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

Genomic redundancy following whole-genome duplication creates opportunities for double-strand misrepair that can lead to chromosomal rearrangements and reductions in chromosome number, known as descending dysploidy. Although flowering plants often undergo post-polyploid rediploidization, the pathways and consequences of descending dysploidy remain poorly understood. Here, we sequence and assemble the genomes of eight Biscutella species ranging from 0.6 to 1.1 Gb and exhibiting chromosome numbers of n = 6, 8 and 9. Our analysis reveals ~11 million years of diploidization from an allotetraploid ancestor with n = 14, characterized by independent descending dysploidy. We identify early-diverging (n = 8/6) and late-diverging (n = 9) genomes that share convergent and divergent features. While both clades show similar levels of gene fractionation and preferential retention of polyploidy-derived genes, the early-diverging genomes exhibit a higher solo-to-intact ratio of Ty3/Gypsy long terminal repeat retrotransposons and fewer conserved topologically associated domains (TADs). We also identify 14 chromosome breakpoints frequently located at TAD boundaries and often associated with transitions between A and B compartments. These results suggest that, although post-polyploid descending dysploidy appears to be independent and superficially stochastic, shared genomic features may predispose recurrent chromosome breakpoints across species.