。整合基因预测结果显示，虎杖基因组共编码55075个功能基因，其中包含6776个在5个被测双子叶植物中保守的基因家族，以及2386个虎杖特有的基因家族。在已鉴定的功能基因中，有4753个被预测为转录因子（transcription factors）。本研究追溯了虎杖的基因复制历史，发现其在约6500万年前和660万年前各经历了一次全基因组复制（whole-genome duplication）事件。虎杖的根部为主要药用组织，转录组（transcriptome）分析显示，共有2173个基因在根部的表达量显著高于地上组织。详细的系统发育分析表明，苯丙烷代谢通路（phenylpropanoid metabolic pathway）中编码芪合酶（stilbene synthase）和查尔酮合酶（chalcone synthase）的基因家族发生了扩张，而该通路与具有重要药理活性的芪类化合物白藜芦醇（resveratrol）的生物合成密切相关。对该草图基因组的分析还鉴定出7个脱落酸（abscisic acid）与水分亏缺胁迫响应编码蛋白基因，以及14个预测参与胁迫应答的富半胱氨酸跨膜模块基因。本研究获得的草图级从头基因组组装（de novo genome assembly）结果，可为虎杖药用成分的分子解析、该重要药用植物的遗传改良，以及其非生物胁迫抗性机制的探究提供宝贵的研究资源。