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

Author

Ogino, Yukiko, Ansai, Satoshi, Watanabe, Eiji, Yasugi, Masaki, Katayama, Yukitoshi, Sakamoto, Hirotaka, Okamoto, Keigo, Okubo, Kataaki, Yamamoto, Yasuhiro, Hara, Ikuyo, Yamazaki, Touko, Kato, Ai, Kamei, Yasuhiro, Naruse, Kiyoshi, Ohta, Kohei, Ogino, Hajime, Sakamoto, Tatsuya, Miyagawa, Shinichi, Sato, Tomomi, Yamada, Gen, Baker, Michael E., and Iguchi, Taisen

Published
2023
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7. Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

Author

Leger, Adrien, Brettell, Ian, Monahan, Jack, Barton, Carl, Wolf, Nadeshda, Kusminski, Natalja, Herder, Cathrin, Aadepu, Narendar, Becker, Clara, Gierten, Jakob, Hammouda, Omar T., Hasel, Eva, Lischik, Colin, Lust, Katharina, Sokolova, Natalia, Suzuki, Risa, Tavhelidse, Tinatini, Thumberger, Thomas, Tsingos, Erika, Watson, Philip, Welz, Bettina, Naruse, Kiyoshi, Loosli, Felix, Wittbrodt, Joachim, Birney, Ewan, and Fitzgerald, Tomas

Published
2022
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8. The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

Author

Fitzgerald, Tomas, Brettell, Ian, Leger, Adrien, Wolf, Nadeshda, Kusminski, Natalja, Monahan, Jack, Barton, Carl, Herder, Cathrin, Aadepu, Narendar, Gierten, Jakob, Becker, Clara, Hammouda, Omar T., Hasel, Eva, Lischik, Colin, Lust, Katharina, Sokolova, Natalia, Suzuki, Risa, Tsingos, Erika, Tavhelidse, Tinatini, Thumberger, Thomas, Watson, Philip, Welz, Bettina, Khouja, Nadia, Naruse, Kiyoshi, Birney, Ewan, Wittbrodt, Joachim, and Loosli, Felix

Published
2022
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10. Sexually dimorphic role of oxytocin in medaka mate choice

Author

Yokoi, Saori, Naruse, Kiyoshi, Kamei, Yasuhiro, Ansai, Satoshi, Kinoshita, Masato, Mito, Mari, Iwasaki, Shintaro, Inoue, Shuntaro, Okuyama, Teruhiro, Nakagawa, Shinichi, Young, Larry J., and Takeuchi, Hideaki

Published
2020

12. Contributors

Author

Allen, Claire, primary, Argenton, Francesco, additional, Astre, Gwendoline, additional, Baumann, Diana P., additional, Beata, Filipek-Górniok, additional, Bischof, John, additional, Blaker, Ellen, additional, Blanco, Ayelén M., additional, Blažek, Radim, additional, Brocca, Marco, additional, D'Angelo, Livia, additional, de Girolamo, Paolo, additional, Del Bene, Filippo, additional, Duroure, Karine, additional, Dyková, Iva, additional, Ellis, Tim, additional, Fujimori, Chika, additional, Gerlai, Robert, additional, Harel, Itamar, additional, Ingalls, Andrew, additional, Ishikawa, Tokiro, additional, Kanda, Shinji, additional, Katsiadaki, Ioanna, additional, Kayo, Daichi, additional, Khosla, Kanav, additional, Kinoshita, Masato, additional, Köhler, Almut, additional, Lars, Bräutigam, additional, Mocho, Jean-Philippe, additional, Moses, Eitan, additional, Murakami, Yu, additional, Nakajo, Mikoto, additional, Naruse, Kiyoshi, additional, Newell, Bruce, additional, Oka, Yoshitaka, additional, Oltova, Jana, additional, Pereira, Nuno, additional, Polačik, Matej, additional, Rajan, Gokul, additional, Reichard, Martin, additional, Schroeder, Paul Georg, additional, Sebire, Marion, additional, Tiso, Natascia, additional, Tsang, Benjamin, additional, Umatani, Chie, additional, Unniappan, Suraj, additional, Valentim, Ana M., additional, Van Eeden, Fredericus J., additional, Varga, Zoltán M., additional, and Žák, Jakub, additional

Published
2022
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13. Genomic and phenotypic characterisation of a wild Medaka population: Establishing an isogenic population genetic resource in fish

Author

Spivakov, Mikhail, Auer, Thomas O., Peravali, Ravindra, Dunham, Ian, Dolle, Dirk, Fujiyama, Asao, Toyoda, Atsushi, Aizu, Tomoyuki, Minakuchi, Yohei, Loosli, Felix, Naruse, Kiyoshi, Birney, Ewan, and Wittbrodt, Joachim

