Updated on 2024/05/23

写真b

 
SAKAKIBARA Keiko
 
*Items subject to periodic update by Rikkyo University (The rest are reprinted from information registered on researchmap.)
Affiliation*
College of Science Department of Life Science
Graduate School of Science Doctoral Program in Life Science
Graduate School of Science Master's Program in Life Science
Title*
Professor
Degree
博士(理学) ( 総合研究大学院大学 )
Research Theme*
  • 陸上植物は約4億7千万年以上前にシャジクモ藻類のような祖先から分かれて進化してきたと考えられている。その過程で、新しい遺伝子の獲得や、もともと持っていた遺伝子が新しい機能を獲得したことが重要な役割を果たした。陸上植物やその近縁種の持っている遺伝子の配列やその遺伝子の機能を調べて比較することで、陸上植物の成立に関わった遺伝子進化の解明をめざす。

  • Research Interests
  • 藻類

  • コケ植物

  • 植物

  • 発生進化学

  • Campus Career*
    • 4 2024 - Present 
      College of Science   Department of Life Science   Professor
    • 4 2024 - Present 
      Graduate School of Science   Master's Program in Life Science   Professor
    • 4 2024 - Present 
      Graduate School of Science   Doctoral Program in Life Science   Professor
    • 4 2016 - 3 2024 
      College of Science   Department of Life Science   Associate Professor
    • 4 2016 - 3 2024 
      Graduate School of Science   Master's Program in Life Science   Associate Professor
    • 4 2016 - 3 2024 
      Graduate School of Science   Doctoral Program in Life Science   Associate Professor

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    Profile

    専門:植物の発生進化学。主にヒメツリガネゴケを用いた形態形成。
    略歴:2003年 総合研究大学院大学で学位取得後、広島大、オーストラリアMonash大にてポスドクを経て
    2009年 ERATO長谷部分化全能性プロジェクトにて技術参事
    2011年 広島大学大学院理学研究科にて特任助教
    2013年 東京大学大学院理学系研究科にて助教
    2016年 立教大学理学部生命理学科にて准教授

    2024年 立教大学理学部生命理学科にて教授

     

    Research History

    • 4 2024 - Present 
      Rikkyo University   College of Science

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    • 4 2016 - Present 
      Rikkyo University   College of Science

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    • 4 2015 - 3 2016 
      Kanazawa University   Career Design Laboratory

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    • 1 2015 - 3 2015 
      東京大学大学院   理学系研究科   研究員

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    • 4 2013 - 1 2015 
      東京大学大学院   理学系研究科   助教

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    • 4 2011 - 3 2013 
      Hiroshima University

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    • 4 2009 - 3 2011 
      ERATO   技術参事

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    • 4 2007 - 3 2009 
      Monash University   Postdoctral researcher

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    •  
      日本学術振興会   特別研究員(PD)

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    Awards

    • 8 2014  
      日本進化学会研究奨励賞  陸上植物の生活史の発生進化学的研究
       
      榊原恵子

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    • 11 2013  
      広島大学  広島大学学長表彰 
       
      榊原恵子

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    • 9 2013  
      日本植物学会  奨励賞  ヒメツリガネゴケをモデルとした発生進化学的解析による陸上植物の異形世代交代を司る分子機構の解明
       
      榊原恵子

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    Papers

    • Sexual reproduction: Is the genetic pathway for female germ cell specification conserved in land plants?

      Emiko Yoro, Keiko Sakakibara

      Current Biology34 ( 6 ) R241 - R244   3 2024

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      Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

      DOI: 10.1016/j.cub.2024.01.062

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    • Protocol: an improved method for inducing sporophyte generation in the model moss Physcomitrium patens under nitrogen starvation. International journal

      Emiko Yoro, Shizuka Koshimizu, Takashi Murata, Keiko Sakakibara

      Plant methods19 ( 1 ) 100 - 100   26 9 2023

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      BACKGROUND: Land plants exhibit a haplodiplontic life cycle, whereby multicellular bodies develop in both the haploid and diploid generations. The early-diverging land plants, known as bryophytes, have a haploid-dominant life cycle, in which a short-lived multicellular body in the diploid generation, known as the sporophyte, develops on the maternal haploid gametophyte tissues. The moss Physcomitrium (Physcomitrella) patens has become one of the most powerful model systems in evolutionary plant developmental studies. To induce diploid sporophytes of P. patens, several protocols are implemented. One of the conventional approaches is to grow approximately one-month-old gametophores for another month on Jiffy-7 pellets made from the peat moss that is difficult to fully sterilize. A more efficient method to obtain all tissues throughout the life cycle should accelerate studies of P. patens. RESULTS: Here, we investigated the effect of nitrogen conditions on the growth and development of P. patens. We provide an improved protocol for the sporophyte induction of P. patens using a BCD-based solid culture medium without Jiffy-7 pellets, based on the finding that the formation of gametangia and subsequent sporophytes is promoted by nitrogen-free growth conditions. The protocol consists of two steps; first, culture the protonemata and gametophores on nitrogen-rich medium under continuous light at 25 °C, and then transfer the gametophores onto nitrogen-free medium under short-day and at 15 °C for sporophyte induction. The protocol enables to shorten the induction period and reduce the culture space. CONCLUSIONS: Our more efficient and shortened protocol for inducing the formation of sporophytes will contribute to future studies into the fertilization or the diploid sporophyte generation of P. patens.

      DOI: 10.1186/s13007-023-01077-z

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    • What can hornworts teach us? International journal

      Eftychios Frangedakis, Alan O Marron, Manuel Waller, Anna Neubauer, Sze Wai Tse, Yuling Yue, Stephanie Ruaud, Lucas Waser, Keiko Sakakibara, Péter Szövényi

      Frontiers in plant science14   1108027 - 1108027   2023

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      Language:English   Publishing type:Research paper (scientific journal)  

      The hornworts are a small group of land plants, consisting of only 11 families and approximately 220 species. Despite their small size as a group, their phylogenetic position and unique biology are of great importance. Hornworts, together with mosses and liverworts, form the monophyletic group of bryophytes that is sister to all other land plants (Tracheophytes). It is only recently that hornworts became amenable to experimental investigation with the establishment of Anthoceros agrestis as a model system. In this perspective, we summarize the recent advances in the development of A. agrestis as an experimental system and compare it with other plant model systems. We also discuss how A. agrestis can help to further research in comparative developmental studies across land plants and to solve key questions of plant biology associated with the colonization of the terrestrial environment. Finally, we explore the significance of A. agrestis in crop improvement and synthetic biology applications in general.

      DOI: 10.3389/fpls.2023.1108027

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    • Phylogenetic distribution and expression pattern analyses identified a divergent basal body assembly protein involved in land plant spermatogenesis Peer-reviewed International journal

      Shizuka Koshimizu, Naoki Minamino, Tomoaki Nishiyama, Emiko Yoro, Mayuko Sato, Mayumi Wakazaki, Kiminori Toyooka, Kazuo Ebine, Keiko Sakakibara, Takashi Ueda, Kentaro Yano

      New Phytologist236 ( 3 ) 1182 - 1196   3 8 2022

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:Wiley  

      Land plant spermatozoids commonly possess characteristic structures such as the spline, which consists of a microtubule array, the multilayered structure (MLS) in which the uppermost layer is a continuum of the spline, and multiple flagella. However, the molecular mechanisms underpinning spermatogenesis remain to be elucidated. We successfully identified candidate genes involved in spermatogenesis, deeply divergent BLD10s, by computational analyses combining multiple methods and omics data. We then examined the functions of BLD10s in the liverwort Marchantia polymorpha and the moss Physcomitrium patens. MpBLD10 and PpBLD10 are required for normal basal body (BB) and flagella formation. Mpbld10 mutants exhibited defects in remodeling of the cytoplasm and nucleus during spermatozoid formation, and thus MpBLD10 should be involved in chromatin reorganization and elimination of the cytoplasm during spermiogenesis. We identified orthologs of MpBLD10 and PpBLD10 in diverse Streptophyta and found that MpBLD10 and PpBLD10 are orthologous to BLD10/CEP135 family proteins, which function in BB assembly. However, BLD10s evolved especially quickly in land plants and MpBLD10 might have acquired additional functions in spermatozoid formation through rapid molecular evolution.

