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

Genome Biology

Philip Watson¹  Natalia Sokolova¹  Clara Becker¹  Erika Tsingos¹  Bettina Welz¹  Omar T. Hammouda¹  Joachim Wittbrodt¹  Jakob Gierten¹  Thomas Thumberger¹  Eva Hasel¹  Colin Lischik¹  Katharina Lust¹  Risa Suzuki¹  Tinatini Tavhelidse¹  Adrien Leger²  Jack Monahan²  Ian Brettell²  Carl Barton²  Ewan Birney²  Cathrin Herder³  Natalja Kusminski³  Nadeshda Wolf³  Felix Loosli³  Narendar Aadepu⁴  Kiyoshi Naruse⁵ 

[1] Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany;European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK;Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany;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;National Institute for Basic Biology, Laboratory of Bioresources, Okazaki, Japan;

关键词: Inbred panel;    Medaka;    Genetics;    Methylation;    Structural variation;    Graph genome;    Long read sequencing;    Pan genome;    Nanopore;   

DOI  :  10.1186/s13059-022-02602-4

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsWe 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.ConclusionsWe 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.

【 授权许可】

CC BY