Basic Information

Email Address

• Email Address

  shirai.kazumasa.7jkyoto-u.ac.jp

Professional Memberships

• SOCIETY OF EVOLUTIONARY STUDIES, JAPAN
• THE JAPANESE SOCIETY OF PLANT PHYSIOLOGISTS

Academic Degree

• 27 Mar. 2012

  九州大学修士（システム生命科学）
• 25 Mar. 2015

  九州大学博士（理学）

Academic Resume (Undergraduate School/Majors)

• 九州大学, 理学部生物学科, 卒業

Research History

• From Sep. 2026, To Present

  Kyoto University, Graduate School of Science, 講師
• From Apr. 2026, To Aug. 2026

  Kyoto University, Graduate School of Science, 特定研究員
• From Oct. 2024, To Mar. 2026

  Kyushu Institute of Technology, Advanced Research and Social Cooperation Headquarters Research Center of Synthetic Biology, 助教
• From Apr. 2024, To Sep. 2024

  Kyoto University, 理学研究科, 特定研究員
• From Apr. 2020, To Mar. 2024

  Kyushu Institute of Technology, School of Computer Science and Systems Engineering Department of Bioscience and Bioinformatics, 研究員
• From Oct. 2017, To Mar. 2020

  Kyushu Institute of Technology, School of Computer Science and Systems Engineering, 特任助教
• From Apr. 2015, To Sep. 2017

  Kyushu Institute of Technology, School of Computer Science and Systems Engineering, 研究員

ID,URL

• J-Global ID

  201801009591637679

researchmap URL

• https://researchmap.jp/kazushirai

Research

Research Interests

• 転写開始点選択
• ダイコン
• 植物ゲノム
• 進化
• ゲノム進化
• 分子進化学
• 集団遺伝学

Research Areas

• Life sciences, Genomics

Papers

• Salicylic acid signaling controls the colonization behavior of Colletotrichum tofieldiae in Arabidopsis thaliana

  Norhafizah Binti Sidek; Shiho Itoh; Toru Aramaki; Yuji Yamasaki; Hisashi Tsujimoto; Kazumasa Shirai; Kousuke Hanada

  Frontiers in Plant Science, 15 Apr. 2026, Peer-reviewed

  
• Arabidopsis LOHN1 peptide modulates lateral root spacing under the control of systemic nitrogen-satiety signaling

  Kazuhiro Ito; Tomoya Sonoda; Yuki Hisanaga; Kentaro P. Iwata; Chieko Goto; Kazumasa Shirai; Mana Goto; Ayu Yamamoto; Atsushi Mabuchi; Takumi Higaki; Boseok Song; Juntaro Negi; Takamasa Suzuki; Hidehiro Fukaki; Kousuke Hanada; Koh Iba; Kensuke Kusumi

  Current Biology, Oct. 2025, Peer-reviewed

  
• Cryptochromes Induce Genome-Wide Changes in Alternative Transcription Start Site Selection in Arabidopsis

  Yoshito Oka; Kazumasa Shirai; Izumi Kimura; Tomoo Shimada; Kousuke Hanada; Tomonao Matsushita

  Biochemical and Biophysical Research Communications, Jun. 2025, Peer-reviewed

  
• Florigen-producing cells express FPF1-LIKE PROTEIN 1 to accelerate flowering and stem growth in Arabidopsis.

  Hiroshi Takagi; Nayoung Lee; Andrew K Hempton; Savita Purushwani; Michitaka Notaguchi; Kota Yamauchi; Kazumasa Shirai; Yaichi Kawakatsu; Susumu Uehara; William G Albers; Benjamin L R Downing; Shogo Ito; Takamasa Suzuki; Takakazu Matsuura; Izumi C Mori; Nobutaka Mitsuda; Daisuke Kurihara; Tomonao Matsushita; Young Hun Song; Yoshikatsu Sato; Mika Nomoto; Naoyuki Uchida; Yasuomi Tada; Kousuke Hanada; Josh T Cuperus; Christine Queitsch; Takato Imaizumi

  Developmental cell, 25 Feb. 2025, Peer-reviewed

  
• Florigen-producing cells express FPF1-LIKE PROTEIN 1 that accelerates flowering and stem growth in long days with sunlight red/far-red ratio in Arabidopsis.

