Research Interests

Evolutionary Developmental Biology (EvoDevo), Axial Patterning, Cell Fate Specification, Comparative Genomics, Single-Cell Transcriptomics, Symbiosis

Current Projects (2022–)

Genetic Regulation of Symbiosis — Regulation of Symbiotic Cell Fate 

We are studying the genomic basis and genetic regulation for the initiation of animal—microbe symbiosis.

Research Directions:

Previous Projects (2005–2022)

Molecular Control of Pluripotent Stem Cells — Regulation of Stem Cell Fate 

We studied stem cell regulation in the acoel Hofstenia miamia using single-cell and epigenetic approaches.

Comparative Genomics and Transcriptomics of Lophotrochozoans — Evolution of Animal Genomes

Brachiopods (lamp shells), phoronids (horseshoe worms), and nemerteans (ribbon worms) are closely related lophotrochozoans. They are poorly studied despite their importance in ecology, evolution, and paleontology. We decoded the genomes of the brachiopod Lingula anatina, the phoronid Phoronis australis, and the nemertean Notospermus geniculatus to gain insights into animal genome evolution. We showed that Lingula lacks genes involved in bone formation, suggesting an independent origin of their phosphate biominerals. We found that lophotrochozoans share many gene families with deuterostomes, implying that lophotrochozoans retain a core set of bilaterian gene repertoire. Based on transcriptomic analyses, we also discovered a possible common origin of bilaterian head patterning. Together, my study reveals a dual nature of lophotrochozoans in which bilaterian-conserved and lineage-specific features shape the evolution of their genomes.

Axial Patterning in Sea Urchins — Evolution of Gene Regulatory Networks in Deuterostomes

Through immunolocalization of a phospho-Smad1/5 antibody, we found that BMP signaling is asymmetrically activated on the left side of the sea urchin larva in the first asymmetrical structure, hydroporic canal. By perturbing BMP signals using pharmaceutical treatments and morpholinos, we showed that BMP signals activate expressions of several transcription factors, which are required for the formation of the hydroporic canal. Our findings suggest that there is a deep evolutionary origin of opposing BMP and Nodal signaling in patterning left–right axis in deuterostomes.

Cell Fate Specification in Amphioxus — Specification of  Germlines and Sensory Neurons in Chordates

Amphioxus is a fish-like basal chordate. It occupies a key position to our understanding of the evolution and development of vertebrates. To study the roles of localized RNAs during germline specification, we quantified the aggregation of the structure so-called pole plasm, which contains Piwi-interacting RNAs including vasa and nanos mRNAs in fertilized eggs. By separating blastomeres at the two-cell stage, we found that absence of inheritance of the pole plasm in one of the twin embryos results in a defect of larval tail development. This observation indicates that the function of Vasa-positive cells derived from pole plasm is also required for differentiation and growth of somatic structures. Furthermore, to study neural specification, we reconstructed a three-dimensional neural structure of the  larva and identified an increase of clustered GABA-positive peripheral neurons after perturbing Notch signaling. Our results also showed that BMP signaling functions upstream of Notch signaling to induce a ventral neurogenic domain. We hypothesize a conserved function for BMP signaling in promoting peripheral neuron formation across bilaterians.

Coral–Dinoflagellate Endosymbiosis — Dynamics of the Lipid Content Between Corals and Algae

Coral–dinoflagellate endosymbiosis is the phenomenon in which algal symbionts live inside the animal host cells. The endosymbiosis occurs specifically in the inner tissue layer, the gastrodermis. To study symbiotic cells, we developed a method to isolate tissue layers in corals. Through this technique, we found that a lipid storage organelle, lipid body, shows a dynamic lipid change in the coral cells under continual light or dark treatments . Using ratiometric imaging with a fluorescent probe, Nile red, we analyzed the content of polar and neutral lipids in the lipid bodies. After inducing coral bleaching, we found a depletion of neutral lipids in the lipid bodies. This result suggests that morphological and compositional changes of lipid bodies reflect the symbiotic status.


Our research has been funded by a range of funders across the globe, including Japan Society for the Promotion of Science (JSPS, Japan), Human Frontier Science Program (HFSP, International), Royal Society (UK), Academia Sinica (Taiwan), and National Science and Technology Council (NSTC, Taiwan).

The current and past direct funding includes: