Complete sequencing of medaka genomes reveals the architecture of centromeric satellites, giant mobile elements, and sex chromosomes
Yoshihiko Suzuki, Kazuki Ichikawa, Yusuke Inoue, Chie Owa, Haruka Kobayashi, Kenji Morikami, Ryohei Nakamura, Takafumi Ikeda, Manabu Fujie, Mayumi Kawamitsu, Nana Arakaki, Eugene W. Myers, Hiroyuki Aburatani, Yusuke Takehana, Masaru Matsuda, Kiyoshi Naruse, Shigehiro Kuraku, Hiroyuki Takeda, Shinichi MorishitaMedaka (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.