  Hiroshi Takagi; Nayoung Lee; Andrew K Hempton; Savita Purushwani; Michitaka Notaguchi; Kota Yamauchi; Kazumasa Shirai; Yaichi Kawakatsu; Susumu Uehara; William G Albers; Benjamin L R Downing; Shogo Ito; Takamasa Suzuki; Takakazu Matsuura; Izumi C Mori; Nobutaka Mitsuda; Daisuke Kurihara; Tomonao Matsushita; Young Hun Song; Yoshikatsu Sato; Mika Nomoto; Yasuomi Tada; Kousuke Hanada; Josh T Cuperus; Christine Queitsch; Takato Imaizumi

  bioRxiv : the preprint server for biology, 29 Apr. 2024

  
• Alternative localization of HEME OXYGENASE 1 in plant cells regulates cytosolic heme catabolism

  Yingxi Chen; Kohji Nishimura; Mutsutomo Tokizawa; Yoshiharu Y Yamamoto; Yoshito Oka; Tomonao Matsushita; Kousuke Hanada; Kazumasa Shirai; Shoji Mano; Takayuki Shimizu; Tatsuru Masuda

  Plant Physiology, 28 May 2024, Peer-reviewed

  
• LHT1/MAC7 contributes to proper alternative splicing under long-term heat stress and mediates variation in the heat tolerance of Arabidopsis

  Kazuho Isono; Kotaro Nakamura; Kousuke Hanada; Kazumasa Shirai; Mao Ueki; Keisuke Tanaka; Takashi Tsuchimatsu; Satoshi Iuchi; Masatomo Kobayashi; Izumi Yotsui; Yoichi Sakata; Teruaki Taji

  PNAS Nexus, 01 Nov. 2023, Peer-reviewed

  
• A de novo gene originating from the mitochondria controls floral transition in Arabidopsis thaliana.

  Tomoyuki Takeda; Kazumasa Shirai; You-Wang Kim; Mieko Higuchi-Takeuchi; Minami Shimizu; Takayuki Kondo; Tomokazu Ushijima; Tomonao Matsushita; Kazuo Shinozaki; Kousuke Hanada

  Plant molecular biology, 28 Oct. 2022, Peer-reviewed

  
• Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants

  Kazumasa Shirai; Mitsuhiko P. Sato; Ranko Nishi; Masahide Seki; Yutaka Suzuki; Kousuke Hanada

  Genome Research, May 2021, Peer-reviewed, Lead author

  
• Genome-Wide Association Study of Local Thai Indica Rice Seedlings Exposed to Excessive Iron

  Reunreudee Kaewcheenchai; Phanchita Vejchasarn; Kousuke Hanada; Kazumasa Shirai; Chatchawan Jantasuriyarat; Piyada Juntawong

  Plants, Apr. 2021, Peer-reviewed

  
• Degree of Functional Divergence in Duplicates Is Associated with Distinct Roles in Plant Evolution

  Akihiro Ezoe; Kazumasa Shirai; Kousuke Hanada

  Molecular Biology and Evolution, Apr. 2021, Peer-reviewed

  
• Contribution of Functional Divergence Through Copy Number Variations to the Inter-Species and Intra-Species Diversity in Specialized Metabolites

  Kazumasa Shirai; Kousuke Hanada

  Frontiers in Plant Science, Nov. 2019, Peer-reviewed, Lead author

  
• Tyr82 Amino Acid Mutation in PB1 Polymerase Induces an Influenza Virus Mutator Phenotype

  Tadasuke Naito; Kazumasa Shirai; Kotaro Mori; Hidetaka Muratsu; Hiroshi Ushirogawa; Ryosuke L. Ohniwa; Kousuke Hanada; Mineki Saito

  Journal of Virology, Sep. 2019, Peer-reviewed

  
• Distinct gene expression signatures induced by viral transactivators of different HTLV-1 subgroups that confer a different risk of HAM/TSP

