FY2023 Annual Report

Evolutionary Neurobiology Unit
Associate Professor Hiroshi Watanabe

(From left to right) Osamu Horiguchi, Kurato Mohri, Ryotaro Nakamura, Hiroshi Watanabe, Hongdi Wang, Chihiro Arasaki, Christine Guzman, Yayoi Hongo, Chihiro Kawano, Minato Miyake, Sen Hedife, Ayumi Yoshikawa


The Evolutionary Neurobiology Unit seeks to clarify the evolutionary origins and early processes of metazoans. Multiple hypotheses addressing these biologically significant questions have been proposed, primarily grounded in histological findings and more recently in the genomic information of various non-model animals. However, many unanswered questions persist, necessitating experimental verification.

Our analysis extends beyond genomic information to encompass the embryonic development process and physiological properties at the cellular level in adults. The unit examines early-branching extant species, focusing on phylogenetically important animal lineages, including ctenophores and cnidarians.

Moreover, we aim to unravel the mysteries of early animal evolution by constructing a novel systematic approach that fully leverages cutting-edge omics technology, including proteomics and metabolomics, alongside bioinformatics and gene function analysis. Additionally, through collaboration with domestic and international laboratories and aquariums, we are establishing new early-branching animal models and further fortifying challenging interdisciplinary research initiatives.

1. Staff

  • Dr. Hiroshi Watanabe, Associate Professor
  • Dr. Kurato Mohri, Staff Scientist
  • Dr. Ryo Nakamura, Postdoctoral Scholar
  • Dr. Hongdi Wang, Postdoctoral Scholar
  • Dr. Ryotaro Nakamura, Research Unit Technician
  • Dr. Yayoi Hongo, Research Unit Technician
  • Chihiro Kawano, Research Unit Technician
  • Osamu Horiguchi, PhD Student (JSPS DC1 fellow)
  • Christine Guzman, PhD Student (JSPS DC1 fellow)
  • Minato Miyake, PhD Student (JSPS DC1 fellow)
  • Sen Hedife, PhD Student
  • Junko Higuchi, Research Assistant
  • Ayumi Yoshikawa, Internship Student (April–August 2023)
  • Chihiro Arasaki, Research Unit Administrator

Past members

  • Dr. Eisuke Hayakawa (April 2016–March 2023. Currently Researcher, RIKEN CSRS, Japan)
  • Kanako Hirata, Research Unit Technician (PoC) (December 2019–March 2023)
  • Mika Ogata, Research Assistant (PoC) (May 2021–March 2023)
  • Asami Kyan, Research Assistant (PoC) (January–April 2023)
  • Ivan Mbogo, PhD Student (September 2015–March 2022. Currently Associate of Hematology Business Development, Sysmex Corporation)
  • Larisa Sheloukhova, PhD Student (September 2015–March 2022. Currently Program-specific researcher at SACI, Kyoto University)
  • Kun-Lung Li, PhD Student (September 2016–September 2021. Currently PostDoc, Institute of Cellular and Organismic Biology, Academia Sinica, Taiwan)
  • Junko Higuchi, Research Assistant (June 2019–May 2022)
  • Akiko Tanimoto, Research Assistant (February 2019–February 2022)
  • Hibiki Fukunaga, Research Assistant (October 2019–March 2021)
  • Rio Zakoh, Research Assistant (April 2018–March 2019)
  • Dr. Mei-Fang Lin, Postdoctoral Scholar (May 2017–July 2020. Currently Assistant Professor, National Sun Yat-sen University, Taiwan)
  • Ms. Erina Kawai, Research Unit Technician (August 2016–October 2019. Currently Research Unit Scientific Diver, OIST Marine Climate Change Unit)
  • Dr. Amol Dahal, Research Unit Technician (May 2016–November 2018. Currently Assistant Professor, Kathmandu University)
  • Dr. Shinya Komoto, Staff Scientist (October 2016–March 2018. Currently Research Support Specialist, OIST Scientific Imaging Section)

