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.

Climate oscillations may drive the divergence of ancestral species through habitat isolation, species distribution patterns, and the cessation of gene flow. However, traditional ecological niche models lack the consideration for the genetic adaptation of species, thus it’s difficult to understand how climate oscillations affect species divergence by changing their climatic suitability and historical demography. We analyzed the impact of climate change on the divergence of two langur species, François’ langur and White-headed langur, using Maxent, Genotype–Environment Association (GEA) models and genomic data. Our results indicate that 1) Climatic suitability for François’ langur and White-headed langur has separated from the Last Interglacial (LIG, 120,000-140,000 years ago) to the Last Glacial Maximum (LGM); 2) Although the effective population size for both species decreased between the LIG and the LGM, the effective population size of François’ langur increased more quickly than that of White-headed langur from the LGM to the present; 3) Historical patterns of climate change have resulted in periods of expanded and contracted climatic suitability, with each species experiencing periods of interspecific genetic isolation and periods of interspecific genetic exchange; and 4) Human activities and future climate change have contracted the range of François’ langur (in China) and White-headed langur. Climate oscillation, population isolation, and in situ evolution in refugia from the LIG to the LGM appear to have played a critical role in langur speciation and adaptive evolution. Overall, our results demonstrate how climatic oscillations and historical demography drive speciation, providing a new perspective on species divergence and conservation.

Lepus oiostolus (L. oiostolus) is a species endemic to the Qinghai-Tibet Plateau. However, the absence of a reference genome limits genetic studies. Here, we report a high-quality L. oiostolus genome assembly, with scaffolds anchored to 24 chromosomes and a total assembled length of 2.80 Gb (contig N50 = 64.24 Mb). We found that transposable elements account for 49.84% of the genome, a total of 22,295 predicted protein-coding genes. Long interspersed nuclear elements (LINEs) constitute a high proportion of the genome, and their expansion is a key contributor to this species’s relatively large genome size. A total of 1,282 genes were found to have expanded into gene families. Comparative analyses indicated that L. oiostolus probably diverged from its close relatives Ochotona curzoniae and Ochotona princeps, approximately 53.1 million years ago (MYA). This study suggested that the Tipin gene enabled Lepus oiostolus to adapt to the high levels of ultraviolet radiation in the Qinghai-Tibet Plateau. As the first chromosome-level genome assembly of Lepus oiostolus, this study will provide a valuable genomic resource for future research on the evolution of the Leporidae.

Repeated homoploid hybrid speciation (HHS) events with the same parental species have rarely been reported. In this study, we used population transcriptome data to test paraphyly and HHS events in one conifer Picea brachytyla. All analyses identified and supported non-sister relationships for the two lineages of P. brachytyla. The southern lineage was placed within the re-circumscribed P. likiangensis species complex (PLSC) while P. brachytyla sensu stricto (s.s.), comprising only the northern lineage, parallels both PLSC and the closely related P. wilsonii. In addition, both phylogenetic and coalescent analyses suggested that P. brachytyla s.s. arose from homoploid hybrid speciation between the ancestor of the PLSC before its diversification (into the current varieties or species), and P. wilsonii, through an intermediate hybrid lineage at an early stage and backcrossing to the ancestral PLSC. These two parental ancestors also produced another homoploid hybrid species, P. purpurea, in the same way but at a later stage, through the same extinct lineage but backcrossing to the other parent, P. wilsonii. We reveal the first case that backcrossing to different parents of the same extinct hybrid lineage produced two different hybrid species. Our results highlight the existence of more reticulate evolution during species diversification in the spruce genus and more complex homoploid hybrid events than have previously been identified.