Sophora japonica is a medium-size deciduous tree belonging to Leguminosae family and famous for its high ecological, economic, and medicinal value. Here, we reveal a draft genome of S. japonica, which was approximately 511.49 Mb long (contig N50 size of 16.15 Mb) based on Illumina, Nanopore and Hi-C data. We reliably assembled 110 contigs into 14 chromosomes, representing 91.62% of the total genome, with an improved N50 size of 31.32 Mb based on Hi-C data. Further investigation identified 271.76 Mb (53.13%) of repetitive sequences and 31,000 protein-coding genes, of which 30,721 (99.1%) were functionally annotated. Phylogenetic analysis indicates that S. japonica separated from Arabidopsis thaliana and Glycine max about 107.53 and 61.24 million years ago, respectively. We detected evidence of species-specific and common-legume WGD events in S. japonica. We further found that multiple TF families (e.g., BBX and PAL) have expanded in S. japonica, which might have led to its enhanced tolerance to abiotic stress. In addition, S. japonica harbors more genes involved in the lignin and cellulose biosynthesis pathways than the other two species. Finally, population genomic analyses revealed no obvious differentiation among geographical groups and the effective population size continuously declined since 2 Ma. Our genomic data provide a powerful comparative framework to study the adaptation, evolution and active ingredients biosynthesis in S. japonica. More importantly, our high-quality S. japonica genome is important for elucidating the biosynthesis of its main bioactive components, and improving its production and/or processing.

 Dimorphic flowers growing on a single individual plant play a critical role in extreme adaption and reproductive assurance in plants and have high ecological and evolutionary significance. However, the omics bases underlying such a differentiation and maintenance remain largely unknown. We aimed to investigate this through genomic, transcriptome and metabolomic analyses of dimorphic flowers in an alpine biennial, Sinoswertia tetraptera (Gentianaceae).  A high-quality chromosome-level genome sequence (903 Mb) was first assembled for S. tetraptera with 31,359 protein-coding genes annotated. Two rounds of recent independent whole-genome duplication (WGD) were revealed. More than 10% of the novel genes from the recent species-specific WGD were found to be differentially expressed in the two types of flowers, and this may have helped contribute to the origin of this innovative trait.  Other contrasting gene expression between flowers included that related to flower development and color, hormones, and iridoid biosynthesis. Metabolomic analyses similarly suggested differential concentrations of both hormones and iridoids in the two types of flowers. The interactions between multiple genes may together lead to contrasting morphology and open versus closed pollination of the dimorphic flowers in this species.  A total of 56 candidate genes were identified from the known iridoid biosynthesis-related pathways. Two hub genes were found to play an essential role in transferring intermediate products between leaves and flowers during iridoid biosynthesis.