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Research

Research

BDR researchers coming from diverse research fields are working together to achieve higher goals.

Seminars & Symposia

Seminars & Symposia

BDR hosts annual symposium and regular seminars inviting international scientists in life science.

Careers & Study

Careers & Study

BDR embraces people from diverse backgrounds, and strives to create an open and supportive setting for research.

Outreach

Outreach

BDR communicates the appeal and significance of our research to society through the use of various media and activities.

News

News

From research, events, people and everything in between, find out what’s going on at RIKEN BDR.

About Us

About Us

Exploring the scientific foundations of life through interdisciplinary approaches to address society’s problems.

Photo of Team leder, Shigehiro Kuraku

Team Leader
Shigehiro Kuraku Ph.D.

Laboratory for Phyloinformatics

Location Kobe / Developmental Biology Buildings

E-mailshigehiro.kuraku[at]riken.jp

Please replace [at] with @.

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

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

Selected Publications

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 13(4), 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 4(2), 261-269 (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 9(1), giz158 (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. Biological sciences 286(1910), 20191828 (2019) doi: 10.1098/rspb.2019.1828

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

Hara Y, Yamaguchi K, Onimaru K, et al.
Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates.
Nature ecology & evolution 2(11), 1761-1771 (2018) doi: 10.1038/s41559-018-0673-5

Onimaru K, Kuraku S.
Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications.
Briefings in functional genomics 17(5), 352-361 (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

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

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 research 41(Web Server issue), W22-8 (2013) doi: 10.1093/nar/gkt389

Members

Shigehiro Kuraku

Team Leader

Mitsutaka Kadota

Technical Scientist

Osamu Nishimura

Technical Scientist

Chiharu Tanegashima

Expert Technician

Kaori Tatsumi

Technical Staff II

Yuta Ohishi

Junior Research Associate

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