Centers & Labs

RIKEN Center for Life Science Technologies

Phyloinformatics Unit

Unit Leader: Shigehiro Kuraku (Ph.D.)
Shigehiro  Kuraku(Ph.D.)

We are the only core facility of RIKEN in western Japan that provides technical support on both next-generation sequencing and mass spectrometry. We host postdoctoral lab experts for sample QC as well as bioinformaticians who process large-scale sequence analysis, and this staff organization has enabled handling of diverse projects in a biologist-oriented manner. Following contributions to international genome consortia for several non-model animals, we aim to conduct original research and technical development by means of molecular evolutionary approaches for sound cross-species comparisons of DNA and protein sequences.

Research Subjects

  • Technical support of a wide range of molecular analyses including large-scale gene expression analysis
  • Development of new solutions for genomics and epigenomics
  • Technical support of bioinformatic analyses including sequence annotation
  • Comparative genomic studies of vertebrates

Selected Publications

  1. Sugahara F, Pascual-Anaya J, Oishi Y, Kuraku S, Aota S, Adachi N, Takagi W, Hirai T, Sato N, Murakami Y, and Kuratani S.:
    “Evidence from cyclostomes for complex regionalization of the ancestral vertebrate brain.”
    Nature, in press (2016).
  2. Moriyama Y, Ito F, Takeda H, Yano T, Okabe M, Kuraku S, Keeley F,W, and Koshiba-Takeuchi K.:
    “Evolution of the fish heart by sub/neofunctionalization of an elastin gene.”
    Nature Communications,7, 10397 (2016).
  3. Kuraku S, Feiner N, Keeley S, and Hara Y.:
    “Incorporating tree-thinking and evolutionary time scale into developmental biology.”
    Development Growth and Differentiation, 58(1),131-142 (2016).
  4. Hara Y, Tatsumi K, Yoshida M, Kajikawa E, Kiyonari H, Kuraku S.:
    “Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation.”
    BMC Genomics., 16(1), 977 (2015).
  5. Noro M, Sugahara F, Kuraku S.:
    “Reevaluating Emx gene phylogeny: homopolymeric amino acid tracts as a potential factor obscuring orthology signals in cyclostome genes.”
    BMC Evol Biol, 15, 78 (2015).
  6. Tatsumi K, Nishimura O, Itomi K, Tanegashima C, and Kuraku S.:
    “Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing”
    Biotechniques, 58(5), 253-257 (2015).
  7. Kuraku S, Zmasek CM, Nishimura O, Katoh K.:
    “aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.”
    Nucleic Acids Res, 41, W22-28 (2013).
  8. Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D, Wang B, Ming Y, Chen Y, Zheng Y, Kuraku S, Pignatelli M, Herrero J, Beal K, Nozawa M, Li Q, Wang J, Zhang H, Yu L, Shigenobu S, Wang J, Liu J, Flicek P, Searle S, Wang J, Kuratani S, Yin Y, Aken B, Zhang G, Irie N.:
    “The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.”
    Nat Genet, 45(6), 701-706 (2013).
  9. Smith J, Kuraku S, …. Flicek P, Bronner M, Warren WC, Clifton SW, Wilson RK, and Li W.:
    “Sequencing of the sea lamprey (Petromyzon marinus) genome provide insights into vertebrate evolution.”
    Nature Genetics 45, 415–421 (2013)
  10. Kuraku S.:
    “Impact of asymmetric gene repertoire between cyclostomes and gnathostomes.”
    Semin Cell Dev Biol, 24(2), 119-127 (2013).

Lab Members

Principal Investigator

Shigehiro Kuraku
Unit Leader

Core Members

Mitsutaka Kadota
Senior Scientist
Osamu Nishimura
Technical Scientist
Reiko Nakagawa
Technical Scientist
Yuichiro Hara
Special Postdoctoral Researcher
Koh Onimaru
Research Scientist
Kazuaki Yamaguchi
Postdoctoral Researcher
Rehab Mohamed
Technical Staff I
Chiharu Tanegashima
Technical Staff II
Kaori Tatsumi
Technical Staff II
Sean Keeley
Technical Staff II
Sayo Saito
Assistant

Contact information

S204 2F RIKEN CDB Bldg.C,
2-2-3 Minatojima-minamimachi, Chuo-ku
Kobe, Hyogo
650-0047 Japan

Email: shigehiro.kuraku [at] riken.jp

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