Evolutionary Functional Genomics / Systems Biology

Darwin proposed the first conclusive theory to explain biodiversity with two principles: adaptation by natural selection, and speciation. However, little is known about the genes responsible for biodiversity, due to the split between laboratory molecular biologists and field evolutionists. The key to synthesize biology is genomics: specifically, evolutionary genomics.

We are taking interdisciplinary approaches to study the molecular basis of biodiversity, and helps start the University Research Priority Program of Systems Biology / Functional Genomics. 

One of the advantages of using plants is the feasibility of ecological studies since they are immobile. The plants we study include a model species Arabidopsis thaliana, an allopolyploid Arabidopsis kamchatica in East Asia, a species-rich genus Cardamine, and Dipterocarpaceae in Malaysia tropical forests.

• The Nagoya Protocol could backfire on the Global South
  Deplazes-Zemp, A; Abiven, S; Schaber, P; Schaepman, M; Schaepman-Strub, G; Schmid, B; Shimizu, KK; Altermatt, F
  NATURE ECOLOGY & EVOLUTION, 2 (6):917-919; 10.1038/s41559-018-0561-z JUN 2018
• Agrobacterium-mediated floral dip transformation of the model polyploid species Arabidopsis kamchatica 
  Yew, Chow-Lih; Kakui, Hiroyuki; Shimizu, Kentaro K. 
  JOURNAL OF PLANT RESEARCH, 131 (2): 349-358, https://doi.org/10.1007/s10265-017-0982-9 MAR 2018 Article (Details)
• 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, https://doi.org/10.1093/dnares/dsx036 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)
• Reference-guided de novo assembly approach improves genome reconstruction for related species 
  Lischer, Heidi E. L.; Shimizu, Kentaro K. 
  BMC BIOINFORMATICS, 18: NOV 10 2017 Article (Details)
• The Cardamine hirsuta genome offers insight into the evolution of morphological diversity 
  Gan, Xiangchao; Hay, Angela; Kwantes, Michiel; et al. 
  NATURE PLANTS, 2 (11): NOV 2016 Article (Details)

• Evolution of reproductive systems
• Self-compatibility
• Genome duplication (speciation)
• Arabidopsis relatives
• Tropical trees (Dipterocarpaceae)

• Evolutionary and ecological functional genomics (EEFG)
• Statistical genetics
• Ecology
• Molecular developmental genetics
• Systems biology