Subjects
Quantitative Biology - Genomics, Quantitative Biology - Populations and Evolution
Abstract

Background Oryzias latipes (Medaka) has been established as a vertebrate genetic model for over a century, and has recently been rediscovered outside its native Japan. The power of new sequencing methods now makes it possible to reinvigorate Medaka genetics, in particular by establishing a near-isogenic panel derived from a single wild population. Results Here we characterise the genomes of wild Medaka catches obtained from a single Southern Japanese population in Kiyosu as a precursor for the establishment of a near isogenic panel of wild lines. The population is free of significant detrimental population structure, and has advantageous linkage disequilibrium properties suitable for establishment of the proposed panel. Analysis of morphometric traits in five representative inbred strains suggests phenotypic mapping will be feasible in the panel. In addition high throughput genome sequencing of these Medaka strains confirms their evolutionary relationships on lines of geographic separation and provides further evidence that there has been little significant interbreeding between the Southern and Northern Medaka population since the Southern/Northern population split. The sequence data suggest that the Southern Japanese Medaka existed as a larger older population which went through a relatively recent bottleneck around 10,000 years ago. In addition we detect patterns of recent positive selection in the Southern population. Conclusions These data indicate that the genetic structure of the Kiyosu Medaka samples are suitable for the establishment of a vertebrate near isogenic panel and therefore inbreeding of 200 lines based on this population has commenced. Progress of this project can be tracked at http://www.ebi.ac.uk/birney-srv/medaka-ref-panel, Comment: 5 figures, 30 pages

Published
2013

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

Author

Takeuchi, Ichiro, primary, Tanase-Nakao, Kanako, additional, Ogawa, Ayame, additional, Sugawara, Tohru, additional, Migita, Osuke, additional, Kashima, Makoto, additional, Yamazaki, Touko, additional, Iguchi, Akihiro, additional, Naiki, Yasuhiro, additional, Uchiyama, Toru, additional, Tamaoki, Junya, additional, Maeda, Hiroki, additional, Shimizu, Hirotaka, additional, Kawai, Toshinao, additional, Taniguchi, Kosuke, additional, Hirata, Hiromi, additional, Kobayashi, Makoto, additional, Matsumoto, Kimikazu, additional, Naruse, Kiyoshi, additional, Hata, Kenichiro, additional, Akutsu, Hidenori, additional, Kato, Takashi, additional, Narumi, Satoshi, additional, Arai, Katsuhiro, additional, and Ishiguro, Akira, additional

Published
2023
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17. A gene regulatory network combining Pax3/7, Sox10 and Mitf generates diverse pigment cell types in medaka and zebrafish

Author

Miyadai, Motohiro, primary, Takada, Hiroyuki, additional, Shiraishi, Akiko, additional, Kimura, Tetsuaki, additional, Watakabe, Ikuko, additional, Kobayashi, Hikaru, additional, Nagao, Yusuke, additional, Naruse, Kiyoshi, additional, Higashijima, Shin-ichi, additional, Shimizu, Takashi, additional, Kelsh, Robert N., additional, Hibi, Masahiko, additional, and Hashimoto, Hisashi, additional

Published
2023
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26. Production of the medaka derived from vitrified whole testes by germ cell transplantation

Author

Seki, Shinsuke, Kusano, Kazunari, Lee, Seungki, Iwasaki, Yoshiko, Yagisawa, Masaru, Ishida, Mariko, Hiratsuka, Tadashi, Sasado, Takao, Naruse, Kiyoshi, Yoshizaki, Goro, Seki, Shinsuke, Kusano, Kazunari, Lee, Seungki, Iwasaki, Yoshiko, Yagisawa, Masaru, Ishida, Mariko, Hiratsuka, Tadashi, Sasado, Takao, Naruse, Kiyoshi, and Yoshizaki, Goro

Abstract

The medaka (Oryzias latipes) is a teleost model distinguished from other model organisms by the presence of inbred strains, wild stocks, and related species. Cryopreservation guarantees preservation of these unique biological resources. However, because of their large size, cryopreservation techniques for their eggs and embryos have not been established. In the present study, we established a methodology to produce functional gametes from cryopreserved testicular cells (TCs). Whole testes taken from medaka were cryopreserved by vitrification. After thawing, the cells dissociated from cryopreserved testicular tissues were intraperitoneally transplanted into sterile triploid hatchlings. Some cells, presumably spermatogonial stem cells, migrated into the genital ridges of recipients and resulted in the production of eggs or sperm, based on sex of the recipient. Mating of recipients resulted in successful production of cryopreserved TC-derived offspring. We successfully produced individuals from the Kaga inbred line, an endangered wild population in Tokyo, and a sub-fertile mutant (wnt4b(-/-)) from cryopreserved their TCs. This methodology facilitates semi-permanent preservation of various medaka strains.

