Basic Information

Affiliated programs (koza)

• Graduate School of Pharmaceutical Sciences, 創発医薬科学専攻 創発医薬科学講座, 助教
• Graduate School of Science, 生物科学専攻 化学生命科学研究領域, 助教

Email Address

• Email Address

  ishii.yuu.6wkyoto-u.ac.jp

Academic Degree

• 04 Sep. 2019

  東北大学博士（生命科学）
• 25 Mar. 2010

  東北大学修士（生命科学）

Academic Resume (Undergraduate School/Majors)

• 東北大学, 理学部生物学科, 卒業

Research History

• From Jan. 2026, To Present

  Kyoto University, Bioinformatics Center, Institute for Chemical Research, Assistant professor
• From Apr. 2023, To Present

  The University of Tokyo, Graduate School of Frontier Sciences, Affiliate Researcher
• From Jul. 2023, To Dec. 2025

  Kyoto University, Graduate School of Agriculture, 特定研究員（学振RPD）
• From Jan. 2023, To Jun. 2023

  Kyoto University, Graduate School of Agriculture, 学振特別研究員（PD）
• From Apr. 2020, To Mar. 2023

  Tohoku University, Graduate School of Life Sciences Department of Ecological Developmental Adaptability Life Sciences, 博士研究員
• From Apr. 2020, To Dec. 2022

  Miyagi University of Education, 学振特別研究員（PD）
• From Oct. 2019, To Mar. 2020

  Tohoku University, Graduate School of Life Sciences, 助教
• From Aug. 2015, To Sep. 2019

  Tohoku University, Graduate School of Life Sciences, 研究支援員

ID,URL

• J-Global ID

  201601017684770067

• External link

  https://sites.google.com/view/yuu-ishii/home

researchmap URL

• https://researchmap.jp/YuuIshii

Research

Research Topics, Overview of the research

• Research Topics

  Evolutionary Mechanisms of Intracellular Symbiosis Between Cnidarians and Unicellular Algae

• Overview of the research

  I am interested in how intracellular symbiosis between cnidarians, such as corals and sea anemones, and unicellular algae known as Symbiodiniaceae has evolved. This symbiotic relationship plays an important role in supporting marine ecosystems in tropical and subtropical regions. My research focuses particularly on the exchange of nutrients and other substances between the symbiotic partners. To understand the mechanisms and evolution of this relationship, I combine omics approaches, chemical analyses, and microscopy.

Research Interests

• interaction
• ecological evolution
• symbiosis
• coral
• Symbiodiniaceae

Research Areas

• Life sciences, Genomics
• Life sciences, Evolutionary biology

Papers

• Ecophysiology of Pavlomulina ranunculiformis (Rappephyceae, Haptophyta): Implications for its fundamental niche

  Akari Miyaura; Sai Koide; So Kobayashi; Yuto Hazui; Masanobu Kawachi; Yuu Ishii; Takashi Yoshida; Ryoma Kamikawa

  Phycological Research, Oct. 2026

  
• Positive Selection of a Starch Synthesis Gene and Phenotypic Differentiation of Starch Accumulation in Symbiotic and Free-Living Coral Symbiont Dinoflagellate Species

  Yuu Ishii; Shunsuke Kanamori; Ryusaku Deguchi; Masakado Kawata; Shinichiro Maruyama; Takashi Yoshida; Ryoma Kamikawa

  Genome Biology and Evolution, 03 Jul. 2025, Peer-reviewed, Lead author, Corresponding author

  
• Molecular diversity of green-colored microbial mats from hot springs of northern Japan.

  Yangtsho Gyaltshen; Yuu Ishii; Sophie Charvet; Eleanor Goetz; Shinichiro Maruyama; Eunsoo Kim

  Extremophiles : life under extreme conditions, 31 Aug. 2024, Peer-reviewed, Lead author

  
• Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards

  Sakamoto, F.; Kanamori, S.; D{\'i}az, L.M.; C{\'a}diz, A.; Ishii, Y.; Yamaguchi, K.; Shigenobu, S.; Nakayama, T.; Makino, T.; Kawata, M.

