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). However, there is little genomic information available for S. flavescens, which has greatly hindered the breeding of S. flavescens and characterisation of bioactive compounds. Therefore, 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). We also annotated 60,485 genes and examined their expression profiles in leaf, stem and root tissues. We also characterised the genes and pathways involved in the biosynthesis of major bioactive compounds, including alkaloids, flavonoids and isoflavonoids. The assembled genome provides valuable resources for conservation, genetic research and breeding of S. flavescens.

The draft genome assembly dataset for Sophora flavescens (Kushen), including: 1) Draft genome assembly: Sfla_v1.chromosomes.fa 2) Draft genome assembly with repeats soft-masked: Sfla_v1.repeat_EDTA.chromosomes_softMasked.fa 3) Gene annotation: Sfla_v1.cdna.gff3 4) Annotated protein sequences: Sfla_v1.proteins.fa 5) Annotated transcripts sequences: Sfla_v1.transcripts.fa 6) Repeat annotation: Sfla_v1.repeat_EDTA.gff3 7) Consensus repeat sequences: Sfla_v1.repeat_EDTA.lib