2. Collaborations

2.1 Gene function analysis in the model ctenophoran Bolinopsis mikado

  • Type of collaboration: Joint research
  • Researchers:
    • Professor Kazuo Inaba and Assistant Professor Kogiku Shiba, Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan

2.2 Genome analysis of Zoantharian species

  • Type of collaboration: Joint research
  • Researchers:
    • Assistant Professor Mei-Fang Lin, National Sun Yat-sen University, Taiwan
    • Associate Professor James Reimer, University of the Ryukyus

2.3 AI-based peptide receptor prediction

  • Type of collaboration: Joint research
  • Researchers:
    • Dr. Honoo Satake and Dr. Akira Shiraishi, Bioorganic Research Institute, Suntroy Foundation for Life Sciences, Kyoto, Japan

3. Activities and Findings

3.1 Analysis of neurotransmitters in basal metazoans

Chemical neurotransmission plays important roles in the nervous system of bilaterian animals. Some primitive neurotransmitters/modulators, including neuropeptides, have been reported to function also in cnidarians, the closest sisters to all bilaterian animals. This suggests that the last common ancestor of Bilateria/Cnidaria was already equipped with chemical neurotransmission. However, the molecular repertoire of neurotransmitters in early-branching taxa including Cnidaria is still unclear. We surveyed molecules in the LC-MS metabolomics of cnidarians to understand the physiological characteristics of the nervous system in pre-bilaterian stages (Figure 1). 

Figure 1: Base peak intensity chromatograms of the cnidarian extracts from c.a. 20 mg of dried a) Nematostella vectensis, b) Aurelia sp. (polyps), c) Aurelia sp. (medusa), and d) Hydra vulgaris, obtained by LC-ESI-MS/MS (positive-ion mode).

3.2 Functional analysis of cnidarian neuropeptides

Peptide hormones are intercellular transmitters that have various physiological roles, and among them, neuropeptides, which are mainly expressed by neurons, are known to have functioned since the early stages of animal evolution. However, much remains unknown about the functions of neuropeptides in pre-bilaterians. In 2022, we reported cnidarian neuropeptides identified using a mass spectrometry-based neuropeptide identification strategy (Figure 2a,b). This year, we used the cnidarian model Nematostella vectensis to experimentally examine the physiological functions of these neuropeptides. A neuropeptide is expressed in the neural networks of the endoderm during planula larval and polyp stages (Figure 2c). Addition of the synthetic peptide to the medium increased the swimming activity of planula larvae (Figure 2d upper). At the young polyp stage, this peptide induced an acute response of contractile behavior along the oral-aboral body axis (Figure 2d lower). These findings reinforce previous knowledge that neuropeptides are involved in controlling various behavioral patterns in cnidarians. In order to comprehensively understand the functions of the peptidergic system, we are currently conducting developmental and behavioral analyses of diverse neuropeptide repertoires.

Figure 2: MS-based identification of amidated short peptides in cnidarians. (b) Single-cell expression profiles of the identified neuropeptides. (c) Immunostaining of a neuropeptide at planula (upper) and young polyp (lower) stages. (d) Effect of addition of synthetic neuropeptide to the culture on planula swimming (upper) and polyp behavior.

3.3 Studies of the neuromuscular organization of benthic ctenophore species

Ctenophora is the earliest metazoan group with neurons and muscles. Therefore, examining the organization of the muscular and nervous systems in this extant lineage provides key insights into understanding the evolutionary origins of these systems essential for animal behavior. Although ctenophores are divided into benthic and pelagic types, studies on the anatomy of the neuromuscular system of ctenophores have mainly focused on pelagic species. This year, we analyzed the detailed neuromuscular tissue of the benthic ctenophore species Vallicula multiformis (Fig. 3a) and compared it with the neuromuscular tissue of a pelagic species (Mohri and Watanabe, accepted). To observe the neural tissue of V. multiformis, we investigated the distribution of neuropeptides. In V. multiformis, which does not have the characteristic comb rows found in pelagic species, we did not detect neurons thought to be involved in comb beating. However, the observed subepithelial and tentacle neural networks were similar to those of pelagic species (Fig. 3b). The similar distribution of these peptides in V. multiformis neurons suggests a common function of these peptides as neuropeptides in ctenophore species. Despite significant differences in morphology and lifestyle, the musculature of V. multiformis closely resembled that of pelagic species (Fig. 3c). These comparative studies contribute to our understanding of the general characteristics of neurons and muscles in ctenophore species.