      DOI: 10.1111/nph.18385

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      Other Link: https://onlinelibrary.wiley.com/doi/full-xml/10.1111/nph.18385

    • An ancestral function of strigolactones as symbiotic rhizosphere signals. Peer-reviewed International journal

      Kyoichi Kodama, Mélanie K Rich, Akiyoshi Yoda, Shota Shimazaki, Xiaonan Xie, Kohki Akiyama, Yohei Mizuno, Aino Komatsu, Yi Luo, Hidemasa Suzuki, Hiromu Kameoka, Cyril Libourel, Jean Keller, Keiko Sakakibara, Tomoaki Nishiyama, Tomomi Nakagawa, Kiyoshi Mashiguchi, Kenichi Uchida, Kaori Yoneyama, Yoshikazu Tanaka, Shinjiro Yamaguchi, Masaki Shimamura, Pierre-Marc Delaux, Takahito Nomura, Junko Kyozuka

      Nature communications13 ( 1 ) 3974 - 3974   8 7 2022

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      Language:English   Publishing type:Research paper (scientific journal)  

      In flowering plants, strigolactones (SLs) have dual functions as hormones that regulate growth and development, and as rhizosphere signaling molecules that induce symbiosis with arbuscular mycorrhizal (AM) fungi. Here, we report the identification of bryosymbiol (BSB), an SL from the bryophyte Marchantia paleacea. BSB is also found in vascular plants, indicating its origin in the common ancestor of land plants. BSB synthesis is enhanced at AM symbiosis permissive conditions and BSB deficient mutants are impaired in AM symbiosis. In contrast, the absence of BSB synthesis has little effect on the growth and gene expression. We show that the introduction of the SL receptor of Arabidopsis renders M. paleacea cells BSB-responsive. These results suggest that BSB is not perceived by M. paleacea cells due to the lack of cognate SL receptors. We propose that SLs originated as AM symbiosis-inducing rhizosphere signaling molecules and were later recruited as plant hormone.

      DOI: 10.1038/s41467-022-31708-3

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    • The complete plastid genome sequence of the enigmatic moss, Takakia lepidozioides (Takakiopsida, Bryophyta): evolutionary perspectives on the largest collection of genes in mosses and the intensive RNA editing Peer-reviewed International journal

      Atsushi Sadamitsu, Yuya Inoue, Keiko Sakakibara, Hiromi Tsubota, Tomio Yamaguchi, Hironori Deguchi, Tomoaki Nishiyama, Masaki Shimamura

      Plant Molecular Biology107 ( 4-5 ) 431 - 449   11 2021

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

      Complete chloroplast genome sequence of a moss, Takakia lepidozioides (Takakiopsida) is reported. The largest collection of genes in mosses and the intensive RNA editing were discussed from evolutionary perspectives. We assembled the entire plastid genome sequence of Takakia lepidozioides (Takakiopsida), emerging from the first phylogenetic split among extant mosses. The genome sequences were assembled into a circular molecule 149,016 bp in length, with a quadripartite structure comprising a large and a small single-copy region separated by inverted repeats. It contained 88 genes coding for proteins, 32 for tRNA, four for rRNA, two open reading frames, and at least one pseudogene (tufA). This is the largest number of genes of all sequenced plastid genomes in mosses and Takakia is the only moss that retains the seven coding genes ccsA, cysA, cysT, petN rpoA, rps16 and trnPGGG. Parsimonious interpretation of gene loss suggests that the last common ancestor of bryophytes had all seven genes and that mosses lost at least three of them during their diversification. Analyses of the plastid transcriptome identified the extraordinary frequency of RNA editing with more than 1100 sites. We indicated a close correlation between the monoplastidy of vegetative tissue and the intensive RNA editing sites in the plastid genome in land plant lineages. Here, we proposed a hypothesis that the small population size of plastids in each vegetative cell of some early diverging land plants, including Takakia, might cause the frequent fixation of mutations in plastid genome through the intracellular genetic drift and that deleterious mutations might be continuously compensated by RNA editing during or following transcription.

      DOI: 10.1007/s11103-021-01214-z

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      Other Link: https://link.springer.com/article/10.1007/s11103-021-01214-z/fulltext.html

    • An Agrobacterium ‐mediated stable transformation technique for the hornwort model Anthoceros agrestis Peer-reviewed International journal

      Eftychios Frangedakis, Manuel Waller, Tomoaki Nishiyama, Hirokazu Tsukaya, Xia Xu, Yuling Yue, Michelle Tjahjadi, Andika Gunadi, Joyce Van Eck, Fay‐Wei Li, Péter Szövényi, Keiko Sakakibara

      New Phytologist232 ( 3 ) 1488 - 1505   19 7 2021

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      Authorship:Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Wiley  

      Despite their key phylogenetic position and their unique biology, hornworts have been widely overlooked. Until recently there was no hornwort model species amenable to systematic experimental investigation. Anthoceros agrestis has been proposed as the model species to study hornwort biology. We have developed an Agrobacterium-mediated method for the stable transformation of A. agrestis, a hornwort model species for which a genetic manipulation technique was not yet available. High transformation efficiency was achieved by using thallus tissue grown under low light conditions. We generated a total of 274 transgenic A. agrestis lines expressing the β-glucuronidase (GUS), cyan, green, and yellow fluorescent proteins under control of the CaMV 35S promoter and several endogenous promoters. Nuclear and plasma membrane localization with multiple color fluorescent proteins was also confirmed. The transformation technique described here should pave the way for detailed molecular and genetic studies of hornwort biology, providing much needed insight into the molecular mechanisms underlying symbiosis, carbon-concentrating mechanism, RNA editing and land plant evolution in general.

      DOI: 10.1111/nph.17524

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      Other Link: https://onlinelibrary.wiley.com/doi/full-xml/10.1111/nph.17524

    • The Hornworts: Morphology, evolution and development Peer-reviewed International journal

      Eftychios Frangedakis, Masaki Shimamura, Juan Carlos Villarreal, Fay‐Wei Li, Marta Tomaselli, Manuel Waller, Keiko Sakakibara, Karen S. Renzaglia, Péter Szövényi

      New Phytologist229 ( 2 ) 735 - 754   15 9 2020

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:Wiley  

      Extant land plants consist of two deeply divergent groups, tracheophytes and bryophytes, which shared a common ancestor some 500 million years ago. While information about vascular plants and the two of the three lineages of bryophytes, the mosses and liverworts, is steadily accumulating, the biology of hornworts remains poorly explored. Yet, as the sister group to liverworts and mosses, hornworts are critical in understanding the evolution of key land plant traits. Until recently, there was no hornwort model species amenable to systematic experimental investigation, which hampered detailed insight into the molecular biology and genetics of this unique group of land plants. The emerging hornwort model species, Anthoceros agrestis, is instrumental in our efforts to better understand not only hornwort biology but also fundamental questions of land plant evolution. To this end, here we provide an overview of hornwort biology and current research on the model plant A. agrestis to highlight its potential in answering key questions of land plant biology and evolution.

