Complete sequencing of medaka genomes reveals the architecture of centromeric satellites, giant mobile elements, and sex chromosomes

Medaka ( Oryzias latipes ) is a small freshwater teleost widely used as a vertebrate model organism. Existing medaka reference genomes, however, contain many gaps and unresolved repetitive regions, hindering precise genome annotation and comparative analyses. Here we present one complete and two near-complete genome assemblies for three inbred medaka strains derived from geographically distant populations. These assemblies provide a comprehensive view of highly repetitive sequences and chromosome-scale genome architecture in medaka. The fully resolved centromeres reveal an intriguing sequence organization characterized by short, distinct SF1+3 satellite arrays flanked by larger homogenized repeats. These short arrays are putatively hypomethylated and conserved across all acrocentric chromosomes, suggesting a functional role in centromere stability. The reconstructed 121 copies of the giant mobile element Teratorn retain complete genes of both a transposon and a herpesvirus, highlighting its unique persistence and impact on host genomes. Moreover, our assemblies reveal extensive structural divergence of medaka Y Chromosomes, yet identify a small (∼24 kb) conserved region encompassing Dmy that may suffice for male determination. Collectively, these (near-)complete medaka genomes provide a powerful resource for exploring the biology of uncharacterized repetitive regions and the molecular basis of phenotypic diversity in vertebrates.