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.

• 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
• …

• Multiple wheat genomes reveal global variation in modern breeding
  Walkowiak, Sean; Gao, Liangliang; Monat, Cecile; Haberer, Georg; Kassa, Mulualem T.; et al.
  Nature   DOI: 10.1038/s41586-020-2961-x  DEC 10 2020
• Metal accumulation and its effect on leaf herbivory in an allopolyploid species Arabidopsis kamchatica inherited from a diploid hyperaccumulator A. halleri
  Shimizu-Inatsugi, Rie; Milosavljevic, Silvija; Shimizu, Kentaro K.; Schaepman-Strub, Gabriela; Tanoi, Keitaro; Sato, Yasuhiro
  Plant Species Biology   DOI: 10.1111/1442-1984.12304  DEC 2020
• Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species
  Rellstab, Christian; Zoller, Stefan; Sailer, Christian; Tedder, Andrew; Gugerli, Felix; Shimizu, Kentaro K; Holderegger, Rolf; Widmer, Alex; Fischer, Martin C
  Molecular Ecology 10.1111/mec.15648 NOV 2020
• A Recently Formed TriploidCardamine insuetaInherits Leaf Vivipary and Submergence Tolerance Traits of Parents
  Sun, Jianqiang; Shimizu-Inatsugi, Rie; Hofhuis, Hugo; Shimizu, Kentaro; Hay, Angela; et al.
  Frontiers In Genetics 10.3389/fgene.2020.567262  OCT 6 2020
• Experimental and Field Data Support Range Expansion in an Allopolyploid Arabidopsis Owing to Parental Legacy of Heavy Metal Hyperaccumulation
  Paape, Timothy; Akiyama, Reiko; Cereghetti, Teo; Onda, Yoshihiko; Hirao, Akira S.; et al.
  Frontiers In Genetics 10.3389/fgene.2020.565854  SEP 30 2020
• Double-Locking Mechanism of Self-Compatibility inArabidopsis thaliana: The Synergistic Effect of Transcriptional Depression and Disruption of Coding Region in the Male Specificity Gene
  Suwabe, Keita; Nagasaka, Kaori; Windari, Endang Ayu; Hoshiai, Chihiro; Ota, Takuma; et al.
  Frontiers In Plant Science  10.3389/fpls.2020.576140  SEP 11 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 10.1002/evl3.166 JUN 2020
• Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana
  Tsuchimatsu, T; Kakui, H; Yamazaki, M; Marona, C; Tsutsui, H; Hedhly, A; Meng, D; Sato, Y; Stadler, T;  Grossniklaus, U; Kanaoka, MM; Lenhard, M; Nordborg, M; Shimizu, KK
  Nature Communications  8 June 2020., 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  AUG 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
• …

• 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