Editorial Marchantia: Past, Present and Future John L. Bowman1,2, Takashi Araki3,* and Takayuki Kohchi3 1
School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA 3 Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan 2
*Corresponding author: E-mail, [email protected]; Fax, +81-75-753-6470.
Why a Liverwort? Few identified macrofossils represent the early colonization of land by plants, but cryptospores dating from the early Middle
Ordovician are plentiful in the fossil record, and are recovered only from terrestrial or near offshore deposits (Wellman and Strother 2015). Cryptospores are a non-phylogenetic assemblage of spores distinct from trilete and monolete spores and pollen grains, but similar to spores of land plants. Ultrastructural and geochemical analyses indicate that crytospore spore walls are chemically similar to those of some extant liverwort spores (Steemans et al. 2010). Thus, the presence of cryptospores is likely to be indicative of the presence of land plants, and, more specifically, liverwort-like bryophytic organisms. Liverwort macrofossils also pre-date those assigned to either mosses or hornworts. Further, cladistic studies of morphology and the fossil record suggest that liverworts are the basalmost lineage of land plants, with hornworts sister to vascular plants, and mosses occupying the middle position of a bryophyte grade (Mishler and Churchill 1984, Kenrick and Crane 1997a). On the other hand, in land plant phylogenies, based on molecular data nearly every possible permutation of bryophyte relationships and their relationships to vascular plants has been proposed. For example, some analyses support the idea of liverworts being the basal lineage in a grade of bryophytes (Qiu et al. 2006), but a recent analysis suggests that hornworts are the basal land plant lineage, with mosses and liverworts forming a sister clade to vascular plants (Wickett et al. 2014). Reconciliation of molecular phylogenies with the fossil record may require broader taxon sampling in the former, or reinterpretation of the latter.
Why Marchantia? The arguments above point to the need for a model liverwort to investigate fundamental events in land plant evolution. The gametophyte body plans of liverworts are more variable than those of either mosses or hornworts—there are simple thalloid, complex thalloid and leafy forms—nearly all are dorsi-ventral (Watson 1964, Schuster 1992, Crandall-Stotler et al. 2009). All liverworts share a short to non-existent protonemal phase and a subsequent prothallus stage prior to differentiating the final gametophyte body, which is produced by apical cells of different anatomies depending upon the body plan. All liverworts also lack stomata and have membrane-bound oil bodies
Plant Cell Physiol. 57(2): 205–209 (2016) doi:10.1093/pcp/pcw023, available online at www.pcp.oxfordjournals.org ! The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: [email protected]
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The evolution of a land flora was a momentous event in shaping our planet by altering the landscape through modulation of geochemical cycles and facilitating the invasion of land by other taxa, such as our own ancestors. By the mid-Ordovican (450 Ma), the appearance of land plants had dramatically changed the terrestrial environment and they rapidly became the dominant ecological force. Between the Ordovician and Devonian there was an explosion in land plant diversification, with the major extant lineages of land plants (liverworts, mosses, hornworts, lycophytes, ferns and seed plants) established by the end of the Devonian (360 Ma). Land plants form a monophyletic clade that nests within a grade of freshwater and terrestrial charophycean algae (also known as streptophyte algae), implying that land plants evolved from a freshwater or terrestrial alga (Pickett-Heaps and Marchant 1972, Karol et al. 2001). Their rapid rise can be attributed to a number of evolved features enabling individuals to survive the terrestrial subaerial environment, such as pigmentation and a ‘sunscreen’ for protection from harsh UV irradiation, and the ability to withstand desiccation for extended periods of time. Many of these physiological adaptations to a terrestrial environment may have evolved with the charophycean algal lineage leading to land plants (Delwiche and Cooper 2015). In contrast, developmental innovations, such as the evolution of an apical cell with more than two cutting faces, enabling the development of three-dimensional growth in the form of complex tissue and organ morphologies including anatomical innovations for water conductance, are a synapomorphy of land plants. Whereas the life cycles of charophycean algae are haplobiontic—a multicellular haploid phase with a singlecelled diploid phase consisting of a zygote that immediately undergoes meiosis—the life cycle of land plants is defined by a complex multicellular diploid sporophyte generation (borne from an embryo), which, combined with the complex multicellular haploid gametophyte generation, led to an alternation of generations. Arguably, the evolution of the sporophyte generation was instrumental in the land plant’s ascent to terrestrial dominance.