Published
2023

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

Author

Takeuchi, Ichiro, Tanase-Nakao, Kanako, Ogawa, Ayame, Sugawara, Tohru, Migita, Osuke, Kashima, Makoto, Yamazaki, Touko, Iguchi, Akihiro, Naiki, Yasuhiro, Uchiyama, Toru, Tamaoki, Junya, Maeda, Hiroki, Shimizu, Hirotaka, Kawai, Toshinao, Taniguchi, Kosuke, Hirata, Hiromi, Kobayashi, Makoto, Matsumoto, Kimikazu, Naruse, Kiyoshi, Hata, Kenichiro, Akutsu, Hidenori, Kato, Takashi, Narumi, Satoshi, Arai, Katsuhiro, and Ishiguro, Akira

Abstract

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, we identified compound heterozygous variants (p.[Asp1131fs];[Thr1891del]) in POLE, encoding Pol ε catalytic subunit A (POLE1), in siblings with a syndromic form of severe congenital transfusion-dependent anaemia. In contrast to Diamond-Blackfan anaemia, marked reticulocytopenia or marked erythroid hypoplasia was not found. Their bone marrow aspirates during infancy revealed erythroid dysplasia with strongly positive TP53 in immunostaining. Repetitive examinations demonstrated trilineage myelodysplasia within 2 years from birth. They had short stature and facial dysmorphism. HEK293 cell-based expression experiments and analyses of patient-derived induced pluripotent stem cells (iPSCs) disclosed a reduced mRNA level of Asp1131fs-POLE1 and defective nuclear translocation of Thr1891del-POLE1. Analysis of iPSCs showed compensatory mRNA upregulation of the other replisome components and increase of the TP53 protein, both suggesting dysfunction of the replisome. We created Pole-knockout medaka fish and found that heterozygous fishes were viable, but with decreased RBCs. Our observations expand the phenotypic spectrum of the Pol ε defect in humans, additionally providing unique evidence linking Pol ε to haematopoiesis.

Published
2024
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30. Ghost introgression in ricefishes of the genus Adrianichthys in an ancient Wallacean lake.

Author

Yamahira, Kazunori, Kobayashi, Hirozumi, Kakioka, Ryo, Montenegro, Javier, Masengi, Kawilarang W. A., Okuda, Noboru, Nagano, Atsushi J., Tanaka, Rieko, Naruse, Kiyoshi, Tatsumoto, Shoji, Go, Yasuhiro, Ansai, Satoshi, and Kusumi, Junko

Subjects
INTROGRESSION (Genetics), REPRODUCTIVE isolation, LAKES, GENE flow, GENETIC speciation
Abstract

Because speciation might have been promoted by ancient introgression from an extinct lineage, it is important to detect the existence of 'ghost introgression' in focal taxa and examine its contribution to their diversification. In this study, we examined possible ghost introgression and its contributions to the diversification of ricefishes of the genus Adrianichthys in Lake Poso, an ancient lake on Sulawesi Island, in which some extinctions are known to have occurred. Population‐genomic analysis revealed that two extant Adrianichthys species, A. oophorus and A. poptae are reproductively isolated from each other. Comparisons of demographic models demonstrated that introgression from a ghost population, which diverged from the common ancestor of A. oophorus and A. poptae, is essential for reconstructing the demographic history of Adrianichthys. The best model estimated that the divergence of the ghost population greatly predated the divergence between A. oophorus and A. poptae, and that the ghost population secondarily contacted the two extant species within Lake Poso more recently. Genome scans and simulations detected a greatly divergent locus, which cannot be explained without ghost introgression. This locus was also completely segregated between A. oophorus and A. poptae. These findings suggest that variants that came from a ghost population have contributed to the divergence between A. oophorus and A. poptae, but the large time‐lag between their divergence and ghost introgression indicates that the contribution of introgression may be restricted. [ABSTRACT FROM AUTHOR]

Published
2023
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33. Development of a screening system for agents that modulate taste receptor expression with the CRISPR-Cas9 system in medaka

