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

    • 1Department of Computational Biology and Medical Sciences, The University of Tokyo, Chiba 277-8561, Japan;
    • 2Department of Biological Sciences, The University of Tokyo, Tokyo 113-0033, Japan;
    • 3Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka 411-8540, Japan;
    • 4Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan;
    • 5Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto 603-8555, Japan;
    • 6Sequencing Section, Core Facilities, Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan;
    • 7Algorithms for Ecological and Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan;
    • 8Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan;
    • 9Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga 526-0829, Japan;
    • 10Center for Bioscience Research and Education, Utsunomiya University, Tochigi 321-8505, Japan;
    • 11Laboratory of Bioresources, National Institute for Basic Biology, Aichi 444-8585, Japan;
    • 12Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Aichi 444-8585, Japan;
    • 13Department of Genetics, The Graduate University for Advanced Studies, Shizuoka 411-8540, Japan
    • Present addresses: 14Research Organization of Information and Systems (ROIS), Tokyo 105-0001, Japan; 15Rhelixa Inc., Tokyo 104-0042, Japan
Published July 1, 2026. https://doi.org/10.1101/gr.281813.125
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cover of Genome Research Vol 36 Issue 7
Current Issue:
July 2026, Vol. 36, No. 7
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Abstract

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.

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