      DOI: 10.1111/nph.16874

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    • Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts Peer-reviewed International journal

      Fay-Wei Li, Tomoaki Nishiyama, Manuel Waller, Eftychios Frangedakis, Jean Keller, Zheng Li, Noe Fernandez-Pozo, Michael S. Barker, Tom Bennett, Miguel A. Blázquez, Shifeng Cheng, Andrew C. Cuming, Jan de Vries, Sophie de Vries, Pierre-Marc Delaux, Issa S. Diop, C. Jill Harrison, Duncan Hauser, Jorge Hernández-García, Alexander Kirbis, John C. Meeks, Isabel Monte, Sumanth K. Mutte, Anna Neubauer, Dietmar Quandt, Tanner Robison, Masaki Shimamura, Stefan A. Rensing, Juan Carlos Villarreal, Dolf Weijers, Susann Wicke, Gane K.-S. Wong, Keiko Sakakibara, Péter Szövényi

      Nature Plants6 ( 3 ) 259 - 272   3 2020

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

      Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.

      DOI: 10.1038/s41477-020-0618-2

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      Other Link: http://www.nature.com/articles/s41477-020-0618-2

    • Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants Peer-reviewed International journal

      Asuka Higo, Tomokazu Kawashima, Michael Borg, Mingmin Zhao, Irene López-Vidriero, Hidetoshi Sakayama, Sean A. Montgomery, Hiroyuki Sekimoto, Dieter Hackenberg, Masaki Shimamura, Tomoaki Nishiyama, Keiko Sakakibara, Yuki Tomita, Taisuke Togawa, Kan Kunimoto, Akihisa Osakabe, Yutaka Suzuki, Katsuyuki T. Yamato, Kimitsune Ishizaki, Ryuichi Nishihama, Takayuki Kohchi, José M. Franco-Zorrilla, David Twell, Frédéric Berger, Takashi Araki

      Nature Communications9 ( 1 ) 5283 - 5283   12 2018

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

      Evolutionary mechanisms underlying innovation of cell types have remained largely unclear. In multicellular eukaryotes, the evolutionary molecular origin of sperm differentiation is unknown in most lineages. Here, we report that in algal ancestors of land plants, changes in the DNA-binding domain of the ancestor of the MYB transcription factor DUO1 enabled the recognition of a new cis-regulatory element. This event led to the differentiation of motile sperm. After neo-functionalization, DUO1 acquired sperm lineage-specific expression in the common ancestor of land plants. Subsequently the downstream network of DUO1 was rewired leading to sperm with distinct morphologies. Conjugating green algae, a sister group of land plants, accumulated mutations in the DNA-binding domain of DUO1 and lost sperm differentiation. Our findings suggest that the emergence of DUO1 was the defining event in the evolution of sperm differentiation and the varied modes of sexual reproduction in the land plant lineage.

      DOI: 10.1038/s41467-018-07728-3

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      Other Link: http://www.nature.com/articles/s41467-018-07728-3

    • Class III HD-Zip activity coordinates leaf development in Physcomitrella patens Peer-reviewed

      Hoichong Karen Yip, Sandra K. Floyd, Keiko Sakakibara, John L. Bowman

      DEVELOPMENTAL BIOLOGY419 ( 1 ) 184 - 197   11 2016

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:ACADEMIC PRESS INC ELSEVIER SCIENCE  

      Land plant bodies develop from meristems, groups of pluripotent stem cells, which may persist throughout the life of a plant or, alternatively, have a transitory existence. Early diverging land plants exhibit indeterminate (persistent) growth in their haploid gametophytic generation, whereas later diverging lineages exhibit indeterminate growth in their diploid sporophytic generation, raising the question of whether genetic machinery directing meristematic functions was co-opted between generations. Class III HD-Zip (C3HDZ) genes are required for the establishment and maintenance of shoot apical meristems in flowering plants. We demonstrate that in the moss Physcomitrella patens, C3HDZ genes are expressed in transitory meristems in both the gametophytic and sporophytic generations, but not in the persistent shoot meristem of the gametyphyte. Loss-of-function of P. patens C3HDZ was engineered using ectopic expression of miR166, an endogenous regulator of C3HDZ gene activity. Loss of C3HDZ gene function impaired the function of gametophytic transitory meristematic activity but did not compromise the functioning of the persistent shoot apical meristem during the gametophyte generation. These results argue against a wholesale co-option of meristematic gene regulatory networks from the gametophyte to the sporophyte during land plant evolution, instead suggesting that persistent meristems with a single apical cell in P. patens and persistent complex meristems in flowering plants are regulated by different genetic programs. (C) 2016 Elsevier Inc. All rights reserved.

      DOI: 10.1016/j.ydbio.2016.01.012

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    • Technological Innovations Give Rise to a New Era of Plant Evolutionary Developmental Biology Peer-reviewed

      K. Sakakibara

      GENOMES AND EVOLUTION OF CHAROPHYTES, BRYOPHYTES, LYCOPHYTES AND FERNS78   3 - 35   2016

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      Authorship:Corresponding author   Language:English   Publishing type:Part of collection (book)   Publisher:ACADEMIC PRESS LTD-ELSEVIER SCIENCE LTD  

      Land plants evolved from freshwater algaelike ancestors approximately 480 million years ago. Land plants developed many new morphological features during the evolution including the origin of a multicellular diploid sporophyte, a sporophytic apical meristem that produces complex body architecture, stomata and the production of lateral organs (leaves), vascular tissue, roots, seeds and flowers. Genetic changes drove the development of these morphological features and recent technological innovations in genomics and genetic modification technologies have allowed us to investigate these genetic changes. Here, I describe recent research on several transcription factors that contributed to the morphological evolution of land plants, including the homeodomain proteins KNOX, BELL and WOX, as well as transcription factors of the bHLH, NAC and FLO/LFY families. I also discuss the conservation of plant hormone signalling, which acts to coordinate the multicellular body plan.

      DOI: 10.1016/bs.abr.2016.01.001

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    • Evolution in the Cycles of Life Invited Peer-reviewed

      John L. Bowman, Keiko Sakakibara, Chihiro Furumizu, Tom Dierschke

      ANNUAL REVIEW OF GENETICS, VOL 5050   133 - 154   2016

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      Language:English   Publishing type:Part of collection (book)   Publisher:ANNUAL REVIEWS  

      The life cycles of eukaryotes alternate between haploid and diploid phases, which are initiated by meiosis and gamete fusion, respectively. In both ascomycete and basidiomycete fungi and chlorophyte algae, the haploid-to-diploid transition is regulated by a pair of paralogous homeodomain protein encoding genes. That a common genetic program controls the haploid-to-diploid transition in phylogenetically disparate eukaryotic lineages suggests this may be the ancestral function for homeodomain proteins. Multicellularity has evolved independently in many eukaryotic lineages in either one or both phases of the life cycle. Organisms, such as land plants, exhibiting a life cycle whereby multicellular bodies develop in both the haploid and diploid phases are often referred to as possessing an alternation of generations. We review recent progress on understanding the genetic basis for the land plant alternation of generations and highlight the roles that homeodomain-encoding genes may have played in the evolution of complex multicellularity in this lineage.

