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.

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

► Google Scholar: https://scholar.google.ch/citations?hl=de&user=rWnq5SEAAAAJ

• A global analysis of matches and mismatches between human genetic and linguistic histories
  C Barbieri, DE Blasi, E Arango-Isaza, AG Sotiropoulos, H Hammarström, et al.
  Proceedings of the National Academy of Sciences 119 (47), e2122084119  2022
• Robustness and the generalist niche of polyploid species: Genome shock or gradual evolution?
  KK Shimizu
  Current Opinion in Plant Biology 69, 102292   2022
• Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade
  AG Sotiropoulos, E Arango-Isaza, T Ban, C Barbieri, S Bourras, C Cowger, ...
  Nature Communications 13 (1), 1-14  2022
• Multiple Wheat Genomes Reveal Novel Gli-2 Sublocus Location and Variation of Celiac Disease Epitopes in Duplicated alpha-Gliadin Genes
  Halstead-Nussloch, Gwyneth; Tanaka, Tsuyoshi; Copetti, Dario; Paape, Timothy; Kobayashi, Fuminori; et al.
  Frontiers In Plant Science 10.3389/fpls.2021.715985  SEP 3 2021
• An Affordable Image-Analysis Platform to Accelerate Stomatal Phenotyping During Microscopic Observation (vol 12,& nbsp;715309, 2021)
  Toda, Yosuke; Tameshige, Toshiaki; Tomiyama, Masakazu; Kinoshita, Toshinori; Shimizu, Kentaro K.
  Frontiers In Plant Science 10.3389/fpls.2021.793369  NOV 3 2021
• Using a two-stage convolutional neural network to rapidly identify tiny herbivorous beetles in the field
  Takimoto, Hironori; Sato, Yasuhiro; Nagano, Atsushi J.; Shimizu, Kentaro K.; Kanagawa, Akihiro
  Ecological Informatics 10.1016/j.ecoinf.2021.101466  DEC 2021
• PRIMA: a rapid and cost-effective genotyping method to detect single-nucleotide differences using probe-induced heteroduplexes
  Kakui, Hiroyuki; Yamazaki, Misako; Shimizu, Kentaro K.
  Scientific Reports 10.1038/s41598-021-99641-x  OCT 24 2021
• The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests
  Ng, Kevin Kit Siong; Kobayashi, Masaki J.; Fawcett, Jeffrey A.; Hatakeyama, Masaomi; Paape, Timothy; et al.
  Communications Biology 10.1038/s42003-021-02682-1  OCT 7 2021
• An Affordable Image-Analysis Platform to Accelerate Stomatal Phenotyping During Microscopic Observation
  Toda, Yosuke; Tameshige, Toshiaki; Tomiyama, Masakazu; Kinoshita, Toshinori; Shimizu, Kentaro K.
  Frontiers In Plant Science 10.3389/fpls.2021.715309 JUL 29 2021
• Ultralong Oxford Nanopore Reads Enable the Development of a Reference-Grade Perennial Ryegrass Genome Assembly
  Frei, Daniel; Veekman, Elisabeth; Grogg, Daniel; Stoffel-Studer, Ingrid; Morishima, Aki; Shimizu-Inatsugi, Rie; Yates, Steven; Shimizu, Kentaro K.; Frey, Juerg E.; Studer, Bruno; Copetti, Dario
  Genome Biology And Evolution 10.1093/gbe/evab159  AUG 2021
• Exploring correlations in genetic and cultural variation across language families in northeast Asia
  Matsumae, Hiromi; Ranacher, Peter; Savage, Patrick E.; Blasi, Damian E.; Currie, Thomas E.; et al.
  Science Advances  10.1126/sciadv.abd9223  AUG 2021
• ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw
  Milosavljevic, Stefan; Kuo, Tony; Decarli, Samuele; Mohn, Lucas; Sese, Jun; Shimizu, Kentaro K.; Shimizu-Inatsugi, Rie; Robinson, Mark D.
  Bmc Genomics, 10.1186/s12864-021-07845-2, JUL 17 2021
• De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium-Resistant Genes in East Asian Genotypes
  Shimizu, Kentaro K.; Copetti, Dario; Okada, Moeko; Wicker, Thomas; Tameshige, Toshiaki; et al.
  Plant And Cell Physiology, 10.1093/pcp/pcaa152, JAN 2021
• Neighbor GWAS: incorporating neighbor genotypic identity into genome-wide association studies of field herbivory
  Sato, Yasuhiro; Yamamoto, Eiji; Shimizu, Kentaro K.; Nagano, Atsushi J.
  Heredity, 10.1038/s41437-020-00401-w, APR 2021
• Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species
  Akiyama, Reiko; Sun, Jianqiang; Hatakeyama, Masaomi; Lischer, Heidi E. L.; Briskine, Roman V.; Hay, Angela; Gan, Xiangchao; Tsiantis, Miltos; Kudoh, Hiroshi; Kanaoka, Masahiro M.; Sese, Jun; Shimizu, Kentaro K.; Shimizu-Inatsugi, Rie
  New Phytologist, 10.1111/nph.17101, MAR 2021
• …

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