Explanipedia

MedakaBase as a unified genomic resource platform for medaka fish biology Open

Kenji Morikami, Yasuhiro Tanizawa, Masaru Yagura, Mika Sakamoto, Shoko Kawamoto , et al. · 2025

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 stra…

Centromere methylation and genome divergence during vertebrate speciation Open

Shinichi Morishita, Yoshihiko Suzuki, Kazuki Ichikawa, Yusuke Inoue, Chie Owa , et al. · 2025

Medaka fish (Oryzias latipes) is a small freshwater teleost widely used as a model organism in developmental and evolutionary biology. Here, we generated complete and near-complete genome assemblies of three inbred medaka strains currently…

Empowering medaka fish biology with versatile genomic resources in MedakaBase Open

Kenji Morikami, Yasuhiro Tanizawa, Masaru Yagura, Mika Sakamoto, Shoko Kawamoto , et al. · 2025

Medaka, a group of small, mostly freshwater fishes in the teleost order Beloniformes, includes the rice fish Oryzias latipes , which is a prominent model organism for diverse biological fields. Chromosome-scale genome sequences of the Hd-r…

From Red Tides to Healthy Ecosystems by Nutrient Management in Ise Bay and Mikawa Bay Open

Ippei Noda, Shinako Iki, Kiyoshi Naruse · 2025

Ise Bay and Mikawa Bay, situated near major urban and industrial areas, have been increasingly affected by water pollution due to human activities. Over time, eutrophication—primarily driven by excess phosphorus (P) and nitrogen (N)—has le…

Natural genetic variation quantitatively regulates heart rate and dimension Open

Jakob Gierten, Bettina Welz, Tomas Fitzgerald, Thomas Thumberger, Rashi Agarwal , et al. · 2025

The polygenic contribution to heart development and function along the health-disease continuum remains unresolved. To gain insight into the genetic basis of quantitative cardiac phenotypes, we utilize highly inbred Japanese rice fish mode…

Discovery and characterisation of gene by environment and epistatic genetic effects in a vertebrate model Open

Bettina Welz, Saul Pierotti, Tomas Fitzgerald, Thomas Thumberger, Risa Suzuki , et al. · 2025

Phenotypic variation arises from the interplay between genetic and environmental factors. However, disentangling these interactions for complex traits remains challenging in observational cohorts such as human biobanks. Instead, model orga…

Photoperiod decoder 1 regulates seasonal changes in energy metabolism through the growth hormone signaling pathway Open

Tomoya Nakayama, T. Yamaguchi, Michiyo Maruyama, Satoshi Ansai, Makoto Kashima , et al. · 2025

Seasonal changes in metabolism are crucial for animals to adapt to annual environmental fluctuations. However, the molecular mechanisms underlying these adaptations remain poorly understood. Here, we identified a novel gene, photoperiod de…

A guide to the use of the Inter-University Bio-Backup Project (IBBP) for the sustainability of individual research, even in the event of natural disasters or other unexpected accidents Open

Kazuo Tsugane, Ai Kato, Naomi Matsubayashi, Kiyoshi Naruse · 2024

Modular control of vertebrate axis segmentation in time and space Open

Ali Seleit, Ian Brettell, Tomas Fitzgerald, Carina Beatrice Vibe, Felix Loosli , et al. · 2024

A transcriptional program underlying the circannual rhythms of gonadal development in medaka Open

Tomoya Nakayama, Miki Tanikawa, Yuki Okushi, Thoma Itoh, Tsuyoshi Shimmura , et al. · 2023

To cope with seasonal environmental changes, organisms have evolved approximately 1-y endogenous circannual clocks. These circannual clocks regulate various physiological properties and behaviors such as reproduction, hibernation, migratio…

Behavioral photosensitivity of multi-color-blind medaka: enhanced response under ultraviolet light in the absence of short-wavelength-sensitive opsins Open

Kiyono Mizoguchi, Mayu Sato, Rina Saito, Mayu Koshikuni, Mana Sakakibara , et al. · 2023

Background The behavioral photosensitivity of animals could be quantified via the optomotor response (OMR), for example, and the luminous efficiency function (the range of visible light) should largely rely on the repertoire and expression…

Congenital anaemia associated with loss-of-function variants in DNA polymerase epsilon 1 Open

Ichiro Takeuchi, Kanako Tanase‐Nakao, Ayame Ogawa, Tohru Sugawara, Osuke Migita , et al. · 2023

DNA polymerase epsilon (Pol ε), a component of the core replisome, is involved in DNA replication. Although genetic defects of Pol ε have been reported to cause immunodeficiency syndromes, its role in haematopoiesis remains unknown. Here, …

High-speed system to generate congenic strains in medaka Open

Minori Shinya, Tetsuaki Kimura, Kiyoshi Naruse · 2023

The congenic strain, an inbred strain containing a small genomic region from another strain, is a powerful tool to assess the phenotypic effect of polymorphisms and/or mutations in the substituted genomic region. Recent substantial progres…

A gene regulatory network combining Pax3/7, Sox10 and Mitf generates diverse pigment cell types in medaka and zebrafish Open

Motohiro Miyadai, Hiroyuki Takada, Akiko Shiraishi, Tetsuaki Kimura, Ikuko Watakabe , et al. · 2023

