Post-polyploid diploidization associated with descending dysploidy and interspecific introgression drives plant genome evolution by unclear mechanisms. Raphanus is an economically and ecologically important Brassiceae genus and model system for studying post-polyploidization genome evolution and introgression. Here, we report the de novo sequence assemblies for 11 genomes covering most of the typical sub-species and varieties of domesticated, wild and weedy radishes from East Asia, South Asia, Europe, and America. Divergence among the species, sub-species, and South/East Asian types coincided with Quaternary glaciations. A genus-level pan-genome was constructed with family-based, locus-based, and graph-based methods, and whole-genome comparisons revealed genetic variations ranging from single-nucleotide polymorphisms (SNPs) to inversions and translocations of whole ancestral karyotype (AK) blocks. Extensive gene flow occurred between wild, weedy, and domesticated radishes. High frequencies of genome reshuffling, biased retention, and large-fragment translocation have shaped the genomic diversity. Most variety-specific gene-rich blocks showed large structural variations. Extensive translocation and tandem duplication of dispensable genes were revealed in two large rearrangement-rich islands. Disease resistance genes mostly resided on specific and dispensable loci. Variations causing the loss of function of enzymes modulating gibberellin deactivation were identified and could play an important role in phenotype divergence and adaptive evolution. This study provides new insights into the genomic evolution underlying post-polyploid diploidization and lays the foundation for genetic improvement of radish crops, biological control of weeds, and protection of wild species' germplasms.

与下降异倍体和种间基因渗入相关的后多倍体二倍体化通过不清楚的机制驱动植物基因组进化。Raphanus是一种经济和生态上重要的芸苔科植物和模型系统，用于研究多倍化后的基因组进化和基因渗入。在这里，我们报告从头11个基因组的序列组装，涵盖了来自东亚、南亚、欧洲和美洲的大部分典型亚种和品种的驯化、野生和杂草萝卜。物种、亚种和南亚/东亚类型之间的差异与第四纪冰川作用相吻合。采用基于家族、基于基因座和基于图的方法构建了属级泛基因组，全基因组比较揭示了从单核苷酸多态性（SNP）到全祖先核型倒位和易位的遗传变异。 AK) 块。野生、杂草和驯化萝卜之间发生了广泛的基因流动。高频率的基因组改组、偏向保留和大片段易位塑造了基因组多样性。大多数特定品种的富含基因的块显示出很大的结构变异。在两个富含重排的大岛中揭示了可有可无的基因的广泛易位和串联重复。抗病基因主要存在于特定和可有可无的基因座上。确定了导致调节赤霉素失活的酶功能丧失的变异，这些变异可能在表型分化和适应性进化中发挥重要作用。该研究为后多倍体二倍体化的基因组进化提供了新的见解，为萝卜作物的遗传改良、杂草生物防治和野生物种种质保护奠定了基础。确定了导致调节赤霉素失活的酶功能丧失的变异，这些变异可能在表型分化和适应性进化中发挥重要作用。该研究为后多倍体二倍体化的基因组进化提供了新的见解，为萝卜作物的遗传改良、杂草生物防治和野生物种种质保护奠定了基础。确定了导致调节赤霉素失活的酶功能丧失的变异，这些变异可能在表型分化和适应性进化中发挥重要作用。该研究为后多倍体二倍体化的基因组进化提供了新的见解，为萝卜作物的遗传改良、杂草生物防治和野生物种种质保护奠定了基础。