Chromosome-scale genomes of water lilies provide evolutionary insights into the aquatic adaptation of angiosperms

Summary The origin and diversification of angiosperms, particularly their ancestral ecological niche, remain an enduring mystery. While competing hypotheses exist, the genomic mechanisms driving repeated transitions to aquatic life are poorly understood. We assembled chromosome-scale genomes for three early-diverging water lilies—Cabomba caroliniana, Barclaya longifolia, and Brasenia schreberi—integrating them with other Nymphaeales genomes for a comparative analysis. Our findings reveal that aquatic adaptation was shaped by ancient whole-genome duplications and functional remodeling of key gene modules. This includes the expansion of photosynthesis and stress-related families, the contraction of nucleotide-binding leucine-rich repeat (NLR) immune receptors, and metabolic reprogramming of terpene-squalene and other stress-associated secondary pathways. These modifications enhanced energy capture, immunity modulation, and resource efficiency in aquatic environments. Collectively, our results underscore the importance of secondary aquatic adaptation in early water lilies, demonstrating that their distinctive aquatic traits can be parsimoniously explained by evolutionary changes associated with adaptation to submerged habitats.