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.

We sought to generate a preliminary demographic framework for Psammochloa villosa to support of future studies of this ecologically important desert grass species, its conservation, and sustainable utilization. Psammochloa villosa occurs in the Inner Mongolian Plateau where it is frequently the dominant species and is involved in sand stabilization and wind breaking. Here, we characterized the genetic diversity and structure of 210 individuals from 43 natural populations of P. villosa using amplified fragment length polymorphism (AFLP) markers. We obtained 1728 well-defined amplified bands from eight pairs of primers, of which 1654 bands (95.72%) were polymorphic.All these values indicate that there is abundant genetic diversity, but limited gene flow in P. villosa. However, an analysis of molecular variance (AMOVA) showed that genetic variation mainly exists within 43 populations of the species (64.16%), and we found that the most genetically similar populations were often not geographically adjacent. Thus, this suggests that the mechanisms of gene flow are surprisingly complex in the species and may occur over long distances. In addition, we predicted the distribution dynamics of P. villosa based on the spatial distribution modeling and found that its range has contracted continuously since the last inter-glacial period. We speculate that dry, cold climates have been critical in determining the geographic distribution of P. villosa during the Quaternary period. Our study provides new insights into the population genetics and evolutionary history of P. villosa in the Inner Mongolian Plateau, which can be used to design in-situ conservation actions and to prioritize sustainable utilization of germplasm resources.