      DOI: 10.1146/annurev-genet-120215-035227

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    • Antagonistic Roles for KNOX1 and KNOX2 Genes in Patterning the Land Plant Body Plan Following an Ancient Gene Duplication Peer-reviewed

      Chihiro Furumizu, John Paul Alvarez, Keiko Sakakibara, John L. Bowman

      PLOS GENETICS11 ( 2 ) ee1004980   2 2015

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:PUBLIC LIBRARY SCIENCE  

      Neofunctionalization following gene duplication is thought to be one of the key drivers in generating evolutionary novelty. A gene duplication in a common ancestor of land plants produced two classes of KNOTTED-like TALE homeobox genes, class I (KNOX1) and class II (KNOX2). KNOX1 genes are linked to tissue proliferation and maintenance of meri-stematic potentials of flowering plant and moss sporophytes, and modulation of KNOX1 activity is implicated in contributing to leaf shape diversity of flowering plants. While KNOX2 function has been shown to repress the gametophytic (haploid) developmental program during moss sporophyte (diploid) development, little is known about KNOX2 function in flowering plants, hindering syntheses regarding the relationship between two classes of KNOX genes in the context of land plant evolution. Arabidopsis plants harboring loss-of-function KNOX2 alleles exhibit impaired differentiation of all aerial organs and have highly complex leaves, phenocopying gain-of-function KNOX1 alleles. Conversely, gain-of-function KNOX2 alleles in conjunction with a presumptive heterodimeric BELL TALE homeobox partner suppressed SAM activity in Arabidopsis and reduced leaf complexity in the Arabidopsis relative Cardamine hirsuta, reminiscent of loss-of-function KNOX1 alleles. Little evidence was found indicative of epistasis or mutual repression between KNOX1 and KNOX2 genes. KNOX proteins heterodimerize with BELL TALE homeobox proteins to form functional complexes, and contrary to earlier reports based on in vitro and heterologous expression, we find high selectivity between KNOX and BELL partners in vivo. Thus, KNOX2 genes confer opposing activities rather than redundant roles with KNOX1 genes, and together they act to direct the development of all above-ground organs of the Arabidopsis sporophyte. We infer that following the KNOX1/KNOX2 gene duplication in an ancestor of land plants, neofunctionalization led to evolution of antagonistic biochemical activity thereby facilitating the evolution of more complex sporophyte transcriptional networks, providing plasticity for the morphological evolution of land plant body plans.

      DOI: 10.1371/journal.pgen.1004980

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    • WOX13-like genes are required for reprogramming of leaf and protoplast cells into stem cells in the moss Physcomitrella patens Peer-reviewed

      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

      DEVELOPMENT141 ( 8 ) 1660 - 1670   4 2014

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      Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:COMPANY OF BIOLOGISTS LTD  

      Many differentiated plant cells can dedifferentiate into stem cells, reflecting the remarkable developmental plasticity of plants. In the moss Physcomitrella patens, cells at the wound margin of detached leaves become reprogrammed into stem cells. Here, we report that two paralogous P. patens WUSCHEL-related homeobox 13-like ( PpWOX13L) genes, homologs of stem cell regulators in flowering plants, are transiently upregulated and required for the initiation of cell growth during stem cell formation. Concordantly, Delta ppwox13l deletion mutants fail to upregulate genes encoding homologs of cell wall loosening factors during this process. During the moss life cycle, most of the Delta ppwox13l mutant zygotes fail to expand and initiate an apical stem cell to form the embryo. Our data show that PpWOX13L genes are required for the initiation of cell growth specifically during stem cell formation, in analogy to WOX stem cell functions in seed plants, but using a different cellular mechanism.

      DOI: 10.1242/dev.097444

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    • Evolution of the Class IV HD-Zip Gene Family in Streptophytes Peer-reviewed

      Christopher S. Zalewski, Sandra K. Floyd, Chihiro Furumizu, Keiko Sakakibara, Dennis W. Stevenson, John L. Bowman

      MOLECULAR BIOLOGY AND EVOLUTION30 ( 10 ) 2347 - 2365   10 2013

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:OXFORD UNIV PRESS  

      Class IV homeodomain leucine zipper (C4HDZ) genes are plant-specific transcription factors that, based on phenotypes in Arabidopsis thaliana, play an important role in epidermal development. In this study, we sampled all major extant lineages and their closest algal relatives for C4HDZ homologs and phylogenetic analyses result in a gene tree that mirrors land plant evolution with evidence for gene duplications in many lineages, but minimal evidence for gene losses. Our analysis suggests an ancestral C4HDZ gene originated in an algal ancestor of land plants and a single ancestral gene was present in the last common ancestor of land plants. Independent gene duplications are evident within several lineages including mosses, lycophytes, euphyllophytes, seed plants, and, most notably, angiosperms. In recently evolved angiosperm paralogs, we find evidence of pseudogenization via mutations in both coding and regulatory sequences. The increasing complexity of the C4HDZ gene family through the diversification of land plants correlates to increasing complexity in epidermal characters.

      DOI: 10.1093/molbev/mst132

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    • KNOX2 Genes Regulate the Haploid-to-Diploid Morphological Transition in Land Plants Peer-reviewed

      Keiko Sakakibara, Sayuri Ando, Hoichong Karen Yip, Yosuke Tamada, Yuji Hiwatashi, Takashi Murata, Hironori Deguchi, Mitsuyasu Hasebe, John L. Bowman

      SCIENCE339 ( 6123 ) 1067 - 1070   3 2013

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      Unlike animals, land plants undergo an alternation of generations, producing multicellular bodies in both haploid (1n: gametophyte) and diploid (2n: sporophyte) generations. Plant body plans in each generation are regulated by distinct developmental programs initiated at either meiosis or fertilization, respectively. In mosses, the haploid gametophyte generation is dominant, whereas in vascular plants-including ferns, gymnosperms, and angiosperms-the diploid sporophyte generation is dominant. Deletion of the class 2 KNOTTED1-LIKE HOMEOBOX (KNOX2) transcription factors in the moss Physcomitrella patens results in the development of gametophyte bodies from diploid embryos without meiosis. Thus, KNOX2 acts to prevent the haploid-specific body plan from developing in the diploid plant body, indicating a critical role for the evolution of KNOX2 in establishing an alternation of generations in land plants.

      DOI: 10.1126/science.1230082

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    • Gametangia development in the moss Physcomitrella patens. Peer-reviewed

      Kofuji R, Yoshimura T, Inoue H, Sakakibara K, Hiwatashi Y, Kurt T, Aoyama T, Ueda K, Hasebe N

      Annual Plant Reviews, Volume36 The moss <i>Physcomitrella patens</i>36   167 - 181   6 2009

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    • Class 1 KNOX genes are not involved in shoot development in the moss Physcomitrella patens but do function in sporophyte development Peer-reviewed

      Keiko Sakakibara, Tomoaki Nishiyama, Hironori Deguchi, Mitsuyasu Hasebe

      EVOLUTION & DEVELOPMENT10 ( 5 ) 555 - 566   9 2008

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      Although the number and form of metazoan organs are determined in the embryo, plants continuously form organs via pluripotent stem cells contained within the meristem. Flowering plants have an indeterminate meristem in their diploid generation, whereas the common ancestor of land plants is inferred to have formed an indeterminate meristem in its haploid generation, as observed in the extant basal land plants, bryophytes, including mosses. It is hypothesized that the underlying gene networks for the diploid meristem were initially present in the haploid generation of the basal land plants and were eventually co-opted for expression in the diploid generation. In flowering plants, the class 1 KNOTTED1-LIKE HOMEOBOX (KNOX) transcription factors are essential for the function of the indeterminate apical meristem. Here, we show that the class 1 KNOX orthologs function in the diploid organ, with determinate growth in the moss Physcomitrella patens, but do not function in the haploid indeterminate meristem. We propose that the genetic networks governing the indeterminate meristem in land plants are variable, and the networks governing the diploid indeterminate meristem with the class 1 KNOX genes likely evolved de novo in the flowering plant lineage.