Figure 3: (a) A benthic ctenophore species Vallicula multiformis.  (b) Distribution of neuropeptide-positive neurons in subepithelial (left) and tentacular (right) nervous system. (c) Actin fibers running at the aboral surface. (d) Schematic diagram of the muscule organization of benthic (V. multiformis) and pelagic (B. mikado) ctenophores.

4. Publications

4.1 Journals

  1. Nakamura, R., Nakamura, R., Watanabe, H. Cnidarian pharyngeal nervous system illustrates prebilaterian neurosecretory regulation of feeding. BioRxiv doi: https://doi.org/10.1101/2023.04.05.535675 (April 2023)
  2. Sheloukhova, L.Watanabe, H. Analysis of cnidarian Gcm suggests a neuronal origin of glial EAAT1 function. Scientific Reports, doi: 10.1038/s41598-023-42046-9 (September 2023)
  3. Hongo, Y., Sekimoto, K. Experiences of Pioneers, Journal of Mass Spectrometry Society of Japan, 71 (1) 19-24, doi: https://doi.org/10.5702/massspec.S23-25 (2023)
  4. Toji, N., Sawai, A., Wang, H., Ji, Y., Sugioka, R., Go, Y., & Wada, K. A predisposed motor bias shapes individuality in vocal learning. Proceedings of the National Academy of Sciences, 121(3), doi: https://doi.org/10.1073/pnas.2308837121 (January 2024)
  5. Mohri, K., Watanabe, H. Neuromuscular organization of the benthic ctenophore, Vallicula multiformis. Zoological Lett., doi: https://doi.org/10.1186/s40851-024-00225-0​ (January 2024)
  6. Nakamura, T., Hongo Y., Harada, K. Mobilize a Proton to Transform the Collision-Induced Dissociation Spectral Pattern of a Cyclic Peptide. Mass Spectrometry, 13 (1), doi: https://doi.org/10.5702/massspectrometry.A0144 (January 2024)