  Ecology and Evolution, 2024, Peer-reviewed

  
• Genetic differentiation and local adaptation of the Japanese honeybee, Apis cerana japonica

  Wakamiya, T.; Kamioka, T.; Ishii, Y.; Takahashi, J.-I.; Maeda, T.; Kawata, M.

  Ecology and Evolution, Oct. 2023, Peer-reviewed

  
• Environmental pH signals the release of monosaccharides from cell wall in coral symbiotic alga

  Ishii, Y.; Ishii, H.; Kuroha, T.; Yokoyama, R.; Deguchi, R.; Nishitani, K.; Minagawa, J.; Kawata, M.; Takahashi, S.; Maruyama, S.

  eLife, 18 Aug. 2023, Peer-reviewed, Lead author

  
• Establishment of a New Model Sea Anemone for Comparative Studies on Cnidarian-Algal Symbiosis

  Mihirogi, Y.; Kaneda, M.; Yamagishi, D.; Ishii, Y.; Maruyama, S.; Nakamura, S.; Shimoyama, N.; Oohori, C.; Hatta, M.

  Zoological Science, 17 Apr. 2023, Peer-reviewed

  
• On the origin of appetite: GLWamide in jellyfish represents an ancestral satiety neuropeptide

  Thoma, V.; Sakai, S.; Nagata, K.; Ishii, Y.; Maruyama, S.; Abe, A.; Kondo, S.; Kawata, M.; Hamada, S.; Deguchi, R.; Tanimoto, H.

  Proceedings of the National Academy of Sciences of the United States of America, 11 Apr. 2023, Peer-reviewed

  
• Does selection occur at the intermediate zone of two insufficiently isolated populations? A whole-genome analysis along an altitudinal gradient

  Yoshida, N.; Morinaga, S.-I.; Wakamiya, T.; Ishii, Y.; Kubota, S.; Hikosaka, K.

  Journal of Plant Research, Mar. 2023, Peer-reviewed

  
• Gene expression alterations from reversible to irreversible stages during coral metamorphosis

  Ishii, Y.; Hatta, M.; Deguchi, R.; Kawata, M.; Maruyama, S.

  Zoological Letters, Dec. 2022, Peer-reviewed, Lead author, Corresponding author

  
• Genetic basis of orange spot formation in the guppy (Poecilia reticulata)

  Kawamoto, M.; Ishii, Y.; Kawata, M.

  BMC Ecology and Evolution, Dec. 2021, Peer-reviewed

  
• Detection of genes positively selected in Cuban Anolis lizards that naturally inhabit hot and open areas and currently thrive in urban areas

  Shunsuke Kanamori; Antonio Cádiz; Luis M. Díaz; Yuu Ishii; Takuro Nakayama; Masakado Kawata

  Ecology and Evolution, Feb. 2021, Peer-reviewed

  
• Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology (Nature Methods, (2020), 17, 5, (481-494), 10.1038/s41592-020-0796-x)

