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.

沙漠对植物施加了强大的选择压力，但生态适应和随后的物种形成的潜在基因组驱动因素在很大程度上仍然未知。在这里，我们生成了从头基因组组装并进行了沙生属Pugionium 的群体基因组分析（十字花科）。我们的结果表明该双特异性属经历了异源多倍体事件，并且两个亲本基因组来自具有不同染色体数目和结构的两个祖先谱系。与非生物胁迫反应和木质素生物合成相关的基因家族的后多倍体扩展促进了该属对沙漠栖息地的环境适应。这两个物种的种群基因组分析进一步揭示了它们最近随着连续基因流的分化，发现差异最大的区域集中在三个高度结构重组的染色体上。这些区域中选择的基因主要位于两个亚基因组之一中，极大地促进了微生境适应的种间差异。