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Leger A, Brettell I, Monahan J, Barton C, Wolf N, Kusminski N, Herder C, Aadepu N, Becker C, Gierten J, Hammouda OT, Hasel E, Lischik C, Lust K, Sokolova N, Suzuki R, Tavhelidse T, Thumberger T, Tsingos E, Watson P, Welz B, Naruse K, Loosli F, Wittbrodt J, Birney E, Fitzgerald T. Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. Genome Biol 2022; 23:58. [PMID: 35189951 PMCID: PMC8862245 DOI: 10.1186/s13059-022-02602-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/05/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The teleost medaka (Oryzias latipes) is a well-established vertebrate model system, with a long history of genetic research, and multiple high-quality reference genomes available for several inbred strains. Medaka has a high tolerance to inbreeding from the wild, thus allowing one to establish inbred lines from wild founder individuals. RESULTS We exploit this feature to create an inbred panel resource: the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. This panel of 80 near-isogenic inbred lines contains a large amount of genetic variation inherited from the original wild population. We use Oxford Nanopore Technologies (ONT) long read data to further investigate the genomic and epigenomic landscapes of a subset of the MIKK panel. Nanopore sequencing allows us to identify a large variety of high-quality structural variants, and we present results and methods using a pan-genome graph representation of 12 individual medaka lines. This graph-based reference MIKK panel genome reveals novel differences between the MIKK panel lines and standard linear reference genomes. We find additional MIKK panel-specific genomic content that would be missing from linear reference alignment approaches. We are also able to identify and quantify the presence of repeat elements in each of the lines. Finally, we investigate line-specific CpG methylation and performed differential DNA methylation analysis across these 12 lines. CONCLUSIONS We present a detailed analysis of the MIKK panel genomes using long and short read sequence technologies, creating a MIKK panel-specific pan genome reference dataset allowing for investigation of novel variation types that would be elusive using standard approaches.
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Affiliation(s)
- Adrien Leger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ian Brettell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jack Monahan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Carl Barton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nadeshda Wolf
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Natalja Kusminski
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Cathrin Herder
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Narendar Aadepu
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany.,Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Clara Becker
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Jakob Gierten
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Omar T Hammouda
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Eva Hasel
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Colin Lischik
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Katharina Lust
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Natalia Sokolova
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Risa Suzuki
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Tinatini Tavhelidse
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Erika Tsingos
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Philip Watson
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Bettina Welz
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Kiyoshi Naruse
- National Institute for Basic Biology, Laboratory of Bioresources, Okazaki, Japan
| | - Felix Loosli
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tomas Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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Fitzgerald T, Brettell I, Leger A, Wolf N, Kusminski N, Monahan J, Barton C, Herder C, Aadepu N, Gierten J, Becker C, Hammouda OT, Hasel E, Lischik C, Lust K, Sokolova N, Suzuki R, Tsingos E, Tavhelidse T, Thumberger T, Watson P, Welz B, Khouja N, Naruse K, Birney E, Wittbrodt J, Loosli F. The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. Genome Biol 2022; 23:59. [PMID: 35189950 PMCID: PMC8862526 DOI: 10.1186/s13059-022-02623-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/31/2022] [Indexed: 12/24/2022] Open
Abstract
Background Unraveling the relationship between genetic variation and phenotypic traits remains a fundamental challenge in biology. Mapping variants underlying complex traits while controlling for confounding environmental factors is often problematic. To address this, we establish a vertebrate genetic resource specifically to allow for robust genotype-to-phenotype investigations. The teleost medaka (Oryzias latipes) is an established genetic model system with a long history of genetic research and a high tolerance to inbreeding from the wild. Results Here we present the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel: the first near-isogenic panel of 80 inbred lines in a vertebrate model derived from a wild founder population. Inbred lines provide fixed genomes that are a prerequisite for the replication of studies, studies which vary both the genetics and environment in a controlled manner, and functional testing. The MIKK panel will therefore enable phenotype-to-genotype association studies of complex genetic traits while allowing for careful control of interacting factors, with numerous applications in genetic research, human health, drug development, and fundamental biology. Conclusions Here we present a detailed characterization of the genetic variation across the MIKK panel, which provides a rich and unique genetic resource to the community by enabling large-scale experiments for mapping complex traits. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02623-z.
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Affiliation(s)
- Tomas Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ian Brettell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Adrien Leger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nadeshda Wolf
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Natalja Kusminski
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Jack Monahan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Carl Barton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Cathrin Herder
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Narendar Aadepu
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany.,Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Jakob Gierten
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Clara Becker
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Omar T Hammouda
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Eva Hasel
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Colin Lischik
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Katharina Lust
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Natalia Sokolova
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Risa Suzuki
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Erika Tsingos
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Tinatini Tavhelidse
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Philip Watson
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Bettina Welz
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Nadia Khouja
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Kiyoshi Naruse
- National Institute for Basic Biology, Laboratory of Bioresources, Okazaki, Japan
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Felix Loosli
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany.
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