      DOI: 10.1111/j.1525-142X.2008.00271.x

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    • The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants Peer-reviewed

      Stefan A. Rensing, Daniel Lang, Andreas D. Zimmer, Astrid Terry, Asaf Salamov, Harris Shapiro, Tomoaki Nishiyama, Pierre-Francois Perroud, Erika A. Lindquist, Yasuko Kamisugi, Takako Tanahashi, Keiko Sakakibara, Tomomichi Fujita, Kazuko Oishi, Tadasu Shin-I, Yoko Kuroki, Atsushi Toyoda, Yutaka Suzuki, Shin-ichi Hashimoto, Kazuo Yamaguchi, Sumio Sugano, Yuji Kohara, Asao Fujiyama, Aldwin Anterola, Setsuyuki Aoki, Neil Ashton, W. Brad Barbazuk, Elizabeth Barker, Jeffrey L. Bennetzen, Robert Blankenship, Sung Hyun Cho, Susan K. Dutcher, Mark Estelle, Jeffrey A. Fawcett, Heidrun Gundlach, Kousuke Hanada, Alexander Heyl, Karen A. Hicks, Jon Hughes, Martin Lohr, Klaus Mayer, Alexander Melkozernov, Takashi Murata, David R. Nelson, Birgit Pils, Michael Prigge, Bernd Reiss, Tanya Renner, Stephane Rombauts, Paul J. Rushton, Anton Sanderfoot, Gabriele Schween, Shin-Han Shiu, Kurt Stueber, Frederica L. Theodoulou, Hank Tu, Yves Van de Peer, Paul J. Verrier, Elizabeth Waters, Andrew Wood, Lixing Yang, David Cove, Andrew C. Cuming, Mitsuyasu Hasebe, Susan Lucas, Brent D. Mishler, Ralf Reski, Igor V. Grigoriev, Ralph S. Quatrano, Jeffrey L. Boore

      SCIENCE319 ( 5859 ) 64 - 69   1 2008

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      We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments ( e. g., flagellar arms); acquisition of genes for tolerating terrestrial stresses ( e. g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant&apos;s unique facility for reverse genetics.

      DOI: 10.1126/science.1150646

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    • Green genes - Comparative genomics of the green branch of life Peer-reviewed

      John L. Bowman, Sandra K. Floyd, Keiko Sakakibara

      CELL129 ( 2 ) 229 - 234   4 2007

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      As more plant genome sequences become available, researchers are increasingly using comparative genomics to address some of the major questions in plant biology. Such questions include the evolution of photosynthesis and multicellularity, the developmental genetic changes responsible for alterations in body plan, and the origin of important plant innovations such as roots, leaves, and vascular tissue.

      DOI: 10.1016/j.cell.2007.04.004

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    • KNOX homeobox genes potentially have similar function in both diploid unicellular and multicellular meristems, but not in haploid meristems Peer-reviewed

      R Sano, CM Juarez, B Hass, K Sakakibara, M Ito, JA Banks, M Hasebe

      EVOLUTION & DEVELOPMENT7 ( 1 ) 69 - 78   1 2005

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      Members of the class 1 knotted-like homeobox (KNOX) gene family are important regulators of shoot apical meristem development in angiosperms. To determine whether they function similarly in seedless plants, three KNOX genes (two class 1 genes and one class 2 gene) from the fern Ceratopteris richardii were characterized. Expression of both class 1 genes was detected in the shoot apical cell, leaf primordia, marginal part of the leaves, and vascular bundles by in situ hybridization, a pattern that closely resembles that of class 1 KNOX genes in angiosperms with compound leaves. The fern class 2 gene was expressed in all sporophyte tissues examined, which is characteristic of class 2 gene expression in angiosperms. All three CRKNOX genes were not detected in gametophyte tissues by RNA gel blot analysis. Arabidopsis plants overexpressing the fern class 1 genes resembled plants that overexpress seed plant class 1 KNOX genes in leaf morphology. Ectopic expression of the class 2 gene in Arabidopsis did not result in any unusual phenotypes. Taken together with phylogenetic analysis, our results suggest that (a) the class 1 and 2 KNOX genes diverged prior to the divergence of fern and seed plant lineages, (b) the class 1 KNOX genes function similarly in seed plant and fern sporophyte meristem development despite their differences in structure, (c) KNOX gene expression is not required for the development of the fern gametophyte, and (d) the sporophyte and gametophyte meristems of ferns are not regulated by the same developmental mechanisms at the molecular level.

      DOI: 10.1111/j.1525-142X.2005.05008.x

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    • Involvement of auxin and a homeodomain-leucine zipper I gene in rhizoid development of the moss Physcomitrella patens Peer-reviewed

      K Sakakibara, T Nishiyama, N Sumikawa, R Kofuji, T Murata, M Hasebe

      DEVELOPMENT130 ( 20 ) 4835 - 4846   10 2003

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      Differentiation of epidermal cells is important for plants because they are in direct contact with the environment. Rhizoids are multicellular filaments that develop from the epidermis in a wide range of plants, including pteridophytes, bryophytes, and green algae; they have similar functions to root hairs in vascular plants in that they support the plant body and are involved in water and nutrient absorption. In this study, we examined mechanisms underlying rhizoid development in the moss, Physcomitrella patens, which is the only land plant in which high-frequency gene targeting is possible. We found that rhizoid development can be split into two processes: determination and differentiation. Two types of rhizoids with distinct developmental patterns (basal and mid-stem rhizoids) were recognized. The development of basal rhizoids from epidermal cells was induced by exogenous auxin, while that of mid-stem rhizoids required an unknown factor in addition to exogenous auxin. Once an epidermal cell had acquired a rhizoid initial cell fate, expression of the homeodomain-leucine zipper I gene Pphb7 was induced. Analysis of Pphb7 disruptant lines showed that Pphb7 affects the induction of pigmentation and the increase in the number and size of chloroplasts, but not the position or number of rhizoids. This is the first report on the involvement of a homeodomain-leucine zipper I gene in epidermal cell differentiation.

      DOI: 10.1242/dev.00644

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    • Characterization of a FLORICAULA/LEAFY homologue of Gnetum parvifolium and its implications for the evolution of reproductive organs in seed plants Peer-reviewed

      S Shindo, K Sakakibara, R Sano, K Ueda, M Hasebe

      INTERNATIONAL JOURNAL OF PLANT SCIENCES162 ( 6 ) 1199 - 1209   11 2001

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:UNIV CHICAGO PRESS  

      The morphological variation among reproductive organs of extant seed plants makes assessment of organ homology difficult. Comparisons of expression patterns of homeotic genes that control organ development will yield new information about the homology of organs to assess inferences deduced from previous morphological studies. In angiosperms, the FLORICAULA/LEAFY (FLO/LFY) genes convert a vegetative shoot meristem to a floral meristem by inducing floral homeotic genes, most of which belong to the MADS-box gene family. To provide insights into the evolution of reproductive organs in seed plants, a FLO/LFY homologue (GpLFY) was cloned from Gnetum parvifolium. GpLFY mRNA was expressed in both the vegetative shoot apex and the female strobilus. The GpLFY mRNA signal was detected in early developmental stages of the collar and the ovule primordium, including the nucellus and three envelopes. A comparison of FLO/LFY gene expression in Gnetum and the conifer Pinus radiata indicates that the Gnetum collar and ovule are homologous with the conifer bract and ovule-ovuliferous scale complex, respectively. Overexpression of GpLFY in transgenic Arabidopsis promoted a conversion of a shoot meristem to a floral primordium. The Arabidopsis LFY null mutant, lfy-26, with a malformed flower, was complemented by overexpression of GpLFY. These results indicate that the inductive pathway from the FLO/LFY gene to the MADS-box genes already existed in the common ancestor of angiosperms and gymnosperms.

