Ancient whole-genome duplication (WGD) or polyploidization is prevalent in plants and has played a crucial role in plant adaptation. However, the underlying genomic basis of ecological adaptation and subsequent diversification after WGD are still poorly understood in most plants. Here, we report a chromosome-scale reference genome assembly for the genus Orinus (Orinus kokonorica as representative) and preformed comparative genomics with its closely related genus Cleistogenes (Cleistogenes songorica as representative), both belonging to a newly named subtribe Orininae of the grass subfamily Chloridoideae. The two genera may share one paleo-allotetraploidy event before 10 million years ago, and their two subgenomes display neither fractionation bias nor global homoeolog expression dominance. Recent expansion of transposable elements and enormous contraction in gene families in O. kokonorica have maintained a similar genome size compared to C. songorica. Further comparative genomic analyses reveal substantial genome rearrangements and extensive structural variations (SVs) between the two species. With comparative transcriptomics, we demonstrate that functional innovations of orthologous genes have played an important role in promoting adaptive evolution and diversification of the two genera after polyploidization. In addition, copy number variations in flower and rhizome development related genes and extensive SVs between orthologs may contribute to the morphological differences between the two genera. Our results provide significant new insights into the adaptive evolution and subsequent diversification of the two genera after polyploidization.

 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.