This Special Focus Issue (Vol. 57, Issue 2) of Plant and Cell Physiology is guest edited by Takayuki Kohchi, John Bowman and Takashi Araki, and brings to the forefront the renaissance of the small model liverwort, Marchantia polymorpha .
Marchantia : Past, Present and Future
John Bowman, Takashi Araki and Takayuki Kochi
This special focus issue is dedicated to the renaissance of the liverwort and model organism Marchantia polymorpha , which is ideally suited for the study land plant evolution and basic cellular mechanisms of development. In this SFI, readers will find a range of enlightening reviews discussing the history and biology of this organism and the plethora of materials and tools currently available to the research community, plus a range of research articles covering multiple aspects of Marchantia biology.
A brief History of Marchantia from Greece to Genomics
Marchantia has been used as a model system for investigating biological processes for nearly two centuries. In this paper, work from the late 18th century through the mid-20th century is reviewed, focusing on the use of Marchantia to uncover sex in bryophytes, and the function and evolution of sex chromosomes in the establishment of cell theory. Also reviewed are the key experiments that elucidated the establishment of polarity in a plant body plan.
Marchantia polymorpha ; Taxonomy, Phylogeny and Morphology of a Model System
One of the classical research plants in plant biology, Marchantia polymorpha , is drawing renewed interest and attention as a model system due to its ease of genetic transformation and ongoing genome sequencing project. Here, a thorough assessment of the taxonomic status, anatomy and developmental morphology of the plant based on a thorough review of the literature and personal observations are presented. Marchantia polymorpha is an attractive model not only for evolutionary biology but also for elucidation of the basic principles of various biological phenomena.
The Naming of Names: Guidelines for Gene Nomenclature in Marchantia
John L. Bowman, Takashi Araki, Mario A. Arteaga-Vazquez, Fred Berger, LiamDolan, Jim Haseloff, Kimitsune Ishizaki, Junko Kyozuka, Shih-Shun Lin, Hideki Nagasaki, Hirofumi Nakagami, Keiji Nakajima, Yasukazu Nakamura, Kyoko Ohashi-Ito, Shinichiro Sawa, Masaki Shimamura, Roberto Solano, Hirokazu Tsukaya, Takashi Ueda, Yuichiro Watanabe, Katsuyuki T. Yamato, Sabine Zachgo, Takayuki Kohchi
To promote consistency and reduce confusion in the scientific literature, community guidelines for M. polymorpha gene and transgene nomenclature are presented. A wiki has been established to facilitate the sharing, canalization, and choosing of unique gene names in M. polymorpha . Finally, with the expectation that other Marchantia species may become subjects of future investigations, we also provide here additional guidelines for the naming of genes in other species of the genus.
Molecular Genetic Tools and Techniques for Marchantia polymorpha Research
Kimitsune Ishizaki, Ryuichi Nishihama, Katsuyuki T. Yamato and Takayuki Kohchi
The liverwort Marchantia polymorpha has been recently revisited for use as a model species due to its critical position in land plant history. Here we review the technologies and resources available for molecular genetic studies in M. polymorpha , which should accelerate the functional characterization of genes and contribute to our knowledge of the evolution and diversification of plant regulatory systems.
Conditional Gene Expression/Deletion Systems for Marchantia polymorpha using its own Heat-shock Promoter and Cre/loxP-Mediated Site-Specific Recombination
Ryuichi Nishihama, Sakiko Ishida, Hiroko Urawa, Yasuhiro Kamei, and Takayuki Kohchi
Marchantia polymorpha is a useful model for genetic analyses, though due to its dominant haploid phase, the analysis of essential genes has been somewhat limited. Here, a conditional gene expression/deletion system that exploits Cre/loxP-mediated site-specific recombination in combination with a newly identified heat-inducible promoter and the glucocorticoid receptor is reported. This system is suited for conditional knockout approaches as well as for cell-lineage analyses.
Efficient and Inducible Use of Artificial MicroRNAs in Marchantia polymorpha
Eduardo Flores-Sandoval, Tom Dierschke, Tom J. Fisher, and John L. Bowman
Artificial microRNAS (amiRNAs) were designed to downregulate genes of interest in M. polymorpha . Over-expression of amiRs against MpARF1 and MpRR-Bs allowed the functional analysis of two conserved hormonal signaling pathways. Further, inducible expression of amiRs against chromatin remodeling factor MpE(z) allowed the study of otherwise lethal mutants, thus demonstrating how inducible and context-dependent expression of amiRs is a useful tool for genetic analysis in Marchantia .
