Research themes

​

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

​

 

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

 

​

3. Advancing genome-wide data acquisition and analysis methods

​

​

​

Major achievements in brief

​

Genomics and evolutionary biology

​​

​・Pioneering analysis of sex chromosomes in sharks and rays:

   We reported the first DNA sequences of sex chromosomes in sharks and rays,  　elucidating their evolutionary origin and investigating sex-determination mechanisms 　using embryonic samples.

　　Niwa et al., 2025. bioRxiv

　　Wu et al., 2024. Cell Genomics 4: 100607

　　Yamaguchi et al., 2023. Genome Res 33:1527-1540

 

・Comprehensive analysis of frequently lost genes in mammalian genomes

　　Our research on mammalian genomes revealed that gene fate is influenced

　　not only by function but also by the surrounding genomic environment.

　　　Hara & Kuraku, 2023. eLife 12: e82290

　　　Hara & Kuraku, 2025. Trends Genet, in press

 

・Analysis of retained yolk proteins in live-bearing sharks

　　Ohishi et al., 2023. Genome Biol. Evol. 15: evad028

 

・Evolution of vision enabling deep-sea diving in the whale shark

　　We identified a novel blue-shift causing residue in rhodopsin, contributing

　　to the understanding of how the largest fish, the whale shark, navigates

　　deep-sea environments. [Coverage in Science]

　　　Yamaguchi et al., 2023. Proc. Natl. Acad. Sci. USA 120: e2220728120

 

・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

​

・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.

​

Methodological achievements

​

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

   　　Kadota et al., 2020. GigaScience 9:1

​

・Webserver aLeaves for efficient homologue sequence search

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

​

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

         Tatsumi et al., 2015. Biotechniques 58:5

​

・Guide of tree-thinking for non-evolutionary biologists

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

​

・Webserver gVolante for evaluating genome and transcriptome sequence assemblies

        Nishimura et al., Bioinformatics, 2017

​