Uncovering the genome evolutionary dynamics of the Mediterranean endemic palm Chamaerops humilis

Background: Chamaerops humilis L. is the only endemic palm species of the western Mediterranean. Here, we present a de novo genome assembly with structural and functional annotation that reveals major structural changes shaping the evolutionary history of this species. Results: The genome, estimated at 3.44 Gbp, comprises 41,738 genes and 2.87 Gbp of repetitive elements. Evolutionary analyses identified a whole-genome duplication event ~ 48.0 Mya, shared with other palms, followed by divergence from its sister genus Phoenix ~ 16.6 Mya. Functional enrichment of rapidly evolving genes highlighted associations with genome plasticity and stress response pathways. Analyses of gene duplication types and KS distributions uncovered recent lineage-specific duplication waves and C. humilis-exclusive duplicated genes, providing novel insights into palm genome evolution and the adaptive potential of this Mediterranean endemic. Conclusions: This study provides a high-quality reference genome for C. humilis and insights into the possible genomic basis for Mediterranean adaptation. Future work combining comparative genomics, pangenomics, and functional studies will be key to fully understanding its evolution.