Empowering medaka fish biology with versatile genomic resources in MedakaBase

Medaka, a group of small, mostly freshwater fishes in the teleost order Beloniformes, includes the rice fishOryzias latipes, which is a prominent model organism for 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 forO. latipesare dispersed across various public databases and lack a centralized 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 versatilein silicosolutions for bench biologists. This initiative led to the launch of MedakaBase (<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://medakabase.nbrp.jp">https://medakabase.nbrp.jp</ext-link>), a web server that enables gene-oriented analysis including exhaustive sequence similarity searches. MedakaBase also provides genome-wide browsing of diverse 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 sevenOryziasspecies, including original data forO. mekongensisandO. luzonensisproduced by the NBRP team. This article outlines technical details behind the data provided by MedakaBase.