The Modern Era Kanji Ohyama (1939–2013) led the early era of plant genomics using Marchantia as a material. Sequencing genomes of chloroplasts (Ohyama et al. 1986) and mitochondria (Oda et al. 1992) from Marchantia culture cells marked important milestones in plant biology. These early structural analyses of organelle genomes indicated that no fully functional enzymes and protein complexes are produced only by the organelle-encoded components and that extensive co-ordination of organelle and nuclear genomes is required in plants. Moreover, M. polymorpha was used for sex chromosome analysis. Marchantia polymorpha has eight autosomes and a single sex chromosome 206
(n = 8 + X in female and Y in male). The gene organization of the Y chromosome provided an insight into sex chromosome structure and evolution in a plant with a haploid system (Yamato et al. 2007). Thus, M. polymorpha has played a leading role as a model for genome analysis. Genome information is a fundamental platform for modern biology, and functional analyses should be done by fully utilizing the available sequence information. The central criteria required for versatile model organisms include forward genetics, reverse genetics, genetic transformation and genome-wide studies. In the past few years, techniques have been established in M. polymorpha that promote this species as a member of the model organism cohort. Forward genetics and subsequent functional analyses of causal genes were reported for air chamber (Ishizaki et al. 2013b) and rhizoid (Proust et al. 2016) development. Reverse genetics approaches were also utilized in studies of auxin signaling (Kato et al. 2015, Flores-Sandoval et al. 2015), phototropin (Komatsu et al. 2014), growth phase transition (Kubota et al. 2014), and so on. Other studies, such as those in secondary metabolism (Takemura et al. 2014) and nuclear-encoded plastid sigma factors (Kanazawa et al. 2013), have also appeared. Efficient Agrobacterium-mediated transformation systems has been developed in M. polymorpha (Ishizaki et al. 2008, Kubota et al. 2013, Tsuboyama and Kodama 2014), enabling reverse genetics tools including artificial microRNAs (amiRs), homologous recombination and genome editing (Ishizaki et al. 2013a, Sugano et al. 2014, Flores-Sandoval et al. 2016). Marchantia polymorpha was also chosen for the community sequencing program at the Joint Genome Institute, Department of Energy, USA. The sequences will be released later this year. Thus, nearly 200 years after it was first used as a biological model, a 21st century Renaissance is reviving M. polymorpha as a superb model with a suite of established, available experimental tools.
In This Issue This Special Focus Issue (SFI) is the first of such introducing M. polymorpha to a broad plant science audience. It includes two reviews, two mini-reviews, four technical articles and four original research articles by researchers working with M. polymorpha. These papers cover several topics, including its history as a study model, taxonomy, phylogeny, morphology and life cycle. It also includes a community proposal for a unified system of gene nomenclature, as well as recent advances in experimental techniques for cell, developmental and genome biology. The first of the two reviews provides a comprehensive overview of Marchantia’s history from its early recognition to its recent rediscovery as a model plant (Bowman 2016). Topics such as the usefulness of Marchantia in discovering cryptogamic sex and spermatozoids (antherozoids), chromosomalbased sex determination and supporting cell theory in plants are all described. Historic research into polarity formation—one of the long-standing questions in developmental biology— using Marchantia gemmalings is also comprehensively described. The second review by Shimamura (2016) covers
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and ventral unicellular rhizoids, except Haplomitrium, which lacks rhizoids. While some early researchers considered the complex thalloids, such as Marchantia polymorpha, to be highly derived, recent molecular phylogenies have indicated the Marchantiopsida, including the complex thalloids, to be basal to most simple and leafy liverwort lineages, with the exception of the Haplomitriopsida comprised of a small number of possibly relict species (Forrest et al. 2006, HeNygre´n et al. 2006). Marchantia polymorpha has been used as a model system for investigating biological processes for nearly two centuries. Prior to its use in what we might consider modern biology following the enlightenment, Marchantia had been described in ancient Greek medical texts as a plant useful to apply to open wounds to prevent infection and inflammation (Dioscorides 1529). While speculative, the basis for this supposition may lie in the chemicals contained in the oil bodies, terpenoids, that have since been shown to reduce fungal and bacterial growth. If so, most liverworts would have sufficed, but due to its abundance, its widespread geographical distribution and its colonization of man-disturbed habitats (Schuster 1992), M. polymorpha was the sole liverwort described in the earliest floras following the Renaissance. In the late 18th century Johann Hedwig and C. Schmidel used M. polymorpha as one of the model species to elucidate the life cycle of liverworts and mosses (Hedwig 1783, Schmidel 1783). At the beginning of the 19th century, a major question was whether the entirety of an organism was composed of cells and how new cells arose. In an attempt to address these questions, Franc¸ois Mirbel followed, in cellular detail, the life cycle of M. polymorpha. While he may not have succeeded in his original aim, his experiments with gemmae (vegetative propagules) of M. polymorpha were perhaps the first to investigate the establishment of dorsiventrality and the body plan of a plant (Mirbel 1835). The remainder of the 19th century was the golden age of anatomy, and M. polymorpha served as a model for studies of motile sperm and fertilization, and culminating in Leitgeb’s detailed studies of liverwort anatomy and development (Leitgeb 1881). The wealth of literature provides a valuable resource for present and future studies of unresolved questions concerning aspects of physiology, development, and evolution.
