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Researcher Information

last modified:2016/09/30

Assistant Professor NISHIYAMA Tomoaki


Faculty, Affiliation

Advanced Science Research Center

College and School Educational Field


Division of Functional Genomics TEL:076-265-2777 FAX:076-234-4537

Academic Background

【Academic background(Doctoral/Master's Degree)】
The University of Tokyo Doctor 200003 Completed
The University of Tokyo Master 199703 Completed
【Academic background(Bachelor's Degree)】
The University of Tokyo 199503


Kanazawa University(2005/04/01-)

Year & Month of Birth


Academic Society

Botanycal Society of Japan



Evolutionary biology、

Speciality Keywords

Genome, Evolution, Streptophytes

Research Themes

Investigation of Early Land Plant Evolution by Comparative Genomics

Unvailing the early evolution of land plants at the gene level by genome sequencing of Physcomitrella pantes and Selaginella moellendorffii and comparisons to other plant genomes. Further studies on charophycean green algae to obtain insight into the earlier events are ongoing.

Genome analyses using next-generation sequencers



  •  The Selaginella genome identifies genetic changes associated with the evolution of vascular plants SCIENCE 332 960-963 2011/05
  •  Digital gene expression profiling by 5'-end sequencing of cDNAs during reprogramming in the moss Physcomitrella patens Nishiyama T, Miyawaki K, Ohshima M, Thompson K, Nagashima A, Hasebe M, Kurata T. PLoS One 7 5 e36471 2012/05
  •  Tagged Mutagenesis and Gene-trap in the Moss, Physcomitrella patens by Shuttle Mutagenesis 7 9-17 2000
  •  Class 1 KNOX genes are not involved in shoot development in the moss Physcomitrella patens but do function in sporophyte development Keiko Sakakibara, Tomoaki Nishiyama, Hironori Deguchi, Mitsuyasu Hasebe EVOLUTION & DEVELOPMENT 10 5  555-566 2008/09
  •  The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T et al. SCIENCE 319 64-69 2008/01

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  •  Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AME 100 8007-8012 2003
  •  Molecular Phylogenetic Analysis Among Bryophytes and Tracheophytes Based on Combined Data of Plastid Coded Genes and the 18S rRNA Gene MOLECULAR BIOLOGY AND EVOLUTION 16 1027-1036 1999
  •  Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions Zimmer AD, Lang D, Buchta K, Rombauts S, Nishiyama T, Hasebe M, Van de Peer Y, Rensing SA, Reski R BMC Genomics 14 498 2013/07
  •  TCC: an R package for comparing tag count data with robust normalization strategies Sun J, Nishiyama T, Shimizu K, Kadota K. BMC Bioinformatics 14 219 2013/07
  •  A normalization strategy for comparing tag count data Kadota K, Nishiyama T, Shimizu K. Algorithms Mol Biol 7 1 5 2012/04
  •  Physcomitrella Cyclin-Dependent Kinase A Links Cell Cycle Reactivation to Other Cellular Changes during Reprogramming of Leaf Cells Ishikawa M, Murata T, Sato Y, Nishiyama T, Hiwatashi Y, Imai A, Kimura M, Sugimoto N, Akita A, Oguri Y, Friedman WE, Hasebe M, Kubo M PLANT CELL 23 8 2924-2938 2011/08
  •  A membrane trafficking pathway regulated by the plant-specific RAB GTPase ARA6 Ebine K, Fujimoto M, Okatani Y, Nishiyama T, Goh T, Ito E, Dainobu T, Nishitani A, Uemura T, Sato MH, Thordal-Christensen H, Tsutsumi N, Nakano A, Ueda T NATURE CELL BIOLOGY 13 853-859 2011/06
  •  Phylogeny, biogeography, and host-plant association in the subfamily Apaturinae (Insecta: Lepidoptera: Nymphalidae) inferred from eight nuclear and seven mitochondrial genes Issei Ohshima, Yukiko Tanikawa-Dodo, Toyohei Saigusa, Tomoaki Nishiyama, Masakazu Kitani, Mitusyasu Hasebe, and Hideo Mohri MOLECULAR PHYLOGENETICS AND EVOLUTION 57 1026-1036 2010/12
  •  A polycomb repressive complex 2 gene regulates apogamy and gives evolutionary insights into early land plant evolution Yosuke Okano, Naoki Aono, Yuji Hiwatashi, Takashi Murata, Tomoaki Nishiyama, Takaaki Ishikawa, Minoru Kubo and Mitsuyasu Hasebe PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AME 106  38  16321-16326 2009/09
  •  The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses. Tsuji S, Ueda K, Nishiyama T, Hasebe M, Yoshikawa S, Konagaya A, Nishiuchi T, Yamaguchi K. JOURNAL OF PLANT RESEARCH 120 2 281-290 2007/03
  •  Chloroplast Phylogeny Indicates that Bryophytes are Monophyletic MOLECULAR BIOLOGY AND EVOLUTION 21 1813-1819 2004
  •  The GID1-mediated gibberellin perception mechanism is conserved in the Lycophyte Selaginella moellendorffii but not in the Bryophyte Physcomitrella patens Hirano K, Nakajima M, Asano K, Nishiyama T, Sakakibara H, Kojima M, Katoh E, Xiang H, Tanahashi T, Hasebe M, Banks JA, Ashikari M, Kitano H, Ueguchi-Tanaka M, Matsuoka M. PLANT CELL 19 10 3058-3079 2007/10
  •  Involvement of auxin and a homeodomain-leucine zipper I gene in rhizoid development of the moss Physcomitrella patens DEVELOPMENT 130 4835-4846 2003
  •  Characterization of MADS-box genes in charophycean green algae and its implication for the evolution of MADS-box genes PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AME 102 2436-2441 2005
  •  Isolation of Homeodomain-Leucine Zipper Genes from the Moss Physcomitrella patens and the Evolution of Homeodomain-Leucine Zipper Genes in Land Plants. MOLECULAR BIOLOGY AND EVOLUTION 8 491-502 2001
  •  Evolution of MADS-box gene induction by FLO/LFY genes JOURNAL OF MOLECULAR EVOLUTION 53 387-393 2001
  •  Establishment of gene-trap and enhancer-trap systems in the moss Physcomitrella patens PLANT JOURNAL 28 105-116 2001
  •  Marked Spatial Genetic Structure in Three Populations of a Weedy Fern, Pteris multifida Poir., and Reestimation of Its Selfing Rate. 12 97-106 1997
  •  Complete Genome Sequence of Burkholderia sp. Strain RPE64, Bacterial Symbiont of the Bean Bug Riptortus pedestris Shibata TF, Maeda T, Nikoh N, Yamaguchi K, Oshima K, Hattori M, Nishiyama T, Hasebe M, Fukatsu T, Kikuchi Y, Shigenobu S. Genome Announcements 1 4  e00441-13  2013/07

Conference Presentations

Arts and Fieldwork


Theme to the desired joint research

Grant-in-Aid for Scientific Research


Classes (Bachelors)

Classes (Graduate Schools)

International Project

International Students

Lecture themes

Others (Social Activities)

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