Kentaro Shimizu

Research Interests

Molecular basis of biodiversity, evolutionary and ecological genomics, evolution of mating systems, speciation by genome duplication (polyploidization), predicting evolutionary and plastic responses in changing environments

CV

Education and Professional Positions

2016 - present Director of PhD Program in Evolutionary Biology
2015 NISTEP Award (Award for nice step researchers) from the Minister of Education, Culture, Sports, Science and Technology, Japan
2015 - present Guest Professor at the Kihara Institute for Biological Research, Yokohama City University, Japan
2015 Visiting Professor at the Center for Ecological Research, Kyoto University, Japan
2015 - present Swiss representative of the Multinational Arabidopsis Steering Committee
2014 - present Faculty of 1000 (Developmental Biology)
2011 - present Associate Professor, Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
2006 - 2011 Assistant Professor, Institute of Plant Biology, University of Zurich, Switzerland
2003 - 2006 Research Scholar, Department of Genetics, North Carolina State University, USA
2002 - 2003 Postdoctoral fellow, Kyoto University, Japan
1997 - 2002 Graduate studies (Ph.D.) in Biology, Kyoto University, Japan
1993 - 1997 Undergraduate studies (B.S.) in Biology, Kyoto University, Japan

Selected Publications

  • Briskine RV., Paape T., Shimizu-Inatsugi R., Nishiyama T., Akama S., Sese J., Shimizu KK. (2016) Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology. Molecular Ecology Notes:Epub ahead of print. DOI: 10.1111/1755-0998.12604
  • Paape T., Hatakeyama M., Shimizu-Inatsugi R., Cereghetti T., Onda Y., Kenta T., Sese J., Shimizu KK. (2016) Conserved but attenuated parental gene expression in allopolyploids: constitutive zinc hyperaccumulation in the allotetraploid Arabidopsis kamchatica. Mol Biol Evol. 2016 Jul 12. pii: msw141. DOI: 10.1093/molbev/msw141
  • Novikova PY., Hohmann N., Nizhynska V., Tsuchimatsu T., Ali J., Muir G., Guggisberg A., Paape T., Schmid K., Fedorenko OM., Holm S., Säll T., Schlötterer C., Marhold K., Widmer A., Sese J., Shimizu KK., Weigel D., Krämer U., Koch MA., Nordborg M. (2016) Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nature Genetics, 48(9):1077-1082. DOI: 10.1038/ng.3617
  • Menardo F., Praz CR., Wyder S., Ben-David R., Bourras S., Matsumae H., McNally KE., Parlange F., Riba A., Roffler S., Schaefer LK., Shimizu KK., Valenti L., Zbinden H., Wicker T., Keller B. (2016) Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species. Nature Genetics, 48(2):201-205. DOI: 10.1038/ng.3485
  • Izuno A., Hatakeyama M., Nishiyama T., Tamaki I., Shimizu-Inatsugi R., Sasaki R., Shimizu KK., Isagi Y. (2016) Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations. Journal of Plant Research, 129(4):727-736. DOI: 10.1007/s10265-016-0822-3
  • Shimizu KK., Tsuchimatsu T. (2015) Evolution of selfing: recurrent patterns in molecular adaptation. Annual Review of Ecology, Evolution and Systematics, 46:593-622. DOI: 10.1146/annurev-ecolsys-112414-054249
  • Takeuchi Y., Chaffron S., Salcher MM., Shimizu-Inatsugi R., Kobayashi MJ., Diway B., von Mering C., Pernthaler J., Shimizu KK. (2015) Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes. Systematic and Applied Microbiology, 38(5):330-339. DOI: 10.1016/j.syapm.2015.05.006
  • Kubo K-I., Paape T., Hatakeyama M., Entani T., Takara A., Kajihara K., Shimizu-Inatsugi R., Shimizu KK., Takayama S. (2015) Evolution of non-self recognition through gene duplication and genetic exchange in S-RNase based self-incompatibility. Nature Plants, 1: 14005
  • Tedder A., Helling M., Pannell JR., Shimizu-Inatsugi R., Kawagoe T., van Campen J., Sese J., Shimizu KK. (2015) Female sterility associated with increased clonal propagation suggests a unique combination of androdioecy and asexual reproduction in populations of Cardamine amara (Brassicaceae). Annals of Botany, 115(5):763-776. DOI: 10.1093/aob/mcv006
  • Tedder A., Carleial S., Gołębiewska M., Kappel C., Shimizu KK., Stift M. (2015) Evolution of the Selfing Syndrome in Arabis alpina (Brassicaceae). PLoS ONE, 10(6):e0126618. DOI: 10.1371/journal.pone.0126618