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RIKEN Center for Biosystems Dynamics Research Laboratory for Phyloinformatics

Team Leader: Shigehiro Kuraku (Ph.D.)

Research Summary

Shigehiro  Kuraku(Ph.D.)

The ‘genome’ stands for a complete set of genetic information per species (or cell) that is a blueprint of our body structure and biological processes at different levels. The genome was not suddenly created but is an interim product of successive modifications over billion years. Every single genome has a history embedded in DNA sequences, and comparisons of the information between species provide clues for past evolutionary events.

By making use of cutting-edge DNA sequencing technologies and bioinformatics, we conduct molecular-level analysis on diversity and evolution of genomes and epigenomes of vertebrates. Our activity includes taking an initiative in whole genome sequencing and analysis projects for some important vertebrate species, which is leading to our fostering of biodiversity literacy from viewpoints of genomics and molecular evolution.

Main Research Fields

  • Biological Sciences

Related Research Fields

  • Complex Systems
  • Biology


  • genome informatics
  • molecular evolution
  • biodiversity

Selected Publications

  • 1. Kajikawa E, Horo U, Ide T, Mizuno K, Minegishi K, Hara Y, Ikawa Y, Nishimura H, Uchikawa M, Kiyonari H, Kuraku S, Hamada H.:
    "Nodal paralogues underlie distinct mechanisms for visceral left-right asymmetry in reptiles and mammals."
    Nature Ecology & Evolution (2020) doi: 10.1038/s41559-019-1072-2
  • 2. Kadota M, Nishimura O, Miura H, Tanaka K, Hiratani I, Kuraku S.:
    "Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?"
    GigaScience (2020) doi: 10.1093/gigascience/giz158
  • 3. Hara Y, Yamaguchi K, Onimaru K, Kadota M, et al.:
    "Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates."
    Nature Ecology and Evolution (2018), doi: 10.1038/s41559-018-0673-5.
  • 4. Hara Y, Takeuchi M, Kageyama Y, et al.:
    "Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes."
    BMC Biology 16.40 (2018)
  • 5. Onimaru K, Kuraku S.:
    "Inference of the ancestral vertebrate phenotype through vestiges of the whole genome duplications."
    Briefings in Functional Genomics (2018)
  • 6. Nishimura O, Hara Y, Kuraku S.:
    "gVolante for standardizing completeness assessment of genome and transcriptome assemblies."
    Bioinformatics 33(22). 3635-3637 (2017)
  • 7. Kadota M, Hara Y, Tanaka K, et al.:
    "CTCF binding landscape in jawless fish with reference to Hox cluster evolution."
    Scientific Reports 7(1). 4957 (2017)
  • 8. Kuraku S, Zmasek CM, Nishimura O, Kato K.:
    "aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity."
    Nucleic Acids Research 41(W1). W22-28 (2013)
  • 9. Smith JJ, Kuraku S, Holt C, et al.:
    "Sequencing of the sea lamprey (Petromyzon marinus) genome provide insights into vertebrate evolution."
    Nature Genetics 45(4). 415-421 (2013)
  • 10. Kuraku S.:
    "Impact of asymmetric gene repertoire between cyclostomes and gnathostomes."
    Seminars in Cell and Developmental Biology 24(2). 119-127 (2013)

Recent Research Results

Related Links

Lab Members

Principal investigator

Shigehiro Kuraku
Team Leader

Core members

Mitsutaka Kadota
Technical Scientist
Osamu Nishimura
Technical Scientist
John James Rozewicki
Technical Scientist
Chiharu Tanegashima
Expert Technician
Kaori Tatsumi
Technical Staff II
Reiko Nakagawa
Research Specialist
Kazuaki Yamaguchi
Research Scientist
Yuta Ohishi
Junior Research Associate

Contact Information

S204, 2F, RIKEN BDR Developmental Biology Bldg.C,
2-2-3 Minatojima-minamimachi, Chuo-ku,
Kobe, Hyogo,
650-0047 Japan
Email: shigehiro.kuraku [at] riken.jp