Allopolyploids have successfully overcome ‘genome shock’, yet how their subgenomes adapt to coexistence remains largely unclear. Here, we constructed high-resolution epigenomic maps for the diploids Brassica rapa (ArAr) and Brassica oleracea (CoCo), and examined epigenomic variation in the allotetraploid Brassica napus (AnAnCnCn) relative to its putative progenitors. We discovered that coordinated genomic and epigenomic reprogramming in B. napus drove convergence of sequence and epigenomic features between An and Cn, significantly reducing expression divergence in homoeologs. Convergent homoeologs were functionally enriched in pathways related to genome stability and abiotic stress responses. Notably, Cn in B. napus exhibited greater sequence conservation and epigenetic homeostasis. Furthermore, transcription factor binding sites (TFBSs) affected by genomic variation in An showed convergent regulatory changes toward Cn, indicating that allopolyploids mitigate subgenomic conflicts through multilayered regulatory coordination. In conclusion, coordinated genomic and epigenomic convergence provides critical insights into the stability and adaptive evolution of allopolyploids.

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