Neural crest cells generate numerous derivatives, including pigment cells, and are a model for studying how fate specification from multipotent progenitors is controlled. In mammals, the core gene regulatory network for melanocytes (their …

Modular control of time and space during vertebrate axis segmentation Open

Ali Seleit, Ian Brettell, Tomas Fitzgerald, Carina Beatrice Vibe, Felix Loosli , et al. · 2023

How temporal and spatial control of developmental processes are linked remains a fundamental question. Do underlying mechanisms form a single functional unit or are these dissociable modules? We address this question by studying the period…

Variation in responses to photoperiods and temperatures in Japanese medaka from different latitudes Open

Ai Shinomiya, Daisuke Adachi, Tsuyoshi Shimmura, Miki Tanikawa, Naoshi Hiramatsu , et al. · 2023

Seasonal changes are more robust and dynamic at higher latitudes than at lower latitudes, and animals sense seasonal changes in the environment and alter their physiology and behavior to better adapt to harsh winter conditions. However, th…

Pax3 and Pax7 function in combination with Mitf to generate melanophores and xanthophores in medaka and zebrafish Open

Motohiro Miyadai, Hiroyuki Takada, Akiko Shiraishi, Tetsuaki Kimura, Ikuko Watakabe , et al. · 2023

Neural crest cells generate numerous derivatives, including pigment cells, and are a model for studying how fate specification from multipotent progenitors is controlled. In mammals, the core gene regulatory network (GRN) for melanocytes (…

Evolutionary differentiation of androgen receptor is responsible for sexual characteristic development in a teleost fish Open

Yukiko Ogino, Satoshi Ansai, Eiji Watanabe, Masaki Yasugi, Yukitoshi Katayama , et al. · 2023

Retinal Cone Mosaic in sws1-Mutant Medaka (Oryzias latipes), A Teleost Open

Megumi Matsuo, Makoto Matsuyama, Tomoe Kobayashi, Shinji Kanda, Satoshi Ansai , et al. · 2022

Comparative observation of sws1-mutant and wild-type retinas revealed that ZPR1 negativity is not a marker for SSCs with SWS1, but SSCs themselves. Loss of functional sws1 did not cause retinal degeneration, indicating that sws1 is not ess…

Evolutionary differentiation of androgen receptor ohnologs is responsible for the development of androgen-dependent unique sexual characteristics in a teleost fish Open

Yukiko Ogino, Satoshi Ansai, Eiji Watanabe, Masaki Yasugi, Yukitoshi Katayama , et al. · 2022

Teleost fishes exhibit complex unique sexual characteristics, such as fin enlargement and courtship display, in response to androgens. However, the molecular mechanisms underlying their evolutionary acquisition remain largely unknown. To a…

Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open

Adrien Léger, Ian Brettell, Jack Monahan, Carl Barton, Nadeshda Wolf , et al. · 2022

The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open

Tomas Fitzgerald, Ian Brettell, Adrien Léger, Nadeshda Wolf, Natalja Kusminski , et al. · 2022

Additional file 9 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open

Adrien Léger, Ian Brettell, Jack Monahan, Carl Barton, Nadeshda Wolf , et al. · 2022

Additional file 9: Table S7. Differentially-methylated regions. Genome coordinates of all significant differentially-methylated regions in 12 MIKK panel lines.

Additional file 1 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open

Adrien Léger, Ian Brettell, Jack Monahan, Carl Barton, Nadeshda Wolf , et al. · 2022

Additional file 1: Table S1. Nanopore sequencing metrics. Metrics from ONT PromethION sequencing.

Additional file 1 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open

Tomas Fitzgerald, Ian Brettell, Adrien Léger, Nadeshda Wolf, Natalja Kusminski , et al. · 2022

Additional file 1: Table S1. MIKK panel lines. Table setting out all MIKK panel lines and the specific analyses each was included in.

Additional file 2 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open

Tomas Fitzgerald, Ian Brettell, Adrien Léger, Nadeshda Wolf, Natalja Kusminski , et al. · 2022

Additional file 2: Table S2. Fecundity data. Table with MIKK panel fecundity data.

Additional file 4 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open

Adrien Léger, Ian Brettell, Jack Monahan, Carl Barton, Nadeshda Wolf , et al. · 2022

Additional file 4: Table S3. Graph segment alignments to reference genomes. Percentage of graph segments aligned to HdrR, HNI, and HSOK reference genomes. and shared across 12 MIKK panel lines.

Additional file 7 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open

Adrien Léger, Ian Brettell, Jack Monahan, Carl Barton, Nadeshda Wolf , et al. · 2022

Additional file 7: Table S6. High-quality graph deletions. Genome coordinates for 16 MIKK panel-specific high quality graph deletions.

Additional file 3 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open

Tomas Fitzgerald, Ian Brettell, Adrien Léger, Nadeshda Wolf, Natalja Kusminski , et al. · 2022

Additional file 3: Table S3. Fish imaging parameters. Table with MIKK panel morphometric data.

Additional file 6 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel Open

Tomas Fitzgerald, Ian Brettell, Adrien Léger, Nadeshda Wolf, Natalja Kusminski , et al. · 2022

Additional file 6: Table S5. High confidence LoF variants. Table of homozygous high-confidence loss-of-function variants in the MIKK panel orthologous to a human dosage-sensitive gene.

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