miRs and their targets in M. polymorpha provide insight into the spectrum of evolutionarily conserved and more lineagerestricted miRs encoded in the M. polymorpha genome (Lin et al. 2016, Tsuzuki et al. 2016). Both research groups identified a core set of conserved miRs, but, due to differential tissue sampling, the overlap of non-conserved miRs was not substantial, implying that there is more to discover.
Perspectives Over the past decade, many researchers worldwide have become increasingly attracted to M. polymorpha due to its unique phylogenetic position amongst plants and to recent advances in the various molecular techniques and tools, making this species a timely and significant model organism of choice. Critical to this trend has been the rapid growth and spread of a research community that exchanges information, materials and people. The expected completion and publication of the genome project this year will further boost research into M. polymorpha, while its promotion as a model basal land plant that is as versatile as the angiosperms, Arabidopsis and rice, will add to our understanding of land plant (embryophytes) evolution and eventually encourage exploration of sister land plant groups (charophycean algal lineages). Similar to Arabidopsis thaliana, we envisage that M. polymorpha will serve as a useful model organism in the broader framework of the eukaryotes, where it could readily lend itself to basic cellular studies or subcellular processes compared with other model organisms. We expect that many ambitious studies will appear in the coming decade and we hope that this SFI will serve as an inspiring taster of what is yet to come.
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phylogeny, taxonomy, life cycle and morphology. It describes the phylogenetic position of Marchantia among bryophytes (liverworts, mosses and hornworts) and summarizes the complicated taxonomy of specific and infraspecific taxa of the genus Marchantia. This account will undoubtedly help those who use M. polymorpha as a model organism to understand its phylogeny and taxonomy. Equally useful are the descriptions of its life cycle and morphology, which include original observations that extend earlier reports such as those described by Kny (1890) and Durand (1908), thus serving as an updated reference work for those especially interested in developmental aspects of this plant. To promote consistency and to reduce confusion in the scientific literature, Bowman et al. (2016) present a community proposal for M. polymorpha gene and transgene nomenclature. This nomenclature was built upon the lessons of the past to suit an organism in the genomic era, and we strongly encourage researchers to follow these guidelines. Next, we have five papers (one mini-review and four original papers) reporting tractable methods for M. polymorpha. Ishizaki et al. (2016) review the current molecular tools and techniques developed for researchers including transformation, overexpression, and gene targeting by homologous recombination and genome editing. The haploid-dominating life cycle facilitates genetic analyses, but conversely limits the ability to isolate mutants of essential genes. To circumvent this issue, Nishihama et al. (2016) describe a system that allows conditional gene expression and deletion using the promoter of a heat shock protein gene and the Cre/loxP site-specific recombination system. Concomitantly, Flores-Sandoval et al. (2016) report that amiRs with primary miR hairpin backbones are efficient for silencing genes, and that adaptation of an estrogen-inducible system permits phenotypic analyses at all stages of the life cycle. In addition to nuclear-encoded genes, chloroplast genes are also targets for genetic studies. Boehm et al. (2016) report the development of a fluorescent reporter system expressed from the chloroplast genome. Finally, Tanaka et al. (2016) report a simple cryopreservation protocol for in vitro grown M. polymorpha gemmae, which should allow long-term preservation of transgenic and mutant lines in M. polymorpha. The remaining four research papers featured in this SFI all describe the