Two telomere-to-telomere Nelumbo genome assemblies reveal domestication history and empower precision breeding.

Lotus (Nelumbo) is an ancient aquatic plant of major ecological, economic, and cultural importance, yet its genomic architecture and domestication history remain incompletely resolved. Here, we generate telomere-to-telomere reference genomes for the two extant species, Asian lotus (N. nucifera) and American lotus (N. lutea). Comparative genomics analysis reveals divergence in centromeric regions and chromosomal structural variation between the two species. Population analysis of 832 globally distributed lotus accessions supports tropical Asia as the primary dispersal cradle of Asian lotus. We detect historical introgression events contributing to modern cultivated gene pools, and identify key loci regulating flower color variation and rhizome enlargement. To support research and breeding, we develop the Nelumbo Multi-omics Genome Platform (NMGP; http://182.92.235.125:18888/lotus/home/ ), integrating multi-omics data with a Pearson correlation-weighted Fusion of machine learning Models for Genomic Prediction (PFMGP) framework. These resources provide foundation for studying lotus evolution and genome-informed breeding.