Abstract
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.
Highlights
Polygonum cuspidatum Sieb. et Zucc., commonly known as Huzhang in Chinese and Japanese knotweed in English, is a medicinal plant that is widely distributed in eastern Asia whose roots have served for centuries as an important traditional Chinese medicine for dispelling wind-evil, damp elimination, analgesic therapy, relieving coughs, and reducing sputum (Peng et al, 2013; Hong et al, 2016)
The genome heterozygosity was estimated to be ca. 1.6%, while the GC content was predicted to be 37.1% (Supplementary Table S2). These results indicate that the P. cuspidatum genome is highly complex, making de novo assembly quite challenging
The assemblies from platanus were more complete than those generated using SOAPdenovo, which is consistent with the observation that platanus performs better for highly heterozygous genomes (Kajitani et al, 2014)
Summary
Polygonum cuspidatum Sieb. et Zucc., commonly known as Huzhang in Chinese and Japanese knotweed in English, is a medicinal plant that is widely distributed in eastern Asia whose roots have served for centuries as an important traditional Chinese medicine for dispelling wind-evil, damp elimination, analgesic therapy, relieving coughs, and reducing sputum (Peng et al, 2013; Hong et al, 2016). In contrast to its medicinal uses, P. cuspidatum is regarded as an invasive plant in Europe and North America due to its aggressive growth, allelopathic effects, and extremely strong abiotic stress tolerance (Murrell et al, 2011; Rouifed et al, 2012; Dommanget et al, 2016). This species shows strong adaptability and tolerance to a wide range of stress conditions, such as dense shade, high temperatures, cold, drought, waterlogging, burning, heavy metals, various soil types, and extreme pH, salt, and high sulfur dioxide conditions (Clements and Ditommaso, 2012; Michalet et al, 2017). Resveratrol, especially in the form of trans-resveratrol, has many pharmacological uses in treating inflammation, HIV, and cardiovascular-related diseases (Hao et al, 2012; Ouyang et al, 2014; Hong et al, 2016)
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