Chromosome‐scale genome assembly of the endangered aquatic plant Ottelia songmingensis elucidates genomic features and conservation implications

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.