Centromere organization and epigenetic regulation in Aristolochia fimbriata

BACKGROUND: Aristolochia fimbriata (A. fimbriata), a magnoliid species similar to Amborella trichopoda, has not undergone additional whole genome duplications since the origin of extant flowering plants. Due to its low genetic redundancy and suitability for large-scale cultivation, A. fimbriata emerges as an exceptional reference and potential model species for comparative and functional genomic studies of angiosperm evolution. RESULTS: Here, we present a complete telomere-to-telomere (T2T) genome assembly of A. fimbriata and characterize its centromeric architecture and epigenetic landscape. Our analysis reveals remarkably short (34-bp) and highly homogenized satellite monomers in its centromeric regions. Furthermore, we identify approximately 1,020 topologically associating domain-like structures and 23,852 non-redundant accessible chromatin regions. Notably, over 50% of accessible chromatin regions participate in long-range chromatin loops that bypass at least one intervening gene, suggesting widespread distal gene regulation in this species. We also demonstrate that an expanded downstream regulatory network of the floral B-class gene APETALA3 (AP3) may contribute to the highly specialized floral features in A. fimbriata. CONCLUSION: Our study not only elucidates the unique centromeric organization and three-dimensional epigenomic architecture of A. fimbriata, but also provides valuable genomic resources for investigating how regulatory network evolution drives phenotypic innovation in flowering plants.