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Researcher Information

last modified:2017/04/18

Assistant Professor NISHIYAMA Tomoaki

Mail

Faculty, Affiliation

Advanced Science Research Center

College and School Educational Field


Laboratory

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

Career

(1997/04/01-2000/03/31)
(2000/04/01-2003/03/31)
(2003/04/01-2005/03/31)
(2003/05/01-2003/09/15)
(2003/09/16-2004/03/31)
(2004/04/01-2005/03/31)
Kanazawa University(2005/04/01-)

Year & Month of Birth

1973/01

Academic Society

Botanycal Society of Japan

Award

Specialities

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

Books

Papers

  •  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

show all

  •  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
  •  Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory Kenji Fukushima, Xiaodong Fang, David Alvarez-Ponce, Huimin Cai, Lorenzo Carretero-Paulet, Cui Chen, Tien-Hao Chang, Kimberly M. Farr, Tomomichi Fujita, Yuji Hiwatashi, Yoshikazu Hoshi, Takamasa Imai, Masahiro Kasahara, Pablo Librado, Likai Mao, Hitoshi Mori, Tomoaki Nishiyama, Masafumi Nozawa, Gergő Pálfalvi, Stephen T. Pollard, Julio Rozas, Alejandro Sánchez-Gracia, David Sankoff, Tomoko F. Shibata, Shuji Shigenobu, Naomi Sumikawa, Taketoshi Uzawa, Meiying Xie, Chunfang Zheng, David D. Pollock, Victor A. Albert, Shuaicheng Li & Mitsuyasu Hasebe Nature Ecology & Evolution 1 0059 2017/02/06
  •  A Lin28 homologue reprograms differentiated cells to stem cells in the moss Physcomitrella patens Chen Li, Yusuke Sako, Akihiro Imai, Tomoaki Nishiyama, Kari Thompson, Minoru Kubo, Yuji Hiwatashi, Yukiko Kabeya, Dale Karlson, Shu-Hsing Wu, Masaki Ishikawa, Takashi Murata, Philip N. Benfey, Yoshikatsu Sato, Yosuke Tamada & Mitsuyasu Hasebe Nature Communications 8 14242 2017/01/27
  •  An adenylyl cyclase with a phosphodiesterase domain in basal plants with a motile sperm system. Masahiro Kasahara, Noriyuki Suetsugu, Yuki Urano, Chiaki Yamamoto, Mikiya Ohmori, Yuki Takada, Shujiro Okuda, Tomoaki Nishiyama, Hidetoshi Sakayama, Takayuki Kohchi & Fumio Takahashi Scientific Reports 6 39232 2016/12/16
  •  APOBEC3A associates with human papillomavirus genome integration in oropharyngeal cancers. Kondo S, Wakae K, Wakisaka N, Nakanishi Y, Ishikawa K, Komori T, Moriyama-Kita M, Endo K, Murono S, Wang Z, Kitamura K, Nishiyama T, Yamaguchi K, Shigenobu S, Muramatsu M, Yoshizaki T. Oncogene 2016/10/03
  •  WOX13-like genes are required for reprogramming of leaf and protoplast cells into stem cells in the moss Physcomitrella patens Keiko Sakakibara, Pascal Reisewitz, Tsuyoshi Aoyama, Thomas Friedrich, Sayuri Ando, Yoshikatsu Sato, Yosuke Tamada, Tomoaki Nishiyama, Yuji Hiwatashi, Tetsuya Kurata, Masaki Ishikawa, Hironori Deguchi, Stefan A. Rensing, Wolfgang Werr, Takashi Murata, Mitsuyasu Hasebe, Thomas Laux Development 141 1660-1670 2014/04
  •  Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology Roman V. Briskine, Timothy Paape, Rie Shimizu-Inatsugi, Tomoaki Nishiyama, Satoru Akama, Jun Sese, Kentaro K. Shimizu Molecular Ecology Resources 2016/09/27
  •  Whole-Genome Sequence of Burkholderia sp. Strain RPE67, a Bacterial Gut Symbiont of the Bean Bug Riptortus pedestris Kazutaka Takeshita, Tomoko F. Shibata, Naruo Nikoh, Tomoaki Nishiyama, Mitsuyasu Hasebe, Takema Fukatsu, Shuji Shigenobu, Yoshitomo Kikuchi Genome Announcements 2 3 e00556-14 2014/06/19
  •  ppdb: plant promoter database version 3.0 Ayaka Hieno, Hushna Ara Naznin, Mitsuro Hyakumachi, Tetsuya Sakurai, Mututomo Tokizawa, Hiroyuki Koyama, Naoki Sato, Tomoaki Nishiyama, Mitsuyasu Hasebe, Andreas D. Zimmer, Daniel Lang, Ralf Reski, Stefan A. Rensing, Junichi Obokata, Yoshiharu Y. Yamamoto Nucleic Acids Research 42 D1 D1188-D1192 2013/11/04
