Integrative Multi-Omics Analysis Reveals the Genetic Architecture of the Floral Characteristics in Anthurium

Anthurium, a highly diverse genus in the Araceae family, is prized for its ornamental spathe and spadix. However, the lack of genomic resources has hindered the studies on its floral traits and evolution. Here, we present the first chromosome-level genomes of A. andraeanum and A. scherzerianum, revealing extensive chromosomal rearrangements and transposable element expansions. Comparative genomics identified two whole-genome duplications and lineage-specific gene family expansions linked to stress adaptation. Population analyses showed a highly admixed structure, reflecting extensive hybridization. Transcriptomic and metabolomic integration uncovered dynamic regulatory networks controlling spathe coloration via flavonoid-anthocyanin pathways and highlighted CER3, KCS1 and KCS3 as key wax biosynthesis regulators. Notably, the loss of SOC1 and AGL6 homologs highlights key transitions in inflorescence evolution. Our findings provide genomic foundations for understanding Anthurium evolution and improving ornamental traits.