      DOI: 10.1086/323417

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    • Isolation of homeodomain-leucine zipper genes from the moss Physcomitrella patens and the evolution of homeodomain-leucine zipper genes in land plants Peer-reviewed

      K. Sakakibara, T. Nishiyama, M. Kato, M. Hasebe

      Molecular Biology and Evolution18 ( 4 ) 491 - 502   2001

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      Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Society for Molecular Biology and Evolution  

      Homeobox genes encode transcription factors involved in many aspects of developmental processes. The homeodomain-leucine zipper (HD-Zip) genes, which are characterized by the presence of both a homeodomain and a leucine zipper motif, form a clade within the homeobox superfamily and were previously reported only from vascular plants. Here we report the isolation of 10 HD-Zip genes (named Pphb1-Pphb10) from the moss Physcomitrella patens. Based on a phylogenetic analysis of the 10 Pphb genes and previously reported vascular plant HD-Zip genes, all of the Pphb genes except Pphb3 belong to three of the four HD-Zip subfamilies (HD-Zip I, II, and III), indicating that these subfamilies originated before the divergence of the vascular plant and moss lineages. Pphb3 is sister to the HD-Zip II subfamily and has some distinctive characteristics, including the difference of the a1 and d1 sites of its leucine zipper motif, which are well conserved in each HD-Zip subfamily. Comparison of the genetic divergence of representative HD-Zip I and II genes showed that the evolutionary rate of HD-Zip I genes was faster than that of HD-Zip II genes.

      DOI: 10.1093/oxfordjournals.molbev.a003828

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    • Tagged mutagenesis and gene-trap in the moss, Physcomitrella patens by shuttle mutagenesis Peer-reviewed

      Tomoaki Nishiyama, Yuji Hiwatashi, Keiko Sakakibara, Masahiro Kato, Mitsuyasu Hasebe

      DNA Research7 ( 1 ) 9 - 17   2000

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:Universal Academy Press Inc.  

      The moss, Physcomitrella patens has been used as a useful material in many fields, because of its simple body plan, ease of gene targeting, and other reasons. Although many mutants have been reported, no method to isolate the corresponding genes was reported. We developed a gene tagging and gene-trap system in P. patens by using the shuttle mutagenesis technique, which has been used in the budding yeast. In 5264 tagged lines, 203 mutants with altered developmental or morphological phenotypes were obtained. In 129 of 4757 gene-trap lines, β-glucuronidase (GUS) activity was detected in some tissue. Although multiple copies of a tag were detected in many tagged lines by Southern analyses, most copies are likely integrated at the same locus according to PCR analyses.

      DOI: 10.1093/dnares/7.1.9

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    Misc.

    • コケ植物が語る過去・現在・未来 1 ツノゴケ-ゲノム解読と形質転換技術が拓く植物進化研究の新機軸

      西山智明, 榊原恵子, 嶋村正樹

      生物の科学 遺伝76 ( 3 )   2022

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    • Hornwort genomes and the developmental evolution of land plants Peer-reviewed

      BSJ-Review12   186 - 195   7 2021

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      Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (other)  

      DOI: 10.24480/bsj-review.12d2.00215

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    • 陸上植物起源研究の最後のフロンティア,ツノゴケの生物学 Invited Peer-reviewed

      嶋村正樹, 西山智明, 榊原恵子

      植物科学最前線12   183 - 185   7 2021

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    • ゲノム解析から見たツノゴケの二酸化炭素濃縮機構とシアノバクテリア,菌類との共生 植物の陸上進出を可能にした生存戦略

      西山智明, 榊原恵子, 嶋村正樹

      化学と生物59 ( 10 )   2021

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    • 古い酒を新しい革袋に~preexisting gene regulatory network の転用による 陸上植物のボディプラン革新 Invited Peer-reviewed

      ISHIZAKI KIMITSUNE, SAKAKIBARA KEIKO

      BSJ-Review7   47 - 54   4 2016

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      Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)   Publisher:日本植物学会  

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    • TALE型ホメオボックス遺伝子族の進化による陸上植物複相の複雑化

      榊原恵子, 古水千尋

      BSJ-Review7B   66 - 77   2016

    • KNOX2遺伝子は陸上植物の世代交代を制御する(一般講演,<特集>日本蘚苔類学会第42回岡山大会)

      榊原 恵子, 安藤 沙友里, Yip Hoichong Karen, 玉田 洋介, 日渡 祐二, 村田 隆, 出口 博則, 長谷部 光泰, Bowman John L.

      蘚苔類研究10 ( 12 ) 426 - 427   11 2013

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      Language:Japanese   Publisher:日本蘚苔類学会  

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    • Alternation of generations in bryophytes and factors regulating alternation of generations

      Sakakibara Keiko

      Bryological research10 ( 12 ) 393 - 397   11 2013

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      Language:Japanese   Publisher:The Bryological Society of Japan  

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    • 日本植物学会第76回大会参加およびシンポジウム開催報告(掲示板)

      嶋村 正樹, 榊原 恵子

      蘚苔類研究10 ( 9 ) 288 - 290   12 2012

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    • ヤマトツノゴケモドキの胞子体の組織発生学的研究(ポスター発表,<特集>日本蘚苔類学会第41回北海道大会)

      奥田 有貴, 榊原 恵子, 嶋村 正樹, 山口 富美夫, 出口 博則

      蘚苔類研究10 ( 9 ) 301 - 301   2012

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      DOI: 10.24474/bryologicalresearch.10.9_301_1

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    • 西表島における生葉上苔類と被着生植物の関係(ポスター発表,<特集>日本蘚苔類学会第41回北海道大会)

      友岡 秀文, 榊原 恵子, 嶋村 正樹, 山口 富美夫, 出口 博則

      蘚苔類研究10 ( 9 ) 303 - 303   2012

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      DOI: 10.24474/bryologicalresearch.10.9_303_2

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    • 蛍光顕微鏡を用いたツノゴケ類胞子体の形態学的研究(ポスター発表,<特集>日本蘚苔類学会第40回奈良大会)

      奥田 有貴, 山口 富美夫, 嶋村 正樹, 榊原 恵子, 出口 博則

      蘚苔類研究10 ( 6 ) 175 - 175   2011

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      DOI: 10.24474/bryologicalresearch.10.6_175_1

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    • Functional analyses of class 2 KNOX genes in Physcomitrella patens

      K Sakakibara, H Deguchi, M Hasebe

      PLANT AND CELL PHYSIOLOGY47   S180 - S180   2006

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      Language:English   Publishing type:Research paper, summary (international conference)   Publisher:OXFORD UNIV PRESS  

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    • Functional analysis of class 1 KNOX genes in Physcomitrella patens

      T Nishiyama, K Sakakibara, M Hasebe

      PLANT AND CELL PHYSIOLOGY46   S198 - S198   2005

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    • Functional Analysis of KNOX class 1 genes in Physcomitrella patens

