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

  • Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop
    Authors: 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
    Source: DNA RESEARCH, 25 (1):39-47; https://doi.org/10.1093/dnares/dsx036 FEB 2018
  • Title: Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop 
    Author(s): Hatakeyama, Masaomi; Aluri, Sirisha; Balachadran, Mathi Thumilan; et al. 
    Source: DNA RESEARCH, 25 (1): 39-47 FEB 2018 
    Document Type: Article (Details)
  • Title: Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology 
    Author(s): Briskine, Roman V.; Paape, Timothy; Shimizu-Inatsugi, Rie; et al. 
    Source: MOLECULAR ECOLOGY RESOURCES, 17 (5): 1025-1036 SEP 2017 
    Document Type: Article (Details)
  • Title: The Cardamine hirsuta genome offers insight into the evolution of morphological diversity 
    Author(s): Gan, Xiangchao; Hay, Angela; Kwantes, Michiel; et al. 
    Source: NATURE PLANTS, 2 (11): NOV 2016 
    Document Type: Article (Details)
  • Title: The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae) 
    Author(s): Izuno, Ayako; Kitayama, Kanehiro; Onoda, Yusuke; et al. 
    Source: MOLECULAR ECOLOGY, 26 (6): 1515-1532 MAR 2017 
    Document Type: Article (Details)
  • Title: Plant adaptive radiation mediated by polyploid plasticity in transcriptomes 
    Author(s): Shimizu-Inatsugi, Rie; Terada, Aika; Hirose, Kyosuke; et al. 
    Source: MOLECULAR ECOLOGY, 26 (1): 193-207 JAN 2017 
    Document Type: 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