Author

Beppu, Kana, Tsutsumi, Rie, Ansai, Satoshi, Ochiai, Nana, Terakawa, Mai, Mori, Marie, Kuroda, Masashi, Horikawa, Kazuki, Tomoi, Takumi, Sakamoto, Joe, Kamei, Yasuhiro, Naruse, Kiyoshi, and Sakaue, Hiroshi

Subjects
CRISPR-Cas9 system, taste 1 receptor 3, fungi, monosodium glutamate, 5-fluorouracil, dysgeusia, medaka (Oryzias latipes)
Abstract

Taste recognition mediated by taste receptors is critical for the survival of animals in nature and is an important determinant of nutritional status and quality of life in humans. However, many factors including aging, diabetes, zinc deficiency, infection with influenza or cold viruses, and chemotherapy can trigger dysgeusia, for which a standard treatment has not been established. We here established an engineered strain of medaka (Oryzias latipes) that expresses green fluorescent protein (GFP) from the endogenous taste 1 receptor 3 (T1R3) gene locus with the use of the CRISPR-Cas9 system. This T1R3-GFP knock-in (KI) strain allows direct visualization of expression from this locus by monitoring of GFP fluorescence. The pattern of GFP expression in the T1R3-GFP KI fish thus mimicked that of endogenous T1R3 gene expression. Furthermore, exposure of T1R3-GFP KI medaka to water containing monosodium glutamate or the anticancer agent 5-fluorouracil resulted in an increase or decrease, respectively, in GFP fluorescence intensity, effects that also recapitulated those on T1R3 mRNA abundance. Finally, screening for agents that affect GFP fluorescence intensity in T1R3-GFP KI medaka identified tryptophan as an amino acid that increases T1R3 gene expression. The establishment of this screening system for taste receptor expression in medaka provides a new tool for the development of potential therapeutic agents for dysgeusia.

Published
2022

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

Author

Matsuo, Megumi, primary, Matsuyama, Makoto, additional, Kobayashi, Tomoe, additional, Kanda, Shinji, additional, Ansai, Satoshi, additional, Kawakami, Taichi, additional, Hosokawa, Erika, additional, Daido, Yutaka, additional, Kusakabe, Takehiro G., additional, Naruse, Kiyoshi, additional, and Fukamachi, Shoji, additional

Published
2022
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39. Evolutionary differentiation of androgen receptor ohnologs is responsible for the development of androgen-dependent unique sexual characteristics in a teleost fish

Author

Ogino, Yukiko, primary, Ansai, Satoshi, additional, Watanabe, Eiji, additional, Yasugi, Masaki, additional, Katayama, Yukitoshi, additional, Sakamoto, Hirotaka, additional, Okamoto, Keigo, additional, Okubo, Kataaki, additional, Yamamoto, Yasuhiro, additional, HARA, Ikuyo, additional, Yamazaki, Touko, additional, Kato, Ai, additional, Kamei, Yasuhiro, additional, Naruse, Kiyoshi, additional, Ohta, Kohei, additional, Ogino, Hajime, additional, Sakamoto, Tatsuya, additional, Miyagawa, Shinichi, additional, SATO, TOMOMI, additional, Yamada, Gen, additional, Baker, Michael, additional, and Iguchi, Taisen, additional

Published
2022
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43. Additional file 10 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

Author

Leger, Adrien, Brettell, Ian, Monahan, Jack, Barton, Carl, Wolf, Nadeshda, Kusminski, Natalja, Herder, Cathrin, Aadepu, Narendar, Becker, Clara, Gierten, Jakob, Hammouda, Omar T., Hasel, Eva, Lischik, Colin, Lust, Katharina, Sokolova, Natalia, Suzuki, Risa, Tavhelidse, Tinatini, Thumberger, Thomas, Tsingos, Erika, Watson, Philip, Welz, Bettina, Naruse, Kiyoshi, Loosli, Felix, Wittbrodt, Joachim, Birney, Ewan, and Fitzgerald, Tomas

Abstract

Additional file 10. Review history.

Published
2022
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44. Additional file 8 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

Author

Leger, Adrien, Brettell, Ian, Monahan, Jack, Barton, Carl, Wolf, Nadeshda, Kusminski, Natalja, Herder, Cathrin, Aadepu, Narendar, Becker, Clara, Gierten, Jakob, Hammouda, Omar T., Hasel, Eva, Lischik, Colin, Lust, Katharina, Sokolova, Natalia, Suzuki, Risa, Tavhelidse, Tinatini, Thumberger, Thomas, Tsingos, Erika, Watson, Philip, Welz, Bettina, Naruse, Kiyoshi, Loosli, Felix, Wittbrodt, Joachim, Birney, Ewan, and Fitzgerald, Tomas

Abstract

Additional file 8: Figure S6. Circos plots. Circos plots for structural variants (DEL, INS, DUP, INV, TRA) discovered by the reference-anchored approach.