comprehensive analyses of Marchantia genes: those encoding SNAREs involved in membrane trafficking (Kanazawa et al. 2016); a transcriptome analysis of developing antheridium (male sexual organ) (Higo et al. 2016); and miRs and their targets (Lin et al. 2016, Tsuzuki et al. 2016). The paper by Kanazawa et al. (2016) clearly demonstrates the phylogenetic importance of M. polymorpha to allow a better understanding of basic subcellular processes in land plants. It also shows the potential of M. polymorpha not only as a model organism for plants, but also of use for studying other organisms. The same is also inferred in the paper by Higo et al. (2016)—this transcriptome analysis is the first to report motile gamete formation in basal land plants and will thus serve as a basis for further comparative analyses among angiosperm plants, basal land plants, and animals. Two papers on
Funding This work was supported by the Australian Research Council [DP130100177 to J.L.B.]; the Japan Society for the Promotion of Science (JSPS) [Bilateral Research Program] and the Ministry of Education, Culture, Sports, Science & Technology (MEXT) [Grant-in-Aid for Scientific Research on Innovative Area (25113005 to T.A and 25113009 to T.K.)].
Acknowledgments We thank Professor Tomoyuki Yamaya, Editor-in-Chief, Plant and Cell Physiology, for providing the opportunity for this Special Focus Issue on Marchantia polymorpha. We wish to acknowledge the authors and reviewers who have contributed to this issue.
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Wellman, C.H. and Strother, P.K. (2015) The terrestrial biota prior to the origin of land plants (Embryophytes)—a review of the evidence. Palaeontology 58: 601–627. Wickett, N.J., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N., et al. (2014) Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc. Natl. Acad. Sci. USA 111: 4859–4868. Yamato, K.T., Ishizaki, K., Fujisawa, M., Okada, S., Nakayama, S., Fujishita, M., et al. (2007) Gene organization of the liverwort Y chromosome reveals distinct sex chromosome evolution in a haploid system. Proc. Natl. Acad. Sci. USA 104: 6472–6477.
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School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA 3 Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan 2
*Corresponding author: E-mail, [email protected]; Fax, +81-75-753-6470.
Why a Liverwort? Few identified macrofossils represent the early colonization of land by plants, but cryptospores dating from the early Middle
Ordovician are plentiful in the fossil record, and are recovered only from terrestrial or near offshore deposits (Wellman and Strother 2015). Cryptospores are a non-phylogenetic assemblage of spores distinct from trilete and monolete spores and pollen grains, but similar to spores of land plants. Ultrastructural and geochemical analyses indicate that crytospore spore walls are chemically similar to those of some extant liverwort spores (Steemans et al. 2010). Thus, the presence of cryptospores is likely to be indicative of the presence of land plants, and, more specifically, liverwort-like bryophytic organisms. Liverwort macrofossils also pre-date those assigned to either mosses or hornworts. Further, cladistic studies of morphology and the fossil record suggest that liverworts are the basalmost lineage of land plants, with hornworts sister to vascular plants, and mosses occupying the middle position of a bryophyte grade (Mishler and Churchill 1984, Kenrick and Crane 1997a). On the other hand, in land plant phylogenies, based on molecular data nearly every possible permutation of bryophyte relationships and their relationships to vascular plants has been proposed. For example, some analyses support the idea of liverworts being the basal lineage in a grade of bryophytes (Qiu et al. 2006), but a recent analysis suggests that hornworts are the basal land plant lineage, with mosses and liverworts forming a sister clade to vascular plants (Wickett et al. 2014). Reconciliation of molecular phylogenies with the fossil record may require broader taxon sampling in the former, or reinterpretation of the latter.
