Academic Journal
Complete sequencing of medaka genomes reveals the architecture of centromeric satellites, giant mobile elements, and sex chromosomes.
| Τίτλος: | Complete sequencing of medaka genomes reveals the architecture of centromeric satellites, giant mobile elements, and sex chromosomes. |
|---|---|
| Συγγραφείς: | Suzuki Y; Department of Computational Biology and Medical Sciences, The University of Tokyo, Chiba 277-8561, Japan., Ichikawa K; Department of Computational Biology and Medical Sciences, The University of Tokyo, Chiba 277-8561, Japan., Inoue Y; Department of Biological Sciences, The University of Tokyo, Tokyo 113-0033, Japan., Owa C; Department of Computational Biology and Medical Sciences, The University of Tokyo, Chiba 277-8561, Japan., Kobayashi H; Department of Computational Biology and Medical Sciences, The University of Tokyo, Chiba 277-8561, Japan., Morikami K; Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka 411-8540, Japan., Nakamura R; Department of Biological Sciences, The University of Tokyo, Tokyo 113-0033, Japan., Ikeda T; Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan.; Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto 603-8555, Japan., Fujie M; Sequencing Section, Core Facilities, Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan., Kawamitsu M; Sequencing Section, Core Facilities, Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan., Arakaki N; Sequencing Section, Core Facilities, Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan., Myers EW; Algorithms for Ecological and Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan., Aburatani H; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan., Takehana Y; Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga 526-0829, Japan., Matsuda M; Center for Bioscience Research and Education, Utsunomiya University, Tochigi 321-8505, Japan., Naruse K; Laboratory of Bioresources, National Institute for Basic Biology, Aichi 444-8585, Japan.; Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Aichi 444-8585, Japan., Kuraku S; Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka 411-8540, Japan.; Department of Genetics, The Graduate University for Advanced Studies, Shizuoka 411-8540, Japan., Takeda H; Department of Biological Sciences, The University of Tokyo, Tokyo 113-0033, Japan; takeda_h@cc.kyoto-su.ac.jp moris@edu.k.u-tokyo.ac.jp.; Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan.; Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto 603-8555, Japan., Morishita S; Department of Computational Biology and Medical Sciences, The University of Tokyo, Chiba 277-8561, Japan; takeda_h@cc.kyoto-su.ac.jp moris@edu.k.u-tokyo.ac.jp. |
| Πηγή: | Genome research [Genome Res] 2026 Aug 03; Vol. 36 (8), pp. 1696-1707. Date of Electronic Publication: 2026 Aug 03. |
| Τύπος έκδοσης: | Journal Article |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9518021 Publication Model: Electronic Cited Medium: Internet ISSN: 1549-5469 (Electronic) Linking ISSN: 10889051 NLM ISO Abbreviation: Genome Res Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press, c1995- |
| Ιατρικοί όροι (MeSH): | Oryzias*/genetics , Centromere*/genetics , Sex Chromosomes*/genetics , DNA, Satellite*/genetics , Genome* , Interspersed Repetitive Sequences*, Animals ; Male ; Female |
| Περίληψη: | Medaka (Oryzias latipes) is a small freshwater teleost widely used as a vertebrate model organism. Existing medaka reference genomes, however, contain many gaps and unresolved repetitive regions, hindering precise genome annotation and comparative analyses. Here we present one complete and two near-complete genome assemblies for three inbred medaka strains derived from geographically distant populations. These assemblies provide a comprehensive view of highly repetitive sequences and chromosome-scale genome architecture in medaka. The fully resolved centromeres reveal an intriguing sequence organization characterized by short, distinct SF1+3 satellite arrays flanked by larger homogenized repeats. These short arrays are putatively hypomethylated and conserved across all acrocentric chromosomes, suggesting a functional role