Scientists have completed a long-standing effort to fully sequence the genome of the medaka, or Japanese rice fish, a widely used model organism in biological research. The work builds on genome sequencing efforts from nearly 10 and 20 years ago, when technological limitations left the genome only partially resolved.
In the first study, researchers used traditional Sanger sequencing, producing reads of about 800 to 1,000 base pairs. This approach left low-quality sequence in parts of the roughly 800 Mb genome and created many gaps. A decade later, in 2017, the team applied PacBio SMRT sequencing to two Japanese medaka strains, Hd-rR and HNI, and one Korean strain, HSOK. The longer reads, spanning tens of kilobases, improved the assembly but still left about 1,000 gaps.
The research, led by scientists from The University of Tokyo and the National Institute of Genetics, part of the Research Organization of Information and Systems (ROIS) in Japan, was published in Genome Research.
According to Yoshihiko Suzuki, primary author of the paper, the goal was to complete the medaka genome sequence and uncover biological information hidden in its gaps, including insights into chromosome stability, mobile DNA and sex determination. Many of these gaps fell within repetitive regions, including centromeres, telomeres, ribosomal DNA arrays, the XY chromosomes and the mobile genetic element Teratorn.
To resolve these regions, the team combined two newer sequencing technologies: PacBio HiFi sequencing, which produces highly accurate long reads, and Oxford Nanopore ultra-long sequencing, which generates reads hundreds of kilobases long. Together, these methods allowed the researchers to fully assemble the Hd-rR strain and nearly complete the HNI and HSOK strains, enabling comparisons of centromeric sequences, transposons and sex chromosomes across strains and species.
The comparisons showed medaka centromeric satellite sequences are more conserved between strains than in other eukaryotic organisms, which may help stabilize kinetochore attachment. The team also found that Teratorn, a herpesvirus genome fused to a transposable element, persists in the genome and can influence nearby gene expression, including medaka fin shape. Genes on the X and Y chromosomes remain paired except near the Y-specific region, a pattern that differs from the threespine stickleback's much older Y chromosome.
Suzuki said the next step is to test the functions of these newly identified regions, with the ultimate goal of using complete genome information to understand how DNA sequence differences shape traits in vertebrates, and eventually to help clarify human genome function.
In the first study, researchers used traditional Sanger sequencing, producing reads of about 800 to 1,000 base pairs. This approach left low-quality sequence in parts of the roughly 800 Mb genome and created many gaps. A decade later, in 2017, the team applied PacBio SMRT sequencing to two Japanese medaka strains, Hd-rR and HNI, and one Korean strain, HSOK. The longer reads, spanning tens of kilobases, improved the assembly but still left about 1,000 gaps.
The research, led by scientists from The University of Tokyo and the National Institute of Genetics, part of the Research Organization of Information and Systems (ROIS) in Japan, was published in Genome Research.
According to Yoshihiko Suzuki, primary author of the paper, the goal was to complete the medaka genome sequence and uncover biological information hidden in its gaps, including insights into chromosome stability, mobile DNA and sex determination. Many of these gaps fell within repetitive regions, including centromeres, telomeres, ribosomal DNA arrays, the XY chromosomes and the mobile genetic element Teratorn.
To resolve these regions, the team combined two newer sequencing technologies: PacBio HiFi sequencing, which produces highly accurate long reads, and Oxford Nanopore ultra-long sequencing, which generates reads hundreds of kilobases long. Together, these methods allowed the researchers to fully assemble the Hd-rR strain and nearly complete the HNI and HSOK strains, enabling comparisons of centromeric sequences, transposons and sex chromosomes across strains and species.
The comparisons showed medaka centromeric satellite sequences are more conserved between strains than in other eukaryotic organisms, which may help stabilize kinetochore attachment. The team also found that Teratorn, a herpesvirus genome fused to a transposable element, persists in the genome and can influence nearby gene expression, including medaka fin shape. Genes on the X and Y chromosomes remain paired except near the Y-specific region, a pattern that differs from the threespine stickleback's much older Y chromosome.
Suzuki said the next step is to test the functions of these newly identified regions, with the ultimate goal of using complete genome information to understand how DNA sequence differences shape traits in vertebrates, and eventually to help clarify human genome function.