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.

Understanding how populations diverge and new species arise is a central question in evolutionary biology. ‘Allopatric’ divergence through geographic isolation is considered to be the commonest mechanism generating species biodiversity in mountainous ecosystems. However, the underlying genomic dynamics, especially genomic islands of elevated divergence and genes that are highly diverged as a result of lineage-specific selection, remain poorly understood. Stellera chamaejasme is widely distributed on the Qinghai-Tibet Plateau and in adjacent regions, making it a good model with which to explore genomic divergence in mountainous ecosystems. We assembled a high-quality, chromosome-level genome for this species and re-sequenced the genomes of 24 populations across its distributional range. Our population genomic analyses recovered four distinct genetic lineages corresponding to geographic distributions with contrasting environments. However, we revealed that continuous gene flow occurred during the diversification of these four lineages and inter-lineage hybrids, and plastome introgressions were frequently found in regions of contact. The elevated genomic divergences were highly heterogeneous across the genome. The formation of such genomic islands showed neither correlation with rate of gene flow nor relationship to time of divergence. The lineage-specific positively selected genes potentially involved in local adaptation were found both within and outside genomic islands. Our results suggest that genomic divergence in S. chamaejasme is likely to have been triggered and further maintained by local selection in addition to geographic isolation.