Laboratory for Phyloinformatics | RIKEN BDR

Laboratory for Phyloinformatics

Team Leader

Shigehiro KurakuPh.D.

Photo of principal investigator

  • Location:Kobe / Developmental Biology Buildings
  • E-mail:shigehiro.kuraku[at]riken.jpPlease replace [at] with @.
  • Lab Website

Genome-wide scope and concepts of molecular evolution for entire life science

Research Summary

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.

Research Theme

  • Biodiversity research based on understanding of life sciences and molecular evolutionary approaches
  • Improvement of genome analysis techniques for chromosome-scale DNA sequencing
  • Vertebrate evolutionary genomics encompassing chromatin organization and regulation
  • Decoding genomes of important organisms with little molecular information

Main Publications List

  • Jayakumar V, Nishimura O, Kadota M, et al.
    Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Common Marmoset.
    Scientific Data 8, 159 (2021) doi: 10.1038/s41597-021-00935-6
  • Ohnishi T, Kiyama Y, Arima-Yoshida F, et al.
    Cooperation of LIM domain-binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia.
    EMBO Molecular Medicine e12574 (2021) doi: 10.15252/emmm.202012574
  • Kajikawa E, Horo U, Ide T, et al.
    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
  • Kadota M, Nishimura O, Miura H, et al.
    Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?
    GigaScience (2020) doi:10.1093/gigascience/giz158
  • Kishida T, Go Y, Tatsumoto S, et al.
    Loss of olfaction in sea snakes provides new perspectives on the aquatic adaptation of amniotes.
    Proceedings of the Royal Society B: Biological Sciences 286 (2019) doi: 10.1098/rspb.2019.1828
  • Hara Y, Yamaguchi K, Onimaru K, 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
  • Hara Y, Takeuchi M, Kageyama Y, et al.
    Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes.
    BMC Biology 16.40 (2018) doi: 10.1186/s12915-018-0509-4
  • Onimaru K, Kuraku S.
    Inference of the ancestral vertebrate phenotype through vestiges of the whole genome duplications.
    Briefings in Functional Genomics (2018) doi: 10.1093/bfgp/ely008
  • Nishimura O, Hara Y, Kuraku S.
    gVolante for standardizing completeness assessment of genome and transcriptome assemblies.
    Bioinformatics 33(22). 3635–3637 (2017) doi: 10.1093/bioinformatics/btx445
  • 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) doi: 10.1038/s41598-017-04506-x
  • 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) doi: 10.1093/nar/gkt389
  • 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) doi: 10.1038/ng.2568
  • Kuraku S.
    Impact of asymmetric gene repertoire between cyclostomes and gnathostomes.
    Seminars in Cell and Developmental Biology 24(2). 119-127 (2013) doi: 10.1016/j.semcdb.2012.12.009


Shigehiro KurakuTeam Leader shigehiro.kuraku[at] CV
Mitsutaka KadotaTechnical Scientist mitsutaka.kadota[at] CV
Osamu NishimuraTechnical Scientist osamu.nishimura[at] CV
John James RozewickiTechnical Scientist    
Chiharu TanegashimaExpert Technician chiharu.tanegashima[at]
Kaori TatsumiTechnical Staff II
Reiko NakagawaResearch Specialist reiko.nakagawa[at] CV
Kazuaki YamaguchiResearch Scientist kazuaki.yamaguchi[at] CV
Yuta OhishiJunior Research Associate yuta.ohishi[at]

*:concurrent / Please replace [at] with @.