Polyploidization and stress response in plants

Evolutionary Genomics

Polyploidization is a frequently observed phenomenon in plant species. It has played an important role as a driving force for evolution in the sense of diversification. Many allopolyploid species have distinct habitats (environmental tolerance), phenotypes or other traits from their parental species. These novel characteristics could have emerged by the combination of multiple genomes. In spite of its interesting role for evolution, polyploidization has not been well studied systematically way, mainly because of the lack of molecular and genomic tools. The recent technical advances, however, are changing the situation.

Our main interest is to reveal how polyploid species adapted to new environment after polyploidization. We focus on transcriptomics, by exploiting the power of latest molecular techniques, e.g. next generation sequencers, to separately detect the expression of homeologs, using genus Arabidopsisand their close relatives. In addition to carrying out molecular research in the wet lab, we collaborate with bioinformaticians, ecologists and cytologists in a multilateral approach to the evolutionary significance of allopolyploidization.

Recent Publications

  • Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica
    Paape, T; Briskine, RV; Halstead-Nussloch, G; Lischer, HEL; Shimizu-Inatsugi, R; Hatakeyama, M; Tanaka, K; Nishiyama, T; Sabirov, R; Sese, J; Shimizu, KK
    NATURE COMMUNICATIONS, 9 10.1038/s41467-018-06108-1 SEP 25 2018
  • Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana
    Y Sato, R Shimizu-Inatsugi, M Yamazaki, KK Shimizu, AJ Nagano
    bioRxiv, 320903,  DOI: 10.1101/320903 2018
  • Patterns of polymorphism, selection and linkage disequilibrium in the subgenomes of the allopolyploid Arabidopsis kamchatica
    Timothy Paape, Roman V Briskine, Heidi EL Lischer, Gwyneth Halstead-Nussloch, Rie Shimizu-Inatsugi, Masaomi Hatekayama, Kenta Tanaka, Tomoaki Nishiyama, Renat Sabirov, Jun Sese, Kentaro K Shimizu
    bioRxiv, 248195 https://doi.org/10.1101/248195 2018 
  • Cost-Effective Discovery of Nucleotide Polymorphisms in Populations of an Allopolyploid Species Using Pool-Seq
    AS Hirao, Y Onda, R Shimizu-Inatsugi, J Sese, KK Shimizu, T Kenta
    American Journal of Molecular Biology 7 (04), 1031 10.4236/ajmb.2017.74012  2017
  • Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop
    Hatakeyama, M; Aluri, S; Balachadran, MT; Sivarajan, SR; Patrignani, A; Gruter, S; Poveda, L; Shimizu-Inatsugi, R; Baeten, J; Francoijs, KJ; Nataraja, KN; Reddy, YAN; Phadnis, S; Ravikumar, RL; Schlapbach, R; Sreeman, SM; Shimizu, KK
    DNA RESEARCH, 25 (1):39-47; https://doi.org/10.1093/dnares/dsx036 FEB 2018
  • Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop 
    Hatakeyama, Masaomi; Aluri, Sirisha; Balachadran, Mathi Thumilan; et al. 
    DNA RESEARCH, 25 (1): 39-47 FEB 2018 Article (Details)
  • Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology 
    Briskine, Roman V.; Paape, Timothy; Shimizu-Inatsugi, Rie; et al. 
    MOLECULAR ECOLOGY RESOURCES, 17 (5): 1025-1036 SEP 2017 Article (Details)
  • The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae) 
    Izuno, Ayako; Kitayama, Kanehiro; Onoda, Yusuke; et al. 
    MOLECULAR ECOLOGY, 26 (6): 1515-1532 MAR 2017 Article (Details)
  • Plant adaptive radiation mediated by polyploid plasticity in transcriptomes 
    Shimizu-Inatsugi, Rie; Terada, Aika; Hirose, Kyosuke; et al. 
    MOLECULAR ECOLOGY, 26 (1): 193-207 JAN 2017 Article (Details)
Rie Shimizu Inatsugi

Dr. Rie Shimizu-Inatsugi
University of Zurich
Department of Evolutionary Biology and Environmental Studies
8008 Zurich

Tel: +41 (0)44 635 47 60

Research topics

  • Polyploidization
  • Transcriptomics
  • Environmental adaptation
  • Stress tolerance
  • Genomics



  • Collaboration with bioinformaticians for NGS data analysis
  • Environmental study in field experiments with ecologists