Genomic and epigenomic coordination maintains subgenome transcriptional balance in allotetraploid Brassica napus

Abstract

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.

Acknowledgements

This work was supported by the National Natural Science Foundation of China (32222063 and 32370636 to L.Z., 31930032 to J.S., 32200471 to Q.Z.), the National Key Research and Development Program of China (2023YFF1000700 and 2021YFF1000100 to L.Z.). We thank the bioinformatics computing platform at National Key Laboratory of Crop Genetic Improvement in Huazhong Agricultural University.

Authors contributions

Conception and design: L.Z. and J.Z.; Data generation: M.M. with the assistance of Q.Z.; Data analysis: J.Z. with the assistance of S.N.; Data interpretation and paper writing: J.Z. and L.Z. with the assistance of M.M., Q.Z., H.Z., J.W., J.S., and T.F..

Data availability

Some B. napus data used in this study were derived from previously published datasets by our team (Table S8). The data for resynthesised B. napus and its diploid progenitors were also sourced from previously published studies [35]. All newly generated sequencing data have been deposited in NCBI GEO under the accession number GSE296743.

Conflicts of interest statement

The authors declare no competing interests.

Supplementary material

Supplementary material is available at Horticulture Research online.

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