A Cyan Fluorescent Reporter Expressed from the Chloroplast Genome of Marchantia polymorpha
Christian R. Boehm, Minoru Ueda, Yoshiki Nishimura, Toshiharu Shikanai, and Jim Haseloff
Investigations of liverwort plastid biology have been complicated by the lack of suitable fluorescent reporter genes. Here, the design and application of a codon-optimized derivative of mTurquoise2 is described. The new reporter gene was successfully expressed from the chloroplast genome of Marchantia polymorpha , and will facilitate plastid-based FRET and ratiometric gene expression analyses.
Cryopreservation of Gemmae from the Liverwort Marchantia polymorpha L.
Daisuke Tanaka, Kimitsune Ishizaki, Takayuki Kohchi and Katsuyuki T. Yamato
Marchantia polymorpha has proven itself as a unique and powerful tool to explore various genetic and developmental aspects of land plants. In this paper a simple and secure protocol to retain valuable transformant and mutant lines via cryopreservation is described. This method should support and further promote research studies using this model organism.
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, and Takashi Ueda
The SNARE protein family is part of the conserved machinery in eukaryotic cells that mediates membrane fusion during membrane trafficking. Kanazawa et al. systematically analyzed SNARE members in Marchantia polymorpha and unraveled conserved and unique features of SNARE proteins in this model plant. The obtained information will be useful for understanding diversification of membrane trafficking pathways among plant lineages.
Transcriptional Framework of Male Gametogenesis in the Liverwort Marchantia polymorpha L.
Asuka Higo, Masaki Niwa, Katsuyuki T. Yamato, Lixy Yamada, Hitoshi Sawada, Tomoaki Sakamoto, Tetsuya Kurata, Makoto Shirakawa, Motomu Endo, Shuji Shigenobu, Katsushi Yamaguchi, Kimitsune Ishizaki, Ryuichi Nishihama, Takayuki Kohchi, and Takashi Araki
The molecular mechanisms underlying sexual reproduction involving an egg and pollen-delivered sperm cell has been well documented in various angiosperm models. Sexual reproduction in basal plants, which similar to animals involves motile sperm, has however remained poorly characterized due to the lack of suitable models. This paper provides the first transcriptional framework on which to study the molecular mechanism of biflagellated motile sperm development in plants using Marchantia polymorpha .
Identification of miRNAs and their Targets in the Liverwort Marchantia polymorpha by Integrating RNA-Seq and Degradome Analyses
Pin-Chun Lin, Chia-Wei Lu, Bing-Nan Shen, Guan-Zong Lee, John L. Bowman, Mario A. Arteaga-Vazquez, Li-Yu Daisy Liu, Syuan-Fei Hong, Chu-Fang Lo, Gong-Min Su, Takayuki Kohchi, Kimitsune Ishizaki, Sabine Zachgo, Felix Althoff, Mizuki Takenaka, Katsuyuki T. Yamato, Shih-Shun Lin
MicroRNAs (miRNAs) regulate gene expression in nearly all eukaryotes and play fundamental roles during plant development. To understand the biological role of miRNAs from an evolutionary perspective, Lin et al. took a comparative transcriptomic approach using the earliest terrestrial plant representative, Marchantia polymorpha , to identify ancient miRNAs in land plants. The combination of RNA-Seq and degradome analyses in M. polymorpha not only enhanced the accuracy of miRNA/target prediction but unveiled a large number of novel miRNAs and targets, which indicates a complex miRNA evolutionary history in embryophytes.
Profiling and Characterization of Small RNAs in the Liverwort, Marchantia polymorpha , Belonging to the First Diverged Land Plants
Masayuki Tsuzuki, Ryuichi Nishihama, Kimitsune Ishizaki, Yukio Kurihara, Minami Matsui, John L. Bowman, Takayuki Kohchi, Takahiro Hamada, and Yuichiro Watanabe
In this paper, Marchantia miRNAs were profiled to determine their abundance and possible roles during Marchantia development. M. polymorpha was found to contain as many as six families each of highly conserved miRNAs and corresponding target mRNAs, and at least 200 unique miRNAs. Overexpression of some miRNAs resulted in abortive thallus development, which strongly indicate that regulation by miRNAs is important for proper body plan formation in Marchantia .