Why Marchantia? The arguments above point to the need for a model liverwort to investigate fundamental events in land plant evolution. The gametophyte body plans of liverworts are more variable than those of either mosses or hornworts—there are simple thalloid, complex thalloid and leafy forms—nearly all are dorsi-ventral (Watson 1964, Schuster 1992, Crandall-Stotler et al. 2009). All liverworts share a short to non-existent protonemal phase and a subsequent prothallus stage prior to differentiating the final gametophyte body, which is produced by apical cells of different anatomies depending upon the body plan. All liverworts also lack stomata and have membrane-bound oil bodies
Plant Cell Physiol. 57(2): 205–209 (2016) doi:10.1093/pcp/pcw023, available online at www.pcp.oxfordjournals.org ! The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: [email protected]
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The evolution of a land flora was a momentous event in shaping our planet by altering the landscape through modulation of geochemical cycles and facilitating the invasion of land by other taxa, such as our own ancestors. By the mid-Ordovican (450 Ma), the appearance of land plants had dramatically changed the terrestrial environment and they rapidly became the dominant ecological force. Between the Ordovician and Devonian there was an explosion in land plant diversification, with the major extant lineages of land plants (liverworts, mosses, hornworts, lycophytes, ferns and seed plants) established by the end of the Devonian (360 Ma). Land plants form a monophyletic clade that nests within a grade of freshwater and terrestrial charophycean algae (also known as streptophyte algae), implying that land plants evolved from a freshwater or terrestrial alga (Pickett-Heaps and Marchant 1972, Karol et al. 2001). Their rapid rise can be attributed to a number of evolved features enabling individuals to survive the terrestrial subaerial environment, such as pigmentation and a ‘sunscreen’ for protection from harsh UV irradiation, and the ability to withstand desiccation for extended periods of time. Many of these physiological adaptations to a terrestrial environment may have evolved with the charophycean algal lineage leading to land plants (Delwiche and Cooper 2015). In contrast, developmental innovations, such as the evolution of an apical cell with more than two cutting faces, enabling the development of three-dimensional growth in the form of complex tissue and organ morphologies including anatomical innovations for water conductance, are a synapomorphy of land plants. Whereas the life cycles of charophycean algae are haplobiontic—a multicellular haploid phase with a singlecelled diploid phase consisting of a zygote that immediately undergoes meiosis—the life cycle of land plants is defined by a complex multicellular diploid sporophyte generation (borne from an embryo), which, combined with the complex multicellular haploid gametophyte generation, led to an alternation of generations. Arguably, the evolution of the sporophyte generation was instrumental in the land plant’s ascent to terrestrial dominance.
The Modern Era Kanji Ohyama (1939–2013) led the early era of plant genomics using Marchantia as a material. Sequencing genomes of chloroplasts (Ohyama et al. 1986) and mitochondria (Oda et al. 1992) from Marchantia culture cells marked important milestones in plant biology. These early structural analyses of organelle genomes indicated that no fully functional enzymes and protein complexes are produced only by the organelle-encoded components and that extensive co-ordination of organelle and nuclear genomes is required in plants. Moreover, M. polymorpha was used for sex chromosome analysis. Marchantia polymorpha has eight autosomes and a single sex chromosome 206
(n = 8 + X in female and Y in male). The gene organization of the Y chromosome provided an insight into sex chromosome structure and evolution in a plant with a haploid system (Yamato et al. 2007). Thus, M. polymorpha has played a leading role as a model for genome analysis. Genome information is a fundamental platform for modern biology, and functional analyses should be done by fully utilizing the available sequence information. The central criteria required for versatile model organisms include forward genetics, reverse genetics, genetic transformation and genome-wide studies. In the past few years, techniques have been established in M. polymorpha that promote this species as a member of the model organism cohort. Forward genetics and subsequent functional analyses of causal genes were reported for air chamber (Ishizaki et al. 2013b) and rhizoid (Proust et al. 2016) development. Reverse genetics approaches were also utilized in studies of auxin signaling (Kato et al. 2015, Flores-Sandoval et al. 2015), phototropin (Komatsu et al. 2014), growth phase transition (Kubota et al. 2014), and so on. Other studies, such as those in secondary metabolism (Takemura et al. 2014) and nuclear-encoded plastid sigma factors (Kanazawa et al. 2013), have also appeared. Efficient Agrobacterium-mediated transformation systems has been developed in M. polymorpha (Ishizaki et al. 2008, Kubota et al. 2013, Tsuboyama and Kodama 2014), enabling reverse genetics tools including artificial microRNAs (amiRs), homologous recombination and genome editing (Ishizaki et al. 2013a, Sugano et al. 2014, Flores-Sandoval et al. 2016). Marchantia polymorpha was also chosen for the community sequencing program at the Joint Genome Institute, Department of Energy, USA. The sequences will be released later this year. Thus, nearly 200 years after it was first used as a biological model, a 21st century Renaissance is reviving M. polymorpha as a superb model with a suite of established, available experimental tools.
