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RIKEN BioResource Research Center Plant-Microbe Symbiosis Research and Development Team

Team Leader: Yasunori Ichihashi (Ph.D.)

Research Summary

Yasunori  Ichihashi(Ph.D.)

Since most agricultural crops grow in soil, where is one of the richest microbial ecosystems on Earth, plants and microbes are strongly associated with each other. Elucidation of the plant-microbe symbiosis should contribute to building a sustainable solution for world food and environmental problems. Our team plan to construct bioresources and experimental systems of plants and microbes for the symbiosis studies, as well as perform large-scale omics studies on agricultural fields. Through collaborative researches with domestic and international communities, we aim to fully understand regulatory mechanism behind the plant-microbe symbiosis and provide a research platform leading to industrial applications.

Main Research Fields

  • Biology

Related Research Fields

  • Agricultural Sciences


  • Plant-Microbe Symbiosis
  • Rhizosphere microbes
  • Mycorrhizal fungi
  • Field-Omics
  • The 21st Century Green Revolution

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

  • 1.Toju, H., Peay, K. G., Yamamichi, M., Narisawa, K., Hiruma, K., Naito, K., Fukuda, S., Ushio, M., Nakaoka, S., Onoda, Y., Yoshida, K., Schlaeppi, K., Bai, Y., Sugiura, R., Ichihashi, Y., Minamisawa, K., Kiers, E. T.:
    "Core microbiomes for sustainable agroecosystems"
    Nat Plants in press. (2018)
  • 2.*Ichihashi, Y., Kusano, M., Kobayashi, M., Suetsugu, K., Yoshida, S., Wakatake, T., Kumaishi, K., Shibata, A., Saito, K., Shirasu, K.:
    “Transcriptomic and Metabolomic Reprogramming from Roots to Haustoria in the Parasitic Plant, Thesium chinense
    Plant Cell Physiol. https://doi.org/10.1093/pcp/pcx200 (2017)
  • 3.*Ichihashi, Y., Mutuku, J. M., Yoshida, S., Shirasu, K.:
    “Transcriptomics exposes the uniqueness of parasitic plants”
    Briefings in Functional Genomics 14, 275-282. (2015)
  • 4.*Townsley, B. T., Covington, M. F., Ichihashi, Y., Zumstein, K., Sinha, N. R.:
    “BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction”
    Front. Plant Sci. 6, 366. (2015)
  • 5.*Ichihashi, Y., Aguilar-Martínez, J. A., Farhi, M., Chitwood, D. H., Kumar, R., Millon, L. V., Peng, J., Maloof, J. N., Sinha, N. R.:
    “Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape”
    Proc. Natl. Acad. Sci. USA. 111, E2616-E2621. (2014)
  • 6.*Ichihashi, Y., Sinha, N. R.:
    “From genome to phenome and back in tomato”
    Curr. Opin. Plant Biol. 18, 9-15. (2014)
  • 7.*Chitwood, D. H., Kumar, R., Headland, L, R., Ranjan, A., Covington, M. F., Ichihashi, Y., Fulop, D., Jiménez-Gómez, J. M., Peng, J., Maloof, J. N., Sinha, N. R.:
    “A quantitative genetic basis for leaf morphology in a set of precisely defined tomato introgression lines”
    Plant Cell 25, 2465-248. (2013)
  • 8.*Kumar, R., Ichihashi, Y., Kimura, S., Chitwood, D. H., Headland, L. R., Peng, J., Maloof, J. N., Sinha, N. R.:
    “A High-Throughput Method for Illumina RNA-Seq Library Preparation”
    Front. Plant Sci. 3, 202. (2012)
  • 9.*Ichihashi, Y., Kawade, K., Usami, T., Horiguchi, G., Takahashi, T., Tsukaya, H.:
    “Key proliferative activity in the junction between the leaf blade and leaf petiole of Arabidopsis”
    Plant Physiol. 157, 1151-1162. (2011)
  • 10.*Ichihashi, Y., Horiguchi, G., Gleissberg, S., Tsukaya, H.:
    “The bHLH transcription factor SPATULA controls final leaf size in Arabidopsis thaliana”
    Plant Cell Physiol. 51, 252-261. (2010)

Related Links

Lab Members

Principal investigator

Yasunori Ichihashi
Team Leader

Core members

Shungo Kobori
Research & Development Scientist
Takumi Sato
Postdoctoral Researcher
Kie Kumaishi
Technical Staff II

Contact Information

BioResource Center Main Building
3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
Email: yasunori.ichihashi [at] riken.jp