Transcriptome analysis reveals that regulation network of the genes related to unique double flowers in tropical viviparous water lily.

Among tropical viviparous water lilies (Nymphaea L.), double-petaled cultivars are exceptionally rare, and the molecular mechanisms underlying their floral organ development remain largely unexplored. In this study, we identified Nymphaea 'Candy Rain' as the sole known tropical water lily cultivar exhibiting a double-petaled phenotype, characterized by complete petaloid conversion of innermost stamens. To elucidate the genetic basis of this unique floral morphology, we performed comparative transcriptome analysis of three distinct petal types in N. 'Candy Rain'. Our investigation further extended to comprehensive identification and characterization of MADS-box gene family members in the reference genome of the tropical viviparous water lily Nymphaea 'Paul Stetson'. Genome-wide analysis revealed 65 NcMADS-box genes unevenly distributed across 25 chromosomes. Phylogenetic and expression analyses implicated several MADS-box gene clades (particularly AGL6, AP2, and AG) in the development of the double-petaled phenotype. Additionally, our data suggest potential involvement of other transcription factor families including WOX, NAC, TCP, MYB, and bHLH in this specialized floral morphogenesis. Notably, we identified multiple phytohormone-related genes (such as IAA16, YUC6, and TCH4) that may participate in the formation of double-petaled flowers, indicating complex hormonal regulation of this trait in tropical viviparous water lilies.