Water lilies are among the most basal groups of angiosperms and retain many morphological and physiological traits of early angiosperms, making them invaluable for studying angiosperm evolution, particularly floral organ development. Here we present the most comprehensive phylogeny of the genus Nymphaea to date, alongside gap-free genome assemblies for three species (Nymphaea colorata, Nymphaea thermarum and Nymphaea caerulea). Our analyses resolve 2 major clades, day-flowering (section A) and night-flowering (section B), which diverged approximately 50 million years ago. Comparative genomics reveals an angiosperm-exclusive pectin lyase gene specifically expressed during pollen tube elongation. Regarding floral traits, we identify the transcription factor NcolMYB75-like as a master regulator of blue anthocyanin biosynthesis. Furthermore, the expansion and diversification of the O-methyltransferase gene family drive the synthesis of species-specific floral scent volatiles. These findings deepen our understanding of early angiosperm innovations and provide a genomic framework for plant breeding and ecological conservation.
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