in centromere stability. The reconstructed 121 copies of the giant mobile element Teratorn retain complete genes of both a transposon and a herpesvirus, highlighting its unique persistence and impact on host genomes. Moreover, our assemblies reveal extensive structural divergence of medaka Y Chromosomes, yet identify a small (∼24 kb) conserved region encompassing Dmy that may suffice for male determination. Collectively, these (near-)complete medaka genomes provide a powerful resource for exploring the biology of uncharacterized repetitive regions and the molecular basis of phenotypic diversity in vertebrates. (© 2026 Suzuki et al.; Published by Cold Spring Harbor Laboratory Press.) |
| References: | Genome Biol. 2013 Jan 30;14(1):R10. (PMID: 23363705) Genetics. 1921 Nov;6(6):554-73. (PMID: 17245975) Nature. 2002 May 30;417(6888):559-63. (PMID: 12037570) G3 (Bethesda). 2014 Mar 20;4(3):433-45. (PMID: 24408034) Science. 2021 Nov 12;374(6569):eabi7489. (PMID: 34762468) Biol Lett. 2021 Aug;17(8):20210212. (PMID: 34343438) Mol Biol Evol. 2021 Sep 27;38(10):4647-4654. (PMID: 34320186) Mol Cell Biol. 1995 Aug;15(8):4009-20. (PMID: 7623797) Nat Biotechnol. 2019 Oct;37(10):1155-1162. (PMID: 31406327) Biol Lett. 2009 Dec 23;5(6):812-6. (PMID: 19586967) Nature. 2024 May;629(8010):136-145. (PMID: 38570684) Nat Methods. 2024 Jun;21(6):967-970. (PMID: 38730258) Nat Commun. 2017 Nov 28;8(1):1833. (PMID: 29184138) Nat Methods. 2026 Apr;23(4):732-739. (PMID: 41286201) PLoS Genet. 2009 Sep;5(9):e1000641. (PMID: 19749981) Curr Biol. 2012 Apr 10;22(7):601-7. (PMID: 22386310) Nature. 2023 May;617(7960):335-343. (PMID: 37165241) Nature. 2007 Jun 7;447(7145):714-9. (PMID: 17554307) Science. 1976 Feb 13;191(4227):528-35. (PMID: 1251186) Nat Commun. 2017 Sep 15;8(1):551. (PMID: 28916771) Genome Res. 2006 Jul;16(7):815-26. (PMID: 16751340) Nat Commun. 2025 Nov 3;16(1):9688. (PMID: 41184258) Genetics. 2025 Dec 10;231(4):. (PMID: 41052773) Zoological Lett. 2023 Jul 22;9(1):16. (PMID: 37480068) Cell Genom. 2026 May 13;6(5):101164. (PMID: 41672067) Genome Biol. 2019 Dec 16;20(1):277. (PMID: 31842948) PLoS Genet. 2010 Feb 12;6(2):e1000844. (PMID: 20169179) Annu Rev Genomics Hum Genet. 2006;7:301-13. (PMID: 16756479) Annu Rev Genet. 2010;44:217-41. (PMID: 20731603) Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):3865-70. (PMID: 17360444) Chromosoma. 2001 Aug;110(4):253-66. (PMID: 11534817) Genome Biol. 2022 Dec 15;23(1):258. (PMID: 36522651) Science. 2022 Apr;376(6588):eabl4178. (PMID: 35357911) Zoolog Sci. 2003 Oct;20(10):1279-91. (PMID: 14569151) Nat Biotechnol. 2020 Sep;38(9):1044-1053. (PMID: 32686750) Cell. 2006 Mar 10;124(5):901-14. (PMID: 16530039) Nucleic Acids Res. 2021 Jan 8;49(D1):D389-D393. (PMID: 33196836) J Cell Biol. 1989 Nov;109(5):1963-73. (PMID: 2808515) Nat Genet. 2023 Jul;55(7):1221-1231. (PMID: 37322109) Genome Res. 2025 Jul 1;35(7):1583-1594. (PMID: 40389285) Bioinformatics. 2020 Jul 1;36(Suppl_1):i93-i101. (PMID: 32657390) Zoolog Sci. 2016 Apr;33(2):125-31. (PMID: 27032677) Zoolog Sci. 2004 Sep;21(9):977-88. (PMID: 15459457) Genome Biol. 2022 Feb 21;23(1):58. (PMID: 35189951) Mol Biol Evol. 1987 May;4(3):203-21. (PMID: 3328815) Science. 2001 Aug 10;293(5532):1098-102. (PMID: 11498581) Nat Commun. 2025 Apr 30;16(1):4062. (PMID: 40307248) Bioinformatics. 2021 Jul 19;37(12):1639-1643. (PMID: 33320174) Genome Res. 2024 Jun 25;34(5):769-777. (PMID: 38866550) Genetics. 2014 Jun;197(2):531-41. (PMID: 24578352) Zoological Lett. 2018 Feb 21;4:6. (PMID: 29484202) PLoS Curr. 2013 Apr 18;5:. (PMID: 23653398) Genomics. 1989 Aug;5(2):332-44. (PMID: 2793186) Genet Res. 2001 Aug;78(1):23-30. (PMID: 11556134) Nature. 2025 Aug;644(8076):430-441. (PMID: 40702183) Genetics. 2000 May;155(1):273-81. (PMID: 10790401) Genome Biol. 2020 Jul 19;21(1):177. (PMID: 32684159) |
| Substance Nomenclature: | 0 (DNA, Satellite) |
| Entry Date(s): | Date Created: 20260701 Date Completed: 20260803 Latest Revision: 20260813 |
| Update Code: | 20260814 |
| PubMed Central ID: | PMC13431155 |
| DOI: | 10.1101/gr.281813.125 |
| PMID: | 42386528 |
| Βάση Δεδομένων: | MEDLINE |
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