Assembly and Annotation of a Draft Genome of the Medicinal Plant Polygonum cuspidatum
Assembly and Annotation of a Draft Genome of the Medicinal Plant Polygonum cuspidatum
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药用植物虎杖基因组草案的组装和注释
DOI：
10.3389/fpls.2019.01274
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发表时间：
2019-10
影响因子：
5.6
通讯作者：
Li Chen
中科院分区：
文献类型：
--
作者：
Zhang Yonghong;Zheng Lanlan;Zheng Yan;Zhou Chao;Huang Ping;Xiao Xiao;Zhao Yongheng;Hao Xincai;Hu Zhubing;Chen Qinhua;Li Hongliang;Wang Xuanbin;Fukushima Kenji;Wang Guodong;Li Chen
虎杖（Polygonum cuspidatum）是一种能产生二苯乙烯和醌等生物活性成分的植物，长期以来一直被认为是传统中草药的重要成分。为了更好地了解这种植物的生物学特性，并对其天然产物的生物合成有深入的了解，我们利用Illumina测序技术组装了虎尾藤的基因组草图。该草图基因组长约2.56 Gb，其中71.54%的基因组被标记为转座元件。综合基因预测表明，虎尾鲟基因组编码55,075个功能基因，其中6,776个基因家族在5个研究物种中保守，2,386个是虎尾鲟所特有的。在鉴定的功能基因中，预计有4,753个编码转录因子。我们追踪了虎尾猿的基因复制历史，并确定它在大约6500万年前和660万年前经历了两次全基因组复制事件。根被认为是主要的药用组织，转录组分析鉴定出2173个基因在根中表达水平高于地上组织。详细的系统发育分析表明，在苯丙素代谢途径中，编码二苯乙烯合成酶和查尔酮合成酶的基因家族扩增，这与白藜芦醇的生物合成有关，白藜芦醇是一种重要的二苯乙烯。基因组草图分析确定了7个脱落酸和水分亏缺胁迫诱导的蛋白质编码基因和14个富含半胱氨酸的跨膜模块基因，预计与胁迫反应有关。本研究构建的虎尾藤基因组图谱为虎尾藤药用成分的分子鉴定、对虎尾藤的改良以及探索虎尾藤的非生物抗逆性提供了宝贵的资源。
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.
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