Pan-genome variations and epigenomic landscape of medaka (Oryzias latipes) with nanopore DNA sequencing

Investigation of pangenomic variations and epigenomic landscape of Oryzias latipes with ONT DNA-sequencing. The teleost medaka (Oryzias latipes) has a high tolerance to inbreeding from the wild, thus allowing one to establish near isogenic lines from wild founder individuals. Ian Brettell et al. have exploited this feature to create an inbred panel resource, the Medaka Inbred KiyosuKarlsruhe (MIKK) panel. Medaka is also a well-established model system, having a long history of genetic research with multiple high quality reference genomes available from different medaka populations (HdrR, HNI and HSOK).

Here they used Oxford Nanopore Technologies (ONT) long-read data to further investigate the genomic and epigenomic landscapes of a subset of the MIKK panel. Nanopore sequencing allowed Ian and his team to identify a much greater variety of high-quality structural variants compared with short reads. We also present results and methods using a pan-genome graph representation of 12 individual medaka lines from the MIKK panel.

This graph-based reference MIKK panel genome revealed novel differences between the MIKK panel lines compared to standard linear reference genomes. The team found additional MIKK panel-specific genomic content that would be missing from linear reference alignment approaches. They were also able to identify and quantify the presence of repeat elements in each of the lines.

Finally, Ian's team investigated line specific CpG methylation and performed differential DNA methylation analysis across the 12 lines analysis different lines. Overall, they 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 the investigation of novel variation types that would be elusive using standard approaches.