Abstract: Aquatic angiosperms represent an important but underexplored lineage for understanding genome evolution, particularly in species with exceptionally large genomes. Here, we present a chromosome-scale genome assembly of the endangered aquatic monocot Ottelia songmingensis (~10.8 Gb), providing a valuable genomic resource for studying genome gigantism and conservation. Using ONT and Hi-C technologies, we anchored 87.7% of the assembly to 11 pseudochromosomes and predicted 35362 protein-coding genes. Comparative genomics revealed two whole-genome duplication events, including a more recent duplication and an ancestral triplication shared within Alismatidae. Repetitive elements constitute 94.3% of the genome, with long terminal repeat retrotransposons alone accounting for over 90%. A recent burst of LTR activity (~6 Mya) combined with a low solo-to-intact ratio (0.61) suggests inefficient transposon removal as a driver of genome expansion. Whole-genome bisulfite sequencing showed globally high DNA methylation levels (CG ~ 85%, CHG ~ 78%), particularly enriched in transposable element-rich regions, highlighting the role of epigenetic regulation in stabilizing large genomes. Population resequencing further indicated extremely low nucleotide diversity (π = 5.31 × 10⁻⁴) and a long-term decline in effective population size since the Middle Pleistocene. Together, these resources provide a genomic foundation for exploring the evolutionary forces underlying genome gigantism and for guiding conservation genomics in endangered aquatic plants.

Key words: endangered monocots, genome stability, ottelia songmingensis, whole-genome duplication