      T Nishiyama, K Sakakibara, M Hasebe

      PLANT AND CELL PHYSIOLOGY45   S162 - S162   2004

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    • The role of Pphb7,a Physcomitrella HD-Zip gene, in rhizoid formation :

      SAKAKIBARA Keiko, HASEBE Mitsuyasu

      Plant and cell physiology42   s50   2001

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      Language:English   Publisher:Japanese Society of Plant Physiologists  

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      Other Link: https://projects.repo.nii.ac.jp/?action=repository_uri&item_id=184659

    • Isolation of MADS genes from the moss. Physcomitrella patens and characterization from gene targeting

      KOFUJI Rumiko, SAKAKIBARA Keiko, NISHIYAMA Tomoaki, HASEBE Mitsuyasu

        21   635 - 635   1 12 1998

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    • Physcomitrella patensにおけるMADS遺伝子の単離と解析

      小藤 累美子, 榊原 恵子, 西山 智明, 長谷部 光泰

      日本植物学会大会研究発表記録 = Proceedings of the annual meeting of the Botanical Society of Japan62   95 - 95   1 9 1998

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    • Physcomiterella patensにおけるホメオボックス遺伝子の単離と解析

      榊原 恵子, 西山 智明, 小藤 累美子, 加藤 雅啓, 長谷部 光泰

      日本植物学会大会研究発表記録 = Proceedings of the annual meeting of the Botanical Society of Japan62   95 - 95   1 9 1998

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    • Physcomitrella patensのタグつき変異体ライブラリーの作成

      西山 智明, 榊原 恵子, 小藤 累美子, 加藤 雅啓, 長谷部 光泰

      日本植物学会大会研究発表記録 = Proceedings of the annual meeting of the Botanical Society of Japan62   156 - 156   1 9 1998

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    Professional Memberships

    •  
      THE JAPANESE SOCIETY OF PLANT PHYSIOLOGISTS

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      SOCIETY OF EVOLUTIONARY STUDIES

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      THE BOTANICAL SOCIETY OF JAPAN

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    Research Projects

    • Key-Molecule-Network in Plant Reproduction

      Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Fund for the Promotion of Joint International Research (International Leading Research ) 

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      12 2022 - 3 2029

      Grant number:22K21352

      Grant amount:\689000000 ( Direct Cost: \530000000 、 Indirect Cost:\159000000 )

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    • Dual function of strigolactones as plant hormones to control growth and as signaling molecules to induce symbiosis: its origin and evolution

      Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research 

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      4 2023 - 3 2028

      Grant number:23H05409

      Grant amount:\612300000 ( Direct Cost: \471000000 、 Indirect Cost:\141300000 )

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    • Genomic dynamics underlying the plastic hermaphroditism in plants: the basis of exploratory reproductive adaptations

      Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research 

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      6 2022 - 3 2027

      Grant number:22H05172

      Grant amount:\317590000 ( Direct Cost: \244300000 、 Indirect Cost:\73290000 )

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    • Sex determination mechanisms underlying evolution of hermaphrodites in haploid generation

      Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Transformative Research Areas (A) 

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      6 2022 - 3 2027

      Grant number:22H05177

      Grant amount:\99970000 ( Direct Cost: \76900000 、 Indirect Cost:\23070000 )

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    • Elucidation of last common ancestor of land plants based on meristem related genes

      Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research 

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      4 2021 - 3 2024

      Grant number:21H02549

      Grant amount:\17550000 ( Direct Cost: \13500000 、 Indirect Cost:\4050000 )

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    • Reformation of evolutionary genomics in land plant evolution: from sequence comparison to functional comparison.

      Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research 

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      6 2019 - 3 2023

      Grant number:19K22448

      Grant amount:\6240000 ( Direct Cost: \4800000 、 Indirect Cost:\1440000 )

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    • Evolution of regulating factor of alternation of generations

      Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research 

      Sakakibara Keiko

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      4 2018 - 3 2022

      Grant number:18K06367

      Grant amount:\4290000 ( Direct Cost: \3300000 、 Indirect Cost:\990000 )

      Land plants exhibit multicellular body both in haploid and diploid generations, which called the alternation of generations. We previously reported the transcription factor regulating alternation of generations, KNOX2 gene. KNOX2 genes were found in Streptophyte algal genomes. Functional analysis of KNOX2 gene in Streptophyte alga Closterium peracerosum-strigosum-littorale is ongoing .
      We reported three hornwort genome informations and transformation method of a hornwort Anthoceros agrestis. KNOX1 gene, which is sister gene to KNOX2 gene, was lost in hornwort genomes.

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    • 細胞壁が制御する幹細胞の運命決定機構の解明

      日本学術振興会  科学研究費助成事業 

      榊原 恵子

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      4 2018 - 3 2020

      Grant number:18H04843

      Grant amount:\9750000 ( Direct Cost: \7500000 、 Indirect Cost:\2250000 )

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    • Elucidation of the mechanism of cell-fate transition by single-cell epigenome analysis

      Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research 

      Tamada Yosuke

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      4 2017 - 3 2020

      Grant number:17H03703

      Grant amount:\17810000 ( Direct Cost: \13700000 、 Indirect Cost:\4110000 )

      Purpose of the research is to understand the epigenome dynamics and the interaction between epigenome and transcriptome, which drive the cell-fate transition including the reprogramming from differentiated cells to stem cells. For this purpose, we performed single-nucleus 4D (3D + time lapse) imaging and single-cell transcriptome analyses during the reprogramming process of the moss Physcomitrella patens. Combined with previously performed ChIP-seq analyses of histone modifications H3K27me3 and H3K4me3, we found that, during the reprogramming process, the transcriptome actively changed during the reprogramming triggered by the physical damage, while the epigenome of the histone modifications did not largely change until the end of the reprogramming process. These data suggest that, at least for the reprogramming of Physcomitrella, the transcriptome changes first and then the epigenome of histone modifications changes toward the cell-fate change.

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    • 植物の新規幹細胞運命決定ロジックの解明

      日本学術振興会  科学研究費助成事業 

      榊原 恵子

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      4 2016 - 3 2018

      Grant number:16H01232

      Grant amount:\10140000 ( Direct Cost: \7800000 、 Indirect Cost:\2340000 )

      多細胞生物は、細胞分裂後に自身と同じ細胞を生み出す自己複製能と別の細胞への分化能の両方を有する幹細胞を持ち、分裂と分化を高度に調整して多細胞体制を構築している。ヒメツリガネゴケ (Physcomitrella patens) は発生段階に応じて露出した単一の幹細胞を形成するため、観察や外部操作が容易である。特に発生初期の胞子体は1個の幹細胞を持ち、後に1個の胞子のうを分化して発生を終了する。幹細胞に隣接する細胞(以後、隣接細胞)は幹細胞にならないことから、幹細胞から何らかの抑制シグナルが隣接細胞に伝えられることで、ボディプランが維持されていると考えられる。ヒメツリガネゴケKNOX1遺伝子は胞子体の幹細胞で発現し、この遺伝子の機能を阻害すると、幹細胞の分裂活性が低下する。さらに、隣接細胞も幹細胞化するBRANCHING (br) 変異株を単離した。この表現型はこれまでに例がなく、BR遺伝子の機能解析を行うことで新規の幹細胞決定因子、抑制因子の単離が期待される。BR遺伝子はホメオボックス転写因子をコードしており、KNOX型転写因子と複合体を形成して核移行することで機能することが推測されている。転写因子BRはKNOX1とともに、幹細胞における抑制シグナルの生合成や輸送か、隣接細胞における幹細胞化の抑制に機能していると考えられる。本研究は、BRタンパク質の局在観察と標的遺伝子の同定、および標的遺伝子の機能解析により、幹細胞制御に関わる新しい分子機構を解明することを目的とする。

