Repetitive genomic regions link structural genomic variation to species diversity
Researchers sequenced the genomes of three medaka, or Japanese rice fish, a common model organism used in biological research, nearly 10 and 20 years ago. While sequencing the genomes was relatively straightforward, assembling them was anything but.
Researchers have sequenced the genomes of three medaka fish, a common model organism in biological research, using advanced sequencing technologies to overcome the challenges posed by repetitive genomic regions. Traditional sequencing methods struggled with these regions, which are found in centromeres, telomeres, ribosomal DNA arrays, X and Y chromosomes, and the giant mobile element Teratorn.
By employing PacBio HiFi sequencing and Oxford Nanopore ultra-long sequencing, the research team was able to generate long, accurate reads that could span these repetitive stretches. This breakthrough allowed them to complete the genome sequence of the medaka fish, which previously contained about 1,000 gaps, and uncover important biological information hidden in these regions.
The study, published in Genome Research, sheds light on how these genomic regions contribute to chromosome stability, mobile DNA survival, and biological sex determination, providing insights into the phenotypic traits of the species.
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