Post-polyploid chromosomal diploidization in plants is affected by clade divergence and constrained by shared genomic features

Genomic redundancy resulting from whole-genome duplication creates opportunities for double-strand misrepair that can lead to chromosomal rearrangements and a reduction in chromosome number, known as descending dysploidy. Although flowering plants often undergo post-polyploid rediploidization, the pathways and consequences of descending dysploidy are still poorly understood. In this study, we sequenced and assembled the genomes of eight Biscutella species varying in size from 0.6 to 1.1 Gb and exhibiting chromosome numbers of n = 6, 8 and 9. Our analysis revealed an estimated 12 million years of diploidization of an allotetraploid ancestral genome ( n = 14) characterized by independent descending dysploidy, resulting in chromosome numbers of n = 9, 8, and 6. We identified clades of early-diverging ( n = 8/6) and late-diverging ( n = 9) genomes that exhibited both convergent and divergent features. While both clades showed similar levels of subgenome fractionation and preferential retention of polyploidy-derived genes, the early-diverging genomes exhibited a higher removal ratio of LTR retrotransposons and greater variability in the size of topologically associated domains (TADs). In addition, we identified 12 chromosome breakage hotspots enriched in LTR retrotransposons and frequently located at TAD boundaries. In addition, we identified 12 chromosome breakpoint hotspots enriched for LTR retrotransposons and frequently located at TAD boundaries. This suggests that although post-polyploid descendig dysploid appears to be an independent and superficially random process, some shared genomic features may favor the occurrence of recurrent chromosome breakpoints in different species.