Breakthrough in Marine Medaka Genome Assembly

Strategic Insights -

A team of researchers from Sungkyunkwan University has achieved a milestone in biotechnology with the development of a chromosome-level genome assembly of the marine medaka (Oryzias melastigma) using Hi-C technology. This achievement is poised to revolutionize genomic and epigenetic research, enabling investigations into toxicogenomic and epigenetic research for environmental studies and precision genome editing in marine organisms.

Key Takeaways:

  • The researchers used Hi-C technology, integrated with PacBio long-read and Illumina short-read sequence data, to assemble the genome of the marine medaka, which has 24 chromosomes and a total length of 873 Mb.
  • The assembled genome has an N50 of 35.9 Mb, and 94.2% of sequences were anchored to 24 chromosomes.
  • Comparative genomic analysis with the related species O. latipes demonstrated strong synteny and species-specific gene expansions.
  • Whole-genome bisulfite sequencing was performed to profile DNA methylation, revealing methylation patterns of O. melastigma across tissues.
  • The research provides a crucial reference for genomic and epigenetic research, enabling investigations into toxicogenomic and epigenetic research for environmental studies and precision genome editing in marine organisms.
  • The study highlights the importance of the marine medaka as a model organism for marine ecotoxicology and genetic or epigenetic studies.
  • The research team included Jin-Sol Lee, Min-Sub Kim, Duck-Hyun Kim, Jordan Jun Chul Park, Alaa El-Din H. Sayed, Xiaoshan Zhu, Youji Wang, Minghua Wang, Zhou Yang, and Jae-Seong Lee.

Statistics:

  • The assembled genome has a total length of 873 Mb.
  • The N50 of the assembled genome is 35.9 Mb.
  • 94.2% of sequences were anchored to the 24 chromosomes.
  • The study used Hi-C technology, PacBio long-read, and Illumina short-read sequence data for genome assembly.
  • The research team conducted comparative genomic analysis with the related species O. latipes.
  • The study included whole-genome bisulfite sequencing to profile DNA methylation.

Sources:

  • Chromosome-level genome assembly of the marine medaka (Oryzias melastigma) using Hi-C technology: Genomic analysis and profiling of DNA methylation for epigenetic study. Comparative Biochemistry and Physiology Part D, 2025;56:101580.
  • Sungkyunkwan University
  • Jin-Sol Lee, Dept. of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
  • Elsevier Science Inc, Ste 800, 230 Park Ave, New York, NY 10169, USA