2026/01/18 by Zhi‐Zhong Li, Zhi‐Hao Qian, Wei Li +1 · 1 voice
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Chromosomal and Genetic Variations #Genome Rearrangement Algorithms #Genomics and Phylogenetic Studies
paper · doi:10.1111/jse.70043
openalex publication_date 2026/01/18 · openalex created_date 2026/01/20 · openalex updated_date 2026/07/28
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.