Abstract
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.
Highlights
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
The analysis consisted of 4 steps: (1) linear draft assembly for each Medaka Inbred Kiyosu-Karlsruhe (MIKK) line using both short and long reads, (2) pangenome graph construction combining known medaka reference genomes and MIKK panel draft assemblies, (3) alignment of Oxford Nanopore Technologies (ONT) reads to the graph, and (4) extraction of complex structural variations
Methylation patterns appear consistent across multiple generations, with the MIKK panel sibling lines clustering together based on their methylation profiles alone. This suggests that, like in other species [46], methylation is a heritable trait in medaka fish capable of persisting across multiple generations and is likely to impact phenotypic traits. With this pilot set of 12 MIKK panel lines, we have demonstrated the feasibility of generating independent assemblies for each of the MIKK panel lines and of interrogating the rich functional differences created by their structural variants
Summary
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. In the companion article published with this one, we provide a detailed genetic characterisation of the 80 individual MIKK panel lines [4], based on the alignment of Illumina short reads to the closest, fully assembled reference genome—the southern Japanese medaka inbred strain, HdrR. This allowed us to discover much of the genetic variation in the MIKK panel relative to HdrR, the approach inevitably kept certain variants hidden, including larger and more complex structural variation—“dark variation”—that is likely to have functional consequences for each of the lines. It makes it difficult to discover complex structural variation, such as large insertions and nested variations
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