In This Issue This Special Focus Issue (SFI) is the first of such introducing M. polymorpha to a broad plant science audience. It includes two reviews, two mini-reviews, four technical articles and four original research articles by researchers working with M. polymorpha. These papers cover several topics, including its history as a study model, taxonomy, phylogeny, morphology and life cycle. It also includes a community proposal for a unified system of gene nomenclature, as well as recent advances in experimental techniques for cell, developmental and genome biology. The first of the two reviews provides a comprehensive overview of Marchantia’s history from its early recognition to its recent rediscovery as a model plant (Bowman 2016). Topics such as the usefulness of Marchantia in discovering cryptogamic sex and spermatozoids (antherozoids), chromosomalbased sex determination and supporting cell theory in plants are all described. Historic research into polarity formation—one of the long-standing questions in developmental biology— using Marchantia gemmalings is also comprehensively described. The second review by Shimamura (2016) covers
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and ventral unicellular rhizoids, except Haplomitrium, which lacks rhizoids. While some early researchers considered the complex thalloids, such as Marchantia polymorpha, to be highly derived, recent molecular phylogenies have indicated the Marchantiopsida, including the complex thalloids, to be basal to most simple and leafy liverwort lineages, with the exception of the Haplomitriopsida comprised of a small number of possibly relict species (Forrest et al. 2006, HeNygre´n et al. 2006). Marchantia polymorpha has been used as a model system for investigating biological processes for nearly two centuries. Prior to its use in what we might consider modern biology following the enlightenment, Marchantia had been described in ancient Greek medical texts as a plant useful to apply to open wounds to prevent infection and inflammation (Dioscorides 1529). While speculative, the basis for this supposition may lie in the chemicals contained in the oil bodies, terpenoids, that have since been shown to reduce fungal and bacterial growth. If so, most liverworts would have sufficed, but due to its abundance, its widespread geographical distribution and its colonization of man-disturbed habitats (Schuster 1992), M. polymorpha was the sole liverwort described in the earliest floras following the Renaissance. In the late 18th century Johann Hedwig and C. Schmidel used M. polymorpha as one of the model species to elucidate the life cycle of liverworts and mosses (Hedwig 1783, Schmidel 1783). At the beginning of the 19th century, a major question was whether the entirety of an organism was composed of cells and how new cells arose. In an attempt to address these questions, Franc¸ois Mirbel followed, in cellular detail, the life cycle of M. polymorpha. While he may not have succeeded in his original aim, his experiments with gemmae (vegetative propagules) of M. polymorpha were perhaps the first to investigate the establishment of dorsiventrality and the body plan of a plant (Mirbel 1835). The remainder of the 19th century was the golden age of anatomy, and M. polymorpha served as a model for studies of motile sperm and fertilization, and culminating in Leitgeb’s detailed studies of liverwort anatomy and development (Leitgeb 1881). The wealth of literature provides a valuable resource for present and future studies of unresolved questions concerning aspects of physiology, development, and evolution.
miRs and their targets in M. polymorpha provide insight into the spectrum of evolutionarily conserved and more lineagerestricted miRs encoded in the M. polymorpha genome (Lin et al. 2016, Tsuzuki et al. 2016). Both research groups identified a core set of conserved miRs, but, due to differential tissue sampling, the overlap of non-conserved miRs was not substantial, implying that there is more to discover.
Perspectives Over the past decade, many researchers worldwide have become increasingly attracted to M. polymorpha due to its unique phylogenetic position amongst plants and to recent advances in the various molecular techniques and tools, making this species a timely and significant model organism of choice. Critical to this trend has been the rapid growth and spread of a research community that exchanges information, materials and people. The expected completion and publication of the genome project this year will further boost research into M. polymorpha, while its promotion as a model basal land plant that is as versatile as the angiosperms, Arabidopsis and rice, will add to our understanding of land plant (embryophytes) evolution and eventually encourage exploration of sister land plant groups (charophycean algal lineages). Similar to Arabidopsis thaliana, we envisage that M. polymorpