Oxford University Press (OUP) Acta Medica Okayama 1340-2838 32 6 2025 MedakaBase as a unified genomic resource platform for medaka fish biology dsaf030 EN Kenji Morikami Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Research Organization of Information and Systems Yasuhiro Tanizawa Genome Informatics Laboratory, National Institute of Genetics, Research Organization of Information and Systems Masaru Yagura Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Research Organization of Information and Systems Mika Sakamoto Genome Informatics Laboratory, National Institute of Genetics, Research Organization of Information and Systems Shoko Kawamoto Department of Genetics, Sokendai (Graduate University for Advanced Studies) Yasukazu Nakamura Genome Informatics Laboratory, National Institute of Genetics, Research Organization of Information and Systems Katsushi Yamaguchi Trans-Omics Facility, National Institute for Basic Biology Shuji Shigenobu Trans-Omics Facility, National Institute for Basic Biology Kiyoshi Naruse Laboratory of Bioresources, National Institute for Basic Biology, National Institutes of Natural Sciences Satoshi Ansai Ushimado Marine Institute, Okayama University Shigehiro Kuraku Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Research Organization of Information and Systems Medaka, a group of small, mostly freshwater fishes in the teleost order Beloniformes, includes the rice fish Oryzias latipes, a useful model organism studied in diverse biological fields. Chromosome-scale genome sequences of the Hd-rR strain of this species were obtained in 2007, and its improved version has facilitated various genome-wide studies. However, despite its widespread utility, omics data for O. latipes are dispersed across various public databases and lack a unified platform. To address this, the medaka section of the National Bioresource Project (NBRP) of Japan established a genome informatics team in 2022 tasked with providing various in silico solutions for bench biologists. This initiative led to the launch of MedakaBase (https://medakabase.nbrp.jp), a web server that enables gene-oriented analysis including exhaustive sequence similarity searches. MedakaBase also provides on-demand browsing of diverse genome-wide datasets, including tissue-specific transcriptomes and intraspecific genomic variations, integrated with gene models from different sources. Additionally, the platform offers gene models optimized for single-cell transcriptome analysis, which often requires coverage of the 3′ untranslated region (UTR) of transcripts. Currently, MedakaBase provides genome-wide data for seven Oryzias species, including original data for O. mekongensis and O. luzonensis produced by the NBRP team. This article outlines technical details behind the data provided by MedakaBase. No potential conflict of interest relevant to this article was reported.