  Tadasuke Naito; Jun-ichirou Yasunaga; Yuichi Mitobe; Kazumasa Shirai; Hiroe Sejima; Hiroshi Ushirogawa; Yuetsu Tanaka; Tatsufumi Nakamura; Kousuke Hanada; Masahiro Fujii; Masao Matsuoka; Mineki Saito

  Retrovirology, Nov. 2018, Peer-reviewed

  
• A Highly Specific Genome-Wide Association Study Integrated with Transcriptome Data Reveals the Contribution of Copy Number Variations to Specialized Metabolites in Arabidopsis thaliana accessions

  Kazumasa Shirai; Fumio Matsuda; Ryo Nakabayashi; Masanori Okamoto; Maho Tanaka; Akihiro Fujimoto; Minami Shimizu; Kazuo Shinozaki; Motoaki Seki; Kazuki Saito; Kousuke Hanada

  MOLECULAR BIOLOGY AND EVOLUTION, Dec. 2017, Peer-reviewed, Lead author

  
• Mutant selection in the self-incompatible plant radish (Raphanus sativus L. var. sativus) using two-step TILLING

  Kaori Kohzuma; Motoko Chiba; Soichiro Nagano; Toyoaki Anai; Miki U. Ueda; Riichi Oguchi; Kazumasa Shirai; Kousuke Hanada; Kouki Hikosaka; Nobuharu Fujii

  BREEDING SCIENCE, Jun. 2017, Peer-reviewed

  
• High prevalence of non-synonymous substitutions in mtDNA of cichlid fishes from Lake Victoria

  Kazumasa Shirai; Nobuyuki Inomata; Shinji Mizoiri; Mitsuto Aibara; Yohey Terai; Norihiro Okada; Hidenori Tachida

  GENE, Dec. 2014, Peer-reviewed, Lead author

  

Misc.

• Evolutionary rates in the Cichlid Fishes of the Three Great Lakes in East Africa

  Kazumasa Shirai; Nobuyuki Inomata; Mitsuto Aibara; Shinji Mizoiri; Yohey Terai; Norihiro Okada; Hidenori Tachida

  GENES & GENETIC SYSTEMS, Dec. 2012

  

Presentations

• Development of prediction model for species specific potential of carbon fixation based on angiosperm genomes

  白井一正

  日本生態学会, 12 Mar. 2026, Invited

  
• 環境変化に応じた植物の転写開始点制御の網羅的解明

  白井一正

  日本進化学会, 31 Aug. 2023

  
• The origin and evolution in Japanese cultivated radishes

  Kazumasa Shirai; Kousuke Hanada

  日本進化学会, 08 Aug. 2019

  
• 栽培ダイコンの起源を探る

  白井一正

  東北大学 セミナー, 21 Nov. 2018, Invited

  