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    • Establishment of hornwort model system for land plant evo-devo studies

      Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research 

      SAKAKIBARA Keiko, FRANGEDAKIS Eftychios

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      4 2014 - 3 2018

      Grant number:26650143

      Grant amount:\4030000 ( Direct Cost: \3100000 、 Indirect Cost:\930000 )

      Hornworts are one of bryophyte group, which locates at an important phylogenetic position in land plants. However the molecular genetic approaches or evo-devo research in hornworts were not well studied yet, because a hornwort model system was not available like other bryophyte groups, a moss Physcomitrella patens a liverwort and Marchantia polymorpha.
      We tried to establish a hornwort model system using a hornwort species, Anthoceros agrestis, which can be induced all developmental stages of the life cycle within 3 months under experimental condition. As the results, we established stable transformation technique via Agrobacterium, generated Anthoceros agrestis draft genome assembly with paired-end library, and perform RNA sequencing using the gametophyte tissue. Also we found KNOX, LFY, and WOX genes, which were identified as sporophyte developmental genes in the moss Physcomitrella patens. We isolated promoter regions of these genes for further expression analysis.

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    • Comprehensive research on Takakia and Haplomitrium based on genomic information

      Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research 

      Shimamura Masaki

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      4 2014 - 3 2018

      Grant number:26291081

      Grant amount:\15990000 ( Direct Cost: \12300000 、 Indirect Cost:\3690000 )

      Comprehensive studies based on genome information of Takakia and Haplomitrium were conducted. Complete sequence of chloroplast genome of T. lepidozioides was annotated and submitted to the database with accession number NC_028738.1. DNA barcoding and phylogenetic analysis of isolated fungi hyphae in mucilage hairs of Takakia lepidozioide indicated that the fungi forming the labyrinthine structure are closely related to Helotiales species isolated from the roots of the Ericaceae species. Although Haplomitrium mnioides has a relatively large genome size (ca. 4.4Gb), it shows relative simplicity of genetic networks, like a model liverwort Marchantia polymoprpha.

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    • Multidimensional Exploration of Logics of Leaf Development

      Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research 

      Tsukaya Hirokazu, SAKAKIBARA Keiko, YAMAGUCHI Takahiro, KAWADE Kensuke, Koga Hiroyuki

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      6 2013 - 3 2018

      Grant number:25113002

      Grant amount:\165750000 ( Direct Cost: \127500000 、 Indirect Cost:\38250000 )

      We could substitute past knowledge or add a new topic to the present textbooks during this research project. Namely, (1) the relationship between the ploidy level regulated by endoredupication and cell size is not as simple as formerly believed (Tsukaya 2013; Katagiri et al. 2016: the latter received The Hirase Award from The Japanese Society of Plant Morphology); (2) spatial-temporal regulation of leaf meristem can be explained by a classic morphogen-like diffusion of AN3 protein (Kawade et al. 2017).

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    • Molecular mechanism regulating the alternation of generations in land plants using the transcription factor

      Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research 

      SAKAKIBARA Keiko

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      4 2012 - 3 2015

      Grant number:24770077

      Grant amount:\4680000 ( Direct Cost: \3600000 、 Indirect Cost:\1080000 )

      Land plants undergo an alternation of generations, producing multicellular bodies in both 1n and 2n generations. We found the transcription factor KNOX2 function in the repression of haploid developmental program in the diploid body. To identify the molecular mechanism regulating the alternation of generations by KNOX2 genes, we performed the comparative transcriptome analysis using the early developing embryos of wild-type and KNOX2 mutant in a moss Physcomitrella patens.
      As the result of comparative transcriprome analysis, we found that the expression level of several transcription factors, secondary metabolic synthetic genes was altered in the KNOX2 mutant embryo. We hypothesize that the control of gene regulatory network and metabolism is important to regulate the alternations of generations in land plants.

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    • Chloroplast phylogenomics to resolve the phylogenetic relationships of major taxonomic groups in bryophytes

      Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research 

      DEGUCHI Hironori, YAMAGUCHI Tomio, TSUBOTA Hiromi, SHIMAMURA Masaki, SAKAKIBARA Keiko, KURABAYASHI Atsushi

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      4 2011 - 3 2014

      Grant number:23370045

      Grant amount:\18590000 ( Direct Cost: \14300000 、 Indirect Cost:\4290000 )

      Chloroplast genomes of seven mosses, two liverworts and one hornworts species were newly sequenced. Comparison of the chloroplast genomes showed that T. lepidozioides had the largest cp genome in the mosses and the gene content was almost identical to those of liverworts and hornworts. Some gene-loss events through the evolution were indicated to be effective for considering the relationships of major moss lineages.
      In addition, we firstly detected linear and circular DNA molecules of chloroplast genome in a Sphagnum moss. Some larger molecules seem to be derived from multimeric conformations of single genomes. The occurrence of linear and multimeric molecules also have been known in some flowering plants. Such structural plasticity of the chloroplast genome seems to be evolutionary conserved across land plants.

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    • 茎頂分裂組織形成遺伝子の解析から陸上植物の胞子体世代延長の誕を探る

      日本学術振興会  科学研究費助成事業 

      森岡 恵子

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      2004 - 2006

      Grant number:04J05131

      Grant amount:\3400000 ( Direct Cost: \3400000 )

      被子植物胞子体の茎頂では、細胞分化を促進する遺伝子と未分化な状態を維持する遺伝子が異なる領域で機能し、未分化な分裂組織を維持しつつ、器官が分化していると推定される。未分化な状態の維持に関わる遺伝子としてKNOXクラス1遺伝子が知られている。KNOXクラス1遺伝子はサイトカイニン合成遺伝子(IPT)、ジベレリン代謝遺伝子(GA2酸化酵素遺伝子)とジベレリン合成遺伝子(GA20酸化酵素遺伝子)といった植物ホルモン生合成系遺伝子を下流に持ち、植物ホルモン量を制御することで茎頂分裂組織の細胞分裂及び伸長を制御し、茎頂分裂組織の未分化な性質を維持すると報告されている。KNOXクラス1遺伝子の関わる分子機構がコケ植物でも保存されているかを調べることで、陸上植物の形態進化を調べることを目的としている。
      コケ植物KNOXクラス1遺伝子3個を単離し、機能解析を行ったところ、これらはいずれも胞子体の初期発生で発現し、細胞分裂・伸長を制御していることがわかった。ヒメツリガネゴケではゲノム計画が進められている。ヒメツリガネゴケKNOXクラス1遺伝子も被子植物と同じく植物ホルモンを制御しているか調べるために、このデータベースからサイトカイニン及びジベレリン関連遺伝子を探索し分子系統解析を行ったところ、ヒメツリガネゴヶゲノム中にGA2酸化酵素相同遺伝子及びGA20酸化酵素相同遺伝子が存在すること、また、被子植物は2種類のIPT遺伝子を持つがヒメツリガネゴケは1種類しか持たないことがわかった。しかし、これらの遺伝子の発現レベルが野生株と三重遺伝子破壊株とで変わらかいことから、ヒメツリガネゴケにおいてはKNOXクラス1遺伝子はジベレリンとサイトカイニンを制御していないことが示唆された。KNOXクラス1遺伝子によるジベレリンとサイトカイニンの制御は維管束植物とコケ植物の分岐の後に維管束植物において獲得されたと推測された。

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