Zhendong Center, Department of Molecular and Biomedical Sciences, The University of Adelaide, Adelaide, 5005, Australia.
Beijing Zhendong Research Institute, Shanxi Zhendong Pharmaceutical Co Ltd, Beijing, 10587, China.
Sci Data. 2023 Aug 29;10(1):572. doi: 10.1038/s41597-023-02490-8.
Sophora flavescens is a medicinal plant in the genus Sophora of the Fabaceae family. The root of S. flavescens is known in China as Kushen and has a long history of wide use in multiple formulations of Traditional Chinese Medicine (TCM). In this study, we used third-generation Nanopore long-read sequencing technology combined with Hi-C scaffolding technology to de novo assemble the S. flavescens genome. We obtained a chromosomal level high-quality S. flavescens draft genome. The draft genome size is approximately 2.08 Gb, with more than 80% annotated as Transposable Elements (TEs), which have recently and rapidly proliferated. This genome size is ~5x larger than its closest sequenced relative Lupinus albus L. . We annotated 60,485 genes and examined their expression profiles in leaf, stem and root tissues, and also characterised the genes and pathways involved in the biosynthesis of major bioactive compounds, including alkaloids, flavonoids and isoflavonoids. The assembled genome highlights the very different evolutionary trajectories that have occurred in recently diverged Fabaceae, leading to smaller duplicated genomes.
苦参是豆科槐属的一种药用植物。苦参的根在中国被称为苦参，在中国传统医学（TCM）的多种配方中有悠久的广泛应用历史。在这项研究中，我们使用第三代纳米孔长读测序技术结合 Hi-C 支架技术从头组装苦参基因组。我们获得了一个染色体级别的苦参高质量基因组草图。基因组草图大小约为 2.08Gb，超过 80%被注释为转座元件（TEs），它们最近迅速增殖。这个基因组大小比最近测序的亲缘种 Lupinus albus L. 大约 5 倍。我们注释了 60485 个基因，并检测了它们在叶、茎和根组织中的表达谱，还研究了参与生物合成主要生物活性化合物的基因和途径，包括生物碱、类黄酮和异黄酮。组装的基因组突出了最近分化的豆科植物中发生的非常不同的进化轨迹，导致较小的重复基因组。
