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 take 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.

• Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana.
  Takashi Tsuchimatsu, Hiroyuki Kakui, Misako Yamazaki, Cindy Marona, Hiroki Tsutsui, Afif Hedhly, Dazhe Meng, Yutaka Sato, Thomas Städler, Ueli Grossniklaus, Masahiro M. Kanaoka, Michael Lenhard, Magnus Nordborg and Kentaro K. Shimizu.
  Nature Communications. 8 June 2020. DOI: 10.1038/s41467-020-16679-7
• Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses
  Hanya, Goro; Tackmann, Janko; Sawada, Akiko; Lee, Wanyi; Pokharel, Sanjeeta Sharma; et al.
  Microbial Ecology  DOI: 10.1007/s00248-020-01515-8 Early Access: APR 2020
• Artificial selection reveals the role of transcriptional constraints in the maintenance of life history variation
  Pick, Joel L.; Hatakeyama, Masaomi; Ihle, Kate E.; Gasparini, Julien; Haussy, Claudy; et al.
  Evolution Letters  DOI: 10.1002/evl3.166  Early Access: APR 2020
• Genet assignment and population structure analysis in a clonal forest-floor herb, Cardamine leucantha, using RAD-seq
  Tsujimoto, Michiaki; Araki, Kiwako S.; Honjo, Mie N.; Yasugi, Masaki; Nagano, Atsushi J.; et al.
  Aob Plants,  DOI: 10.1093/aobpla/plz080 Published: FEB 2020
• Genetic relationships and linguistic diversity in present-day populations of South America
  Barbieri, Chiara; Barquera, Rodrigo; Arias, Leonardo; Sandoval, Jose R.; Acosta, Oscar; et al.
  American Journal Of Physical Anthropology Vol 171 Pages: 17-18 Supplement: 69 MAR 2020
• The Current Genomic Landscape of Western South America: Andes, Amazonia, and Pacific Coast
  Barbieri, Chiara; Barquera, Rodrigo; Arias, Leonardo; Sandoval, Jose R.; Acosta, Oscar; et al.
  Molecular Biology And Evolution,  DOI: 10.1093/molbev/msz174, DEC 2019
• Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence
  Izuno, Ayako; Wicker, Thomas; Hatakeyama, Masaomi; Copetti, Dario; Shimizu, Kentaro K.
  G3-genes Genomes Genetics, 10.1534/g3.119.400643
• Transcriptional Variation in Glucosinolate Biosynthetic Genes and Inducible Responses to Aphid Herbivory on Field-Grown Arabidopsis thaliana
  Sato, Y; Tezuka, A; Kashima, M; Deguchi, A; Shimizu-Inatsugi, R; Yamazaki, M; Shimizu, KK; Nagano, AJ
  FRONTIERS IN GENETICS, 10 10.3389/fgene.2019.00787 SEP 11 2019
• A stigmatic gene confers interspecies incompatibility in the Brassicaceae
  Fujii, S; Tsuchimatsu, T; Kimura, Y; Ishida, S; Tangpranomkorn, S; Shimosato-Asano, H; Iwano, M; Furukawa, S; Itoyama, W; Wada, Y; Shimizu, KK; Takayama, S
  NATURE PLANTS, 5 (7):731-741; 10.1038/s41477-019-0444-6 JUL 2019
• Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana
  Sato, Y; Shimizu-Inatsugi, R; Yamazaki, M; Shimizu, KK; Nagano, AJ
  BMC PLANT BIOLOGY, 19 10.1186/s12870-019-1705-2 APR 27 2019
• Molecular basis of flowering under natural long-day conditions in Arabidopsis
  Song, YH; Kubota, A; Kwon, MS; Covington, MF; Lee, N; Taagen, ER; Cintron, DL; Hwang, DY; Akiyama, R; Hodge, SK; Huang, H; Nguyen, NH; Nusinow, DA; Millar, AJ; Shimizu, KK; Imaizumi, T
  NATURE PLANTS, 4 (10):824-835; 10.1038/s41477-018-0253-3 OCT 2018
• 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 
• 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
• 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

• 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