  Faktorov{\'a}, D.; Nisbet, R.E.R.; Fern{\'a}ndez Robledo, J.A.; Casacuberta, E.; Sudek, L.; Allen, A.E.; Ares, M.; Arest{\'e}, C.; Balestreri, C.; Barbrook, A.C.; Beardslee, P.; Bender, S.; Booth, D.S.; Bouget, F.-Y.; Bowler, C.; Breglia, S.A.; Brownlee, C.; Burger, G.; Cerutti, H.; Cesaroni, R.; Chiurillo, M.A.; Clemente, T.; Coles, D.B.; Collier, J.L.; Cooney, E.C.; Coyne, K.; Docampo, R.; Dupont, C.L.; Edgcomb, V.; Einarsson, E.; Elustondo, P.A.; Federici, F.; Freire-Beneitez, V.; Freyria, N.J.; Fukuda, K.; Garc{\'i}a, P.A.; Girguis, P.R.; Gomaa, F.; Gornik, S.G.; Guo, J.; Hampl, V.; Hanawa, Y.; Haro-Contreras, E.R.; Hehenberger, E.; Highfield, A.; Hirakawa, Y.; Hopes, A.; Howe, C.J.; Hu, I.; Iba{\~n}ez, J.; Irwin, N.A.T.; Ishii, Y.; Janowicz, N.E.; Jones, A.C.; Kachale, A.; Fujimura-Kamada, K.; Kaur, B.; Kaye, J.Z.; Kazana, E.; Keeling, P.J.; King, N.; Klobutcher, L.A.; L; er, N.; Lassadi, I.; Li, Z.; Lin, S.; Lozano, J.-C.; Luan, F.; Maruyama, S.; Matute, T.; Miceli, C.; Minagawa, J.; Moosburner, M.; Najle, S.R.; Nanjappa, D.; Nimmo, I.C.; Noble, L.; Nov{\'a}k Vanclov{\'a}, A.M.G.; Nowacki, M.; Nu{\~n}ez, I.; Pain, A.; Piersanti, A.; Pucciarelli, S.; Pyrih, J.; Rest, J.S.; Rius, M.; Robertson, D.; Ruaud, A.; Ruiz-Trillo, I.; Sigg, M.A.; Silver, P.A.; Slamovits, C.H.; Jason Smith, G.; Sprecher, B.N.; Stern, R.; Swart, E.C.; Tsaousis, A.D.; Tsypin, L.; Turkewitz, A.; Turn?ek, J.; Valach, M.; Verg{\'e}, V.; von Dassow, P.; von der Haar, T.; Waller, R.F.; Wang, L.; Wen, X.; Wheeler, G.; Woods, A.; Zhang, H.; Mock, T.; Worden, A.Z.; Luke?, J.

  Nature Methods, May 2020, Peer-reviewed

  
• Genetic tool development in marine protists: emerging model organisms for experimental cell biology

  Faktorov{\'a}, D.; Nisbet, R.E.R.; Fern{\'a}ndez Robledo, J.A.; Casacuberta, E.; Sudek, L.; Allen, A.E.; Ares, M.; Arest{\'e}, C.; Balestreri, C.; Barbrook, A.C.; Beardslee, P.; Bender, S.; Booth, D.S.; Bouget, F.-Y.; Bowler, C.; Breglia, S.A.; Brownlee, C.; Burger, G.; Cerutti, H.; Cesaroni, R.; Chiurillo, M.A.; Clemente, T.; Coles, D.B.; Collier, J.L.; Cooney, E.C.; Coyne, K.; Docampo, R.; Dupont, C.L.; Edgcomb, V.; Einarsson, E.; Elustondo, P.A.; Federici, F.; Freire-Beneitez, V.; Freyria, N.J.; Fukuda, K.; Garc{\'i}a, P.A.; Girguis, P.R.; Gomaa, F.; Gornik, S.G.; Guo, J.; Hampl, V.; Hanawa, Y.; Haro-Contreras, E.R.; Hehenberger, E.; Highfield, A.; Hirakawa, Y.; Hopes, A.; Howe, C.J.; Hu, I.; Iba{\~n}ez, J.; Irwin, N.A.T.; Ishii, Y.; Janowicz, N.E.; Jones, A.C.; Kachale, A.; Fujimura-Kamada, K.; Kaur, B.; Kaye, J.Z.; Kazana, E.; Keeling, P.J.; King, N.; Klobutcher, L.A.; L; er, N.; Lassadi, I.; Li, Z.; Lin, S.; Lozano, J.-C.; Luan, F.; Maruyama, S.; Matute, T.; Miceli, C.; Minagawa, J.; Moosburner, M.; Najle, S.R.; Nanjappa, D.; Nimmo, I.C.; Noble, L.; Nov{\'a}k Vanclov{\'a}, A.M.G.; Nowacki, M.; Nu{\~n}ez, I.; Pain, A.; Piersanti, A.; Pucciarelli, S.; Pyrih, J.; Rest, J.S.; Rius, M.; Robertson, D.; Ruaud, A.; Ruiz-Trillo, I.; Sigg, M.A.; Silver, P.A.; Slamovits, C.H.; Jason Smith, G.; Sprecher, B.N.; Stern, R.; Swart, E.C.; Tsaousis, A.D.; Tsypin, L.; Turkewitz, A.; Turn?ek, J.; Valach, M.; Verg{\'e}, V.; von Dassow, P.; von der Haar, T.; Waller, R.F.; Wang, L.; Wen, X.; Wheeler, G.; Woods, A.; Zhang, H.; Mock, T.; Worden, A.Z.; Luke?, J.