  •  Methylome Diversification through Changes in DNA Methyltransferase Sequence Specificity  Yoshikazu Furuta, Hiroe Namba-Fukuyo, Tomoko F. Shibata, Tomoaki Nishiyama, Shuji Shigenobu, Yutaka Suzuki, Sumio Sugano, Mitsuyasu Hasebe, Ichizo Kobayashi PLoS Genetics 10 4 e1004272 2014/04/10
  •  Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge Oleg Gusev, Yoshitaka Suetsugu, Richard Cornette, Takeshi Kawashima, Maria D. Logacheva, Alexey S. Kondrashov, Aleksey A. Penin, Rie Hatanaka, Shingo Kikuta, Sachiko Shimura, Hiroyuki Kanamori, Yuichi Katayose, Takashi Matsumoto, Elena Shagimardanova, Dmitry Alexeev, Vadim Govorun, Jennifer Wisecaver, Alexander Mikheyev, Ryo Koyanagi, Manabu Fujie, Tomoaki Nishiyama, Shuji Shigenobu, Tomoko F. Shibata, Veronika Golygina, Mitsuyasu Hasebe, Takashi Okuda, Nori Satoh, Takahiro Kikawada Nature Communications 5 4784 2014/09/12
  •  SNARE Molecules in Marchantia polymorpha: Unique and Conserved Features of the Membrane Fusion Machinery Takehiko Kanazawa, Atsuko Era, Naoki Minamino, Yu Shikano, Masaru Fujimoto, Tomohiro Uemura, Ryuichi Nishihama, Katsuyuki T. Yamato, Kimitsune Ishizaki, Tomoaki Nishiyama, Takayuki Kohchi, Akihiko Nakano, Takashi Ueda Plant & Cell Physiology 57 2 307-324 2015/05/27
  •  Detection of hypermutated human papillomavirus type 16 genome by Next-Generation Sequencing Kousho Wakae, Satoru Aoyama, Zhe Wang, Kouichi Kitamura, Guangyan Liu, Ahasan Md. Monjurul, Miki Koura, Mieko Imayasu, Naoya Sakamoto, Mitsuhiro Nakamura, Satoru Kyo, Satoru Kondo, Hiroshi Fujiwara, Tomokazu Yoshizaki, Iwao Kukimoto, Katsushi Yamaguchi, Shuji Shigenobu, Tomoaki Nishiyama, Masamichi Muramatsu Virology 485 460–466 2015/11
  •  Algal ancestor of land plants was preadapted for symbiosis Pierre-Marc Delaux, Guru V. Radhakrishnan, Dhileepkumar Jayaraman, Jitender Cheema, Mathilde Malbreil, Jeremy D. Volkening, Hiroyuki Sekimoto, Tomoaki Nishiyama, Michael Melkonian, Lisa Pokorny, Carl J. Rothfels, Heike Winter Sederoff, Dennis W. Stevenson, Barbara Surek, Yong Zhang, Michael R. Sussman, Christophe Dunand, Richard J. Morris, Christophe Roux, Gane Ka-Shu Wong, Giles E. D. Oldroyd, Jean-Michel Ané Proceedings of the National Academy of Sciences of the United States of America 112 43 13390–13395 2015/10/05
  •  Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations Ayako Izuno, Masaomi Hatakeyama, Tomoaki Nishiyama, Ichiro Tamaki, Rie Shimizu-Inatsugi, Ryuta Sasaki, Kentaro K. Shimizu, Yuji Isagi Journal of Plant Research 129 4 727–736 2016/04/06
  •  The Polycomb group protein CLF emerges as a specific tri-methylase of H3K27 regulating gene expression and development in Physcomitrella patens Idan Pereman, Assaf Mosquna, 1, Aviva Katz, Gertrud Wiedemann, Daniel Lang, Eva L. Decker, Yosuke Tamada, Takaaki Ishikawa, Tomoaki Nishiyama, Mitsuyasu Hasebe, Ralf Reski, Nir Ohad Biochimica et Biophysica Acta (BBA) 1859 7 860–870 2016/07
  •  Diversification of a Transcription Factor Family Led to the Evolution of Antagonistically Acting Genetic Regulators of Root Hair Growth  Holger Breuninger , Anna Thamm , Susanna Streubel , Hidetoshi Sakayama , Tomoaki Nishiyama , Liam Dolan Current Biology 26 12 1622–1628 2016/06/20

Conference Presentations

Arts and Fieldwork

Patent

Theme to the desired joint research

Grant-in-Aid for Scientific Research

○「植物の多細胞体制進化の鍵となったゲノム進化の特定」(2008-2009) 
○「多数の核マーカーによる陸上植物の初期系統分化の解明」(2007-2008) 
○「植物の多細胞体制進化の鍵となったゲノム進化の特定」(2006-2007) 
○「小葉類葉緑体ゲノムにおけるRNAエディティングの全体像とその生物情報学的解析」(2006-2007) 
○「非モデル生物におけるゲノム解析法の確立」(2010-2015) 
○「次世代シーケンサーによる系統解析の革新」(2011-2012) 

Classes (Bachelors)

○Functional Plant Science(2016)
○Physiology 1(2016)
○Experiments in Biology(2016)
○Experiments in Biology(2016)

Classes (Graduate Schools)

International Project

International Students

Lecture themes

Others (Social Activities)

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