Integrative multi-omics analysis reveals the genetic architecture of floral traits in <i>Anthurium</i>

<i>Anthurium</i>, a highly diverse genus in the family Araceae, is well known for its ornamental spathes and spadices. However, limited genomic resources hinder the study of floral traits and their evolutionary histories. Here, we present high-quality chromosome-level genome assemblies of <i>Anthurium andraeanum</i> and <i>Anthurium scherzerianum</i>. Comparative genomics revealed extensive chromosomal rearrangements and species-specific transposon expansions, which likely contributed to genome divergence. Two lineage-specific whole-genome duplications were identified, associated with gene family expansions linked to stress adaptation. Population structure analysis uncovered strong genetic admixture, reflecting widespread historical hybridization. Integrated transcriptomic and metabolomic analyses revealed dynamic regulatory networks governing spathe coloration through flavonoid-anthocyanin pathways. In addition, <i>CER3</i>, <i>KCS1</i>, and <i>KCS3</i> were identified as key regulators involved in wax biosynthesis. Notably, inflorescence evolution correlates with the loss of the floral identity genes <i>SOC1</i> and <i>AGL6</i>, highlighting conserved developmental pathways and lineage-specific innovations. Our findings provide foundational genomic resources for understanding <i>Anthurium</i> evolution, offer molecular targets for breeding programs, and elucidate transposon-driven genome expansion mechanisms that advance our knowledge of speciation in tropical epiphytes with exceptionally large genomes.