Books and Other Publications

• The Synthetic Biology Handbook

  木賀 大介; 蓮沼 誠久; 木賀 大介; 瀧ノ上 正浩; 大竹 和正; 豊田 太郎; 赤嶺 柚希; 車 兪澈; 市橋 伯一; Praful Gagrani; 上村 淳; 小林 徹也; 遠藤 慧; 齊藤 博英; 小野 紘貴; 清水 義宏; 小坂 唯心; 青木 航; 野地 博行; 皆川 慶嘉; 相馬 悠希; 清水 浩; 西田 敬二; 相澤 康則; 金子 真也; 野村M. 慎一郎; 松林 英明; 堀 豊; 山村 雅幸; 松田 史生; 浜田 道昭; 蓮沼 誠久; 柘植 謙爾; 柿澤 茂行; 石川 聖人; 松永 朋子; 青木 遼太; 松永 幸大; 井上 真男; 三宅 良磨; 大木 健二; 金岡 良典; 堀 克敏; 吉本 将悟; 籠谷 勇紀; 重廣 司; 伊川 友活; 田村 あずみ; Aa Haeruman Azam; 千原 康太郎; 氣駕 恒太郎; 浦島 匡; 鯵坂 勝美; 阪中 幹祥; 佐藤 文彦; 山田 泰之; Ogbonna Sochi Judith; 金井 貴蓉; 山野–足立 範子; 大政 健史; 坂井 伶平; 白井 一正; 花田 耕介; Much Zaenal Fanani; 關 光; 松村 浩由; 木下 俊則; 林 優紀; 田中 謙也; 鈴木 研志; 花井 泰三; 駒 大輔; 大橋 博之; 藤原 良介; 棟方 涼介; 南 博道; 中川 明; 武田 知己; 山本 碩満; 湯澤 賢; 加藤 俊介; 本田 孝祐; 戸谷 吉博; 由里本 博也; 阪井 康能; 渡辺 智; 中西 周次; 田畑 裕; 中島田 豊; 福居 俊昭; 若井 暁; 庄司 信一郎; 金森 崇; 末次 正幸; 中町 優斗; 加藤 敬行; 菅 裕明; 古橋 麻衣; 竹内 昌治; 酒井 友希; 守屋 健太; 石崎 公庸; 岩崎 秀雄; 廣田 隆一; 村中 俊哉; 小保方 潤一; 畑 貴之; 佐藤 壮一郎; 松尾 充啓; 野尻 秀昭; 新谷 政己; 前田 太郎; 松尾 真紀子; 小宮 健; 太田 努; 竹下 あすか; 久保田 唯史; 高江 可奈子; 田中 幹人; 川本 思心; 林 真理; 吉澤 剛; 見上 公一; 村瀬 泰菜; 菱山 豊; 四ノ宮 成祥; 三成 寿作; 標葉 隆馬; 藤原 慶, Joint work, 第2章 植物学・農業分野への応用 第1節 植物の合成生物学

  (株)エヌ・ティー・エス, Jun. 2026

  Find Kyoto University's collection of books :

  

Awards

• 04 Oct. 2021

  優秀発表賞（植物インフォマティクス研究会）
• 12 Dec. 2020

  口頭発表優秀賞（日本育種学会中国地域育種談話会）

External funds: Kakenhi

• 沖縄産野生ダイコンが持つ高温耐性遺伝子の解明

  Grant-in-Aid for Scientific Research (C)

  Basic Section 39030:Horticultural science-related

  Kyoto University

  白井 一正

  From 01 Apr. 2026, To 31 Mar. 2029, Granted

  高温耐性;環境適応;遺伝資源;アブラナ科;新規ゲノム構築

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-26K08788/
• Identification of genes controlling potential of carbon fixation in angiosperm based on genome analysis

  Grant-in-Aid for Transformative Research Areas (A)

  Transformative Research Areas, Section (IV)

  Kyushu Institute of Technology;Kyoto University

  白井 一正

  From 01 Apr. 2024, To 31 Mar. 2026, Granted

  遺伝子ファミリー;炭素固定能力;被子植物

  https://kaken.nii.ac.jp/grant/KAKENHI-PUBLICLY-24H01519/
• Identification of genes related to root development of Japanese cultivated radish

  Grant-in-Aid for Early-Career Scientists

  Basic Section 39010:Science in plant genetics and breeding-related

  Kyushu Institute of Technology

  白井 一正

  From 01 Apr. 2022, To 31 Mar. 2026, Granted

  ダイコン;進化;ゲノム;栽培化;人為選択

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22K14870/
• Development of prediction model for species specific potential of carbon fixation based on angiosperm genomes

  Grant-in-Aid for Transformative Research Areas (A)

  Transformative Research Areas, Section (IV)

  Kyushu Institute of Technology

  白井 一正

  From 16 Jun. 2022, To 31 Mar. 2024, Project Closed

  炭素固定能力;被子植物;機械学習;ゲノム;遺伝子ファミリー

  https://kaken.nii.ac.jp/grant/KAKENHI-PUBLICLY-22H05731/
• Exhaustive search of anti-pathogenic peptides in Musa acuminata

  Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))

  Medium-sized Section 39:Agricultural and environmental biology and related fields

  Kyushu Institute of Technology

  Kousuke Hanada

  From 09 Oct. 2018, To 31 Mar. 2022, Project Closed

  バナナ;抗菌性ペプチド;フザリウム;短い遺伝子;抗菌ペプチド;ペプチド

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-18KK0176/