start-ver=1.4
cd-journal=joma
no-vol=32
cd-vols=
no-issue=6
article-no=
start-page=dsaf030
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2025
dt-pub=20251022
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=MedakaBase as a unified genomic resource platform for medaka fish biology
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=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.
en-copyright=
kn-copyright=

en-aut-name=MorikamiKenji
en-aut-sei=Morikami
en-aut-mei=Kenji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=TanizawaYasuhiro
en-aut-sei=Tanizawa
en-aut-mei=Yasuhiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=YaguraMasaru
en-aut-sei=Yagura
en-aut-mei=Masaru
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=SakamotoMika
en-aut-sei=Sakamoto
en-aut-mei=Mika
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=KawamotoShoko
en-aut-sei=Kawamoto
en-aut-mei=Shoko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=NakamuraYasukazu
en-aut-sei=Nakamura
en-aut-mei=Yasukazu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

en-aut-name=YamaguchiKatsushi
en-aut-sei=Yamaguchi
en-aut-mei=Katsushi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=

en-aut-name=ShigenobuShuji
en-aut-sei=Shigenobu
en-aut-mei=Shuji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=

en-aut-name=NaruseKiyoshi
en-aut-sei=Naruse
en-aut-mei=Kiyoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=

en-aut-name=AnsaiSatoshi
en-aut-sei=Ansai
en-aut-mei=Satoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=

en-aut-name=KurakuShigehiro
en-aut-sei=Kuraku
en-aut-mei=Shigehiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=

affil-num=1
en-affil=Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Research Organization of Information and Systems
kn-affil=

affil-num=2
en-affil=Genome Informatics Laboratory, National Institute of Genetics, Research Organization of Information and Systems
kn-affil=

affil-num=3
en-affil=Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Research Organization of Information and Systems
kn-affil=

affil-num=4
en-affil=Genome Informatics Laboratory, National Institute of Genetics, Research Organization of Information and Systems
kn-affil=

affil-num=5
en-affil=Department of Genetics, Sokendai (Graduate University for Advanced Studies)
kn-affil=

affil-num=6
en-affil=Genome Informatics Laboratory, National Institute of Genetics, Research Organization of Information and Systems
kn-affil=

affil-num=7
en-affil=Trans-Omics Facility, National Institute for Basic Biology
kn-affil=

affil-num=8
en-affil=Trans-Omics Facility, National Institute for Basic Biology
kn-affil=

affil-num=9
en-affil=Laboratory of Bioresources, National Institute for Basic Biology, National Institutes of Natural Sciences
kn-affil=

affil-num=10
en-affil=Ushimado Marine Institute, Okayama University
kn-affil=

affil-num=11
en-affil=Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Research Organization of Information and Systems
kn-affil=
en-keyword=medaka
kn-keyword=medaka
en-keyword=comparative genomics
kn-keyword=comparative genomics
en-keyword=genome browser
kn-keyword=genome browser
en-keyword=MedakaBase
kn-keyword=MedakaBase
en-keyword=Beloniformes
kn-keyword=Beloniformes
END