Orchid genome evolution and trait innovation

Orchidaceae, one of the largest and most morphologically diverse angiosperm families, showcases unique evolutionary adaptations in morphology, ecology, and function. Recent advances in molecular and genomic research have greatly reshaped our understanding of orchid evolution, revealing how genome dynamics, ecological interactions, and developmental plasticity jointly shaped their exceptional diversification. Phylogenomic frameworks derived from various genomic datasets have reconstructed the evolutionary history, revealing the influence of geological, climatic, and biotic factors on ancient divergences and global distributions. Comprehensive genomic studies have uncovered substantial variation in genome size, structure, and composition, largely driven by repetitive elements and whole-genome duplication events that facilitated adaptive radiations. Key innovations, including epiphytism, mycoheterotrophy, and deceptive pollination, are linked to gene family evolution and modifications in pathways related to CAM photosynthesis, mycorrhizal symbiosis, and floral morphogenesis. Integrative multi-omics approaches further illuminate mechanisms underlying speciation hotspots, coevolution with pollinators and fungi, and the molecular basis of developmental diversity. Overall, this review synthesizes current genomic, phylogenetic, and functional insights into orchid evolution, providing a theoretical foundation and future research framework for understanding their molecular diversification.