Research themes

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Our group aims to infer the molecular-level history of complex life, based on molecular phylogenetic approaches to evolutionarily dissecting biodiversity with increasing knowledge of cellular events from genome-wide profiling. We mainly focus on vertebrates including elusive wild species with unique phenotypes. Our interests are categorized into these themes.

 

1. Deciphering the evolutionary history of genomes by comparing DNA sequence information of various organisms

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2. Formulating genome evolution mechanism based on understanding of cellular events

 

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3. Advancing genome-wide data acquisition and analysis methods

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Major achievements in brief

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Genomics and evolutionary biology

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・First-ever comprehensive genome analysis of multiple shark species

　　that revealed the Hox C gene retention and peculiarity of whale shark vision
　　　Hara et al., 2018. Nat. Ecol. & Evol. 2: 1761-1771

・Promotion of previously unrecognized laboratory animals

      from evolutionary and genomic viewpoints

          Bamboo shark: Onimaru et al., Dev. Dyn. 2018.

          Gecko:  Hara et al., BMC Biol. 2018

・Introduction of the conjecture for inferring the phenotype of the vertebrate ancestor

          Onimaru & Kuraku, 2018. Briefings Func. Genomics. 17: 352-361.

・Genome-wide analysis of CTCF binding in the lamprey

          Kadota et al., 2017. Scientific Reports 7: 4957.

・Identification of the genes lost from the human ancestor

       including Bmp16, Pax10, FoxG2

          Feiner et al., 2014. Genome Biol. Evol. 19: 1635-1651, etc.

          Reviewed in Kuraku et al., 2016. Diff. Growth Dev. 58: 131-142

・Revealing the peculiarity of the lamprey genome

      as part of the international genome analysis consortium

          Smith, Kuraku, et al., 2013. Nature Genetics 45: 415-421

          Reviewed in Manousaki et al., 2017. Jawless Fishes of the World, vol.1

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・Documentaiton of the history of numerous genes

       responsible for animal development, physiology, and endocrinology

          Moriyama et al., 2016. Nature Comm. 7:10397

          Kajikawa et al., Nat. Ecol. & Evol. 2020, etc.

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Methodological achievements

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・Optimized Hi-C protocol 'iconHi-C' covering both laboratory and in silico steps

   　　Kadota et al., 2020. GigaScience 9:1

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・Webserver aLeaves for efficient homologue sequence search

         Kuraku et al., 2013. Nuc. Acids. Res. 41: W22-28.

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・Optimized cost-saving mate-pair library preparation protocol iMate

         Tatsumi et al., 2015. Biotechniques 58:5

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・Guide of tree-thinking for non-evolutionary biologists

         Kuraku et al. 2016. Dev. Growth Diff., 58: 131-42.

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・Webserver gVolante for evaluating genome and transcriptome sequence assemblies

        Nishimura et al., Bioinformatics, 2017

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