Deserts exert strong selection pressures on plants, but the underlying genomic drivers of ecological adaptation and subsequent speciation remain largely unknown. Here, we generated de novo genome assemblies and conducted population genomic analyses of the psammophytic genus Pugionium (Brassicaceae). Our results indicated that this bispecific genus had undergone an allopolyploid event, and the two parental genomes were derived from two ancestral lineages with different chromosome numbers and structures. The postpolyploid expansion of gene families related to abiotic stress responses and lignin biosynthesis facilitated environmental adaptations of the genus to desert habitats. Population genomic analyses of both species further revealed their recent divergence with continuous gene flow, and the most divergent regions were found to be centered on three highly structurally reshuffled chromosomes. Genes under selection in these regions, which were mainly located in one of the two subgenomes, contributed greatly to the interspecific divergence in microhabitat adaptation.

Central European Institute of Technology Masaryk University 625 00 Brno Czech Republic

Institute of Evolution University of Haifa Mount Carmel Haifa 3498838 Israel

Key Laboratory for Bio Resource and Eco Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu 610065 China

Key Laboratory for Bio Resource and Eco Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu 610065 China;

State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating Gansu Desert Control Research Institute Lanzhou 730000 China

State Key Laboratory of Grassland Agro Ecosystem Innovation Institute of Ecology and Life Sciences Lanzhou University Lanzhou 730000 China

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