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

  1. Wang, H., Watanabe, H., The genomic features underpinning early neurogenesis origin during Metazoan evolution, May15-18, 2023, HHMI Janelia research campus, US (Poster)
  2.  Mohri, K., Miyake, M., Watanabe, H., 動物の筋肉は進化上どのように生じたのか:クシクラゲT-box転写因子による筋分化制御にみられる保存性 (How did the muscles evolve in metazoan: A conserved T‐boxtranscription factor‐mediating muscle differentiation in Ctenophora), The 25th Annual Meeting of Society of Evolutionary Studies, Japan, August 31, 2023, Okinawa, Japan (Oral)
  3.  Miyake, M., Horiguchi, O., Watanabe, H.  Insights into the evolutionary origins of neurons: Lessons from ctenophore neurogenesis. The 25th of Annual Meeting of the Society of Evolutionary Studies, Japan, Okinawa, Japan, August 31-September 3, 2023    (Oral)
  4.  Mohri, K., Miyake, M., Watanabe, H., カブトクラゲ T-box転写因子による筋分化制御と多細胞動物における筋分化制御機構の共通性 (Regulation of muscle differentiation by T-box transcription factors in ctenophore.), The 94th Annual Meeting of the Zoological Society of Japan, September 9, 2023, Yamagata, Japan (Oral)
  5.  Miyake, M., Horiguchi, O., Watanabe, H. Functional analysis of Ctenophora transcription factors and evolutionary origins of the nervous system. The 94th Annual Meeting of the Zoological Society of Japan, September 9, 2023, Yamagata, Japan (Oral)
  6.  Watanabe, H., Nakamura, R., Nakamura, R. Development of semi-centralized nervous system of Nematostella. The 94th Annual Meeting of the Zoological Society of Japan, Yamagata, Japan September 7-9, 2023 (Oral)
  7.  Nakamura, R., Watanabe, H. Cnidarian pharyngeal nervous system illustrates prebilaterian neurosecretory regulation of feeding. International Workshop "EVOLUTION OF RESILIENCE, REGENERATION, AND ANIMAL COMPLEXITY - INSIGHTS FROM BASAL METAZOANS", Evangelishe Akademie Tuzting, Germany September 18-21, 2023 (Oral)
  8.  Guzman, C., Watanabe, H. From diffusion to network: A Neurexin view of the Origin of Neural Synapse.International Workshop "EVOLUTION OF RESILIENCE, REGENERATION, AND ANIMAL COMPLEXITY - INSIGHTS FROM BASAL METAZOANS", Evangelishe Akademie Tuzting, Germany, September 18-21, 2023 (Poster)
  9.  Hongo, Y., Nakamura, R., Watanabe, H., Unpredicted metabolism of aromatic L-amino acids in Cnidaria, Nematostella vectensis. The 47th The Japan Society for Comparative Endocrinology Symposium, Nov. 17–19, 2023, Fukuoka, Japan (Poster)
  10.  Nakamura, R., et al., 刺胞動物ネマトステラにおける神経ペプチドの時空間的動態と機能解析. The 47th The Japan Society for Comparative Endocrinology Symposium, Nov. 17–19, 2023, Fukuoka, Japan (Poster)
  11.  Hongo, Y. LC-ESI-MS/MS で覗いた動物の代謝進化, RIKEN Symposium, December 12, 2024 (Oral) 
  12.  Watanabe, H. Evolutionary Origin of the Central Nervous System: Insights from the development and function of cnidarian Pharyngeal Nervous System. The 3rd AsiaEvo Conference, Dec 15-19, 2023. Singapore (Oral)
  13. Miyake, M., Horiguchi, O., Watanabe, H., Insights into the evolutionary origins of neurons from functions of putative neurogenic transcription factors in Ctenophora. The 3rd AsiaEvo Conference, Dec 15-19, 2023. Singapore (Poster)

5. Intellectual Property Rights and Other Specific Achievements

External Fundings

  • Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science (JSPS), “Evolutionary origins of the integrated nervous system: developmental, physiological, and functional analysis of the pharyngeal nervous system of cnidarians (刺胞動物の咽頭神経系の発生・生理・機能学的解析で迫る集積神経系の進化的起源)” Grant No. 23H02533, Lead PI: H. Watanabe, Amount 18,720,000 JPY, Period: Apr. 2023 – Mar. 2026
  • Grant-in-Aid for Early-Career Scientists, Japan Society for the Promotion of Science (JSPS), “Ancestral Functions of PRXamide Neuropeptides and Evolutionary Origin of Endocrine Systems: Insights from Functional Analysis in a Model Sea Anemone (刺胞動物を用いた内分泌系の起源解明:PRXamide 神経ペプチドの祖先的機能は何か?)” Grant No. 23K14244, Lead PI: R. Nakamura, Amount 4,680,000JPY, Period: Apr. 2023 – Mar. 2026
  • Grant-in-Aid for JSPS Fellows, Japan Society for the Promotion of Science (JSPS), “Pou-class gene functions in Ctenophora and their implications in nervous system evolution (クシクラゲPou転写因子群の機能解析で迫る神経の進化的起源)” Grant No. 23KJ2140, Lead PI: M. Miyake, Amount 3,000,000JPY, Period: Apr. 2023–Mar.2026

6. Meetings and Events

Nothing to report

7. Other

Nothing to report.