  Nature Methods, 2020

  
• Human-specific mutations in VMAT1 confer functional changes and multi-directional evolution in the regulation of monoamine circuits.

  Daiki X Sato; Yuu Ishii; Tomoaki Nagai; Kazumasa Ohashi; Masakado Kawata

  BMC evolutionary biology, 02 Dec. 2019, Peer-reviewed

  
• Global shifts in gene expression profiles accompanied with environmental changes in cnidarian-dinoflagellate endosymbiosis

  Ishii, Y.; Maruyama, S.; Takahashi, H.; Aihara, Y.; Yamaguchi, T.; Yamaguchi, K.; Shigenobu, S.; Kawata, M.; Ueno, N.; Minagawa, J.

  G3: Genes, Genomes, Genetics, 01 Jul. 2019, Peer-reviewed, Lead author

  
• Isolation of uracil auxotroph mutants of coral symbiont alga for symbiosis studies

  Ishii, Y.; Maruyama, S.; Fujimura-Kamada, K.; Kutsuna, N.; Takahashi, S.; Kawata, M.; Minagawa, J.

  Scientific Reports, Dec. 2018, Peer-reviewed, Lead author

  

Misc.

• 褐虫藻は共生していることをどう感じているのか

  石井悠

  BSJ-review, Nov. 2022, Peer-reviewed, Lead author

  
• 褐虫藻が低pH条件でグルコースを分泌するメカニズムと意義

  石井悠; 石井悠; 石井宏憲; 高橋俊一; 高橋俊一; 黒羽剛; 篠原直貴; 横山隆亮; 出口竜作; 西谷和彦; 皆川純; 皆川純; 河田雅圭; 丸山真一朗

  藻類, 2021

  
• サンゴ共生藻と環境との対話,宿主との対話

  石井悠; 丸山真一朗

  光合成研究, Apr. 2020, Peer-reviewed, Lead author

  
• サンゴ共生藻における形質転換技術開発の現状と展望

  石井 悠; 丸山 真一朗

  BSJ-review, Nov. 2017, Peer-reviewed, Lead author

  

Awards

• 08 Sep. 2023

  日本動物学会女性研究者奨励OM賞
• 02 Jun. 2018

  International Society for Evolutionary Protistology meeting 2018 Travel Award

Education

Teaching subject(s)

• From 01 Apr. 2026, To 31 Mar. 2027

  Seminar on Bioinformatics IIC

  9067, Spring, Graduate School of Science, 1
• From 01 Apr. 2026, To 31 Mar. 2027

  Seminar on Bioinformatics IIB

  9066, Fall, Graduate School of Science, 1
• From 01 Apr. 2026, To 31 Mar. 2027

  Seminar on Bioinformatics IIA

  9065, Spring, Graduate School of Science, 1
• From 01 Apr. 2026, To 31 Mar. 2027

  Seminar on Bioinformatics IID

  9068, Fall, Graduate School of Science, 1
• From 01 Apr. 2026, To 31 Mar. 2027

  Seminar on Bioinformatics IA

  9061, Spring, Graduate School of Science, 1
• From 01 Apr. 2026, To 31 Mar. 2027

  Seminar on Bioinformatics ID

  9064, Fall, Graduate School of Science, 1
• From 01 Apr. 2026, To 31 Mar. 2027

  Seminar on Bioinformatics IC

  9063, Spring, Graduate School of Science, 1
• From 01 Apr. 2026, To 31 Mar. 2027

  Seminar on Bioinformatics IB

  9062, Fall, Graduate School of Science, 1
• From 01 Apr. 2026, To 31 Mar. 2027

  Bioinformatics

  3768, Spring, Faculty of Science, 2
• From 01 Apr. 2026, To 31 Mar. 2027

  Advanced Course on Biological Science B

  9012, Fall, Graduate School of Science, 2
• From 01 Apr. 2026, To 31 Mar. 2027

  Bioinformatics

  9136, Spring, Graduate School of Science, 2
• From 01 Apr. 2026, To 31 Mar. 2027

  Genome Informatics

  C408, Spring, Faculty of Pharmaceutical Sciences, 2