Published
2022
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45. Additional file 10 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

Author

Fitzgerald, Tomas, Brettell, Ian, Leger, Adrien, Wolf, Nadeshda, Kusminski, Natalja, Monahan, Jack, Barton, Carl, Herder, Cathrin, Aadepu, Narendar, Gierten, Jakob, Becker, Clara, Hammouda, Omar T., Hasel, Eva, Lischik, Colin, Lust, Katharina, Sokolova, Natalia, Suzuki, Risa, Tsingos, Erika, Tavhelidse, Tinatini, Thumberger, Thomas, Watson, Philip, Welz, Bettina, Khouja, Nadia, Naruse, Kiyoshi, Birney, Ewan, Wittbrodt, Joachim, and Loosli, Felix

Abstract

Additional file 10. Review history.

Published
2022
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46. Additional file 8 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

Author

Fitzgerald, Tomas, Brettell, Ian, Leger, Adrien, Wolf, Nadeshda, Kusminski, Natalja, Monahan, Jack, Barton, Carl, Herder, Cathrin, Aadepu, Narendar, Gierten, Jakob, Becker, Clara, Hammouda, Omar T., Hasel, Eva, Lischik, Colin, Lust, Katharina, Sokolova, Natalia, Suzuki, Risa, Tsingos, Erika, Tavhelidse, Tinatini, Thumberger, Thomas, Watson, Philip, Welz, Bettina, Khouja, Nadia, Naruse, Kiyoshi, Birney, Ewan, Wittbrodt, Joachim, and Loosli, Felix

Subjects
mental disorders, population characteristics, human activities, geographic locations, humanities
Abstract

Additional file 8: Figure S9. Copenhagen plot. Plot showing genomic positions of significant eQTL SNPs.

Published
2022
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47. Additional file 2 of Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

Author

Leger, Adrien, Brettell, Ian, Monahan, Jack, Barton, Carl, Wolf, Nadeshda, Kusminski, Natalja, Herder, Cathrin, Aadepu, Narendar, Becker, Clara, Gierten, Jakob, Hammouda, Omar T., Hasel, Eva, Lischik, Colin, Lust, Katharina, Sokolova, Natalia, Suzuki, Risa, Tavhelidse, Tinatini, Thumberger, Thomas, Tsingos, Erika, Watson, Philip, Welz, Bettina, Naruse, Kiyoshi, Loosli, Felix, Wittbrodt, Joachim, Birney, Ewan, and Fitzgerald, Tomas

Abstract

Additional file 2: Figures S1-S5. Supplementary figures. Various supplementary figures.

Published
2022
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48. Additional file 4 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

Author

Fitzgerald, Tomas, Brettell, Ian, Leger, Adrien, Wolf, Nadeshda, Kusminski, Natalja, Monahan, Jack, Barton, Carl, Herder, Cathrin, Aadepu, Narendar, Gierten, Jakob, Becker, Clara, Hammouda, Omar T., Hasel, Eva, Lischik, Colin, Lust, Katharina, Sokolova, Natalia, Suzuki, Risa, Tsingos, Erika, Tavhelidse, Tinatini, Thumberger, Thomas, Watson, Philip, Welz, Bettina, Khouja, Nadia, Naruse, Kiyoshi, Birney, Ewan, Wittbrodt, Joachim, and Loosli, Felix

Abstract

Additional file 4: Figures S1-S8. Supplementary figures. Various supplementary figures.

Published
2022
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49. Additional file 9 of The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

Author

Fitzgerald, Tomas, Brettell, Ian, Leger, Adrien, Wolf, Nadeshda, Kusminski, Natalja, Monahan, Jack, Barton, Carl, Herder, Cathrin, Aadepu, Narendar, Gierten, Jakob, Becker, Clara, Hammouda, Omar T., Hasel, Eva, Lischik, Colin, Lust, Katharina, Sokolova, Natalia, Suzuki, Risa, Tsingos, Erika, Tavhelidse, Tinatini, Thumberger, Thomas, Watson, Philip, Welz, Bettina, Khouja, Nadia, Naruse, Kiyoshi, Birney, Ewan, Wittbrodt, Joachim, and Loosli, Felix

Abstract

Additional file 9: Figure S10. Haploview plots. Linkage disequilibrium (LD) plots generated with Haploview for each of the 24 medaka chromosomes, showing r2 values in the MIKK panel for each pair of SNPs within 1 Mb of one another.

Published
2022
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