Evolutionary Genomics

Polyploidization is a frequently observed phenomenon in plant species. It has played an important role as a driving force for evolution in the sense of diversification. Many allopolyploid species have distinct habitats (environmental tolerance), phenotypes or other traits from their parental species. These novel characteristics could have emerged by the combination of multiple genomes. In spite of its interesting role for evolution, polyploidization has not been well studied systematically way, mainly because of the lack of molecular and genomic tools. The recent technical advances, however, are changing the situation.

Our main interest is to reveal how polyploid species adapted to new environment after polyploidization. We focus on transcriptomics, by exploiting the power of latest molecular techniques, e.g. next generation sequencers, to separately detect the expression of homeologs, using genus Arabidopsisand their close relatives. In addition to carrying out molecular research in the wet lab, we collaborate with bioinformaticians, ecologists and cytologists in a multilateral approach to the evolutionary significance of allopolyploidization.

• 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, KK; Frey, JE; Studer, B; Copetti, Dario
  Genome Biology And Evolution, 10.1093/gbe/evab159; 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
• 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
• 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
• 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
• 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
• Trait-dependent resemblance of the flowering phenology and floral morphology of the allopolyploid Cardamine flexuosa to those of the parental diploids in natural habitats
  Akiyama, Reiko; Milosavljevic, Stefan; Leutenegger, Matthias; Shimizu-Inatsugi, Rie
  Journal Of Plant Research 133(2): 147-155 DOI: 10.1007/s10265-019-01164-0  MAR 2020
• 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
• Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars
  Kuon, JE; Qi, WH; Schlapfer, P; Hirsch-Hoffmann, M; von Bieberstein, PR; Patrignani, A; Poveda, L; Grob, S; Keller, M; Shimizu-Inatsugi, R; Grossniklaus, U; Vanderschuren, H; Gruissem, W
  BMC BIOLOGY, 17 (1):10.1186/s12915-019-0697-6 SEP 18 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
• 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
• …

• Polyploidization
• Transcriptomics
• Environmental adaptation
• Stress tolerance
• Genomics

• Collaboration with bioinformaticians for NGS data analysis
• Environmental study in field experiments with ecologists