# Integrative multi-omics analysis reveals the genetic architecture of floral traits in Anthurium

## TL;DR

This study provides high-quality genome assemblies for two Anthurium species and reveals genetic factors influencing floral traits and evolution.

## Contribution

The paper presents chromosome-level genome assemblies and identifies key genes and transposon-driven mechanisms in Anthurium evolution.

## Key findings

- Genome assemblies revealed chromosomal rearrangements and transposon expansions contributing to genome divergence.
- Lineage-specific gene family expansions linked to stress adaptation were identified.
- Flavonoid–anthocyanin pathways and wax biosynthesis regulators were found to govern spathe coloration.

## Abstract

Anthurium, 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 Anthurium andraeanum and Anthurium scherzerianum. 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, CER3, KCS1, and KCS3 were identified as key regulators involved in wax biosynthesis. Notably, inflorescence evolution correlates with the loss of the floral identity genes SOC1 and AGL6, highlighting conserved developmental pathways and lineage-specific innovations. Our findings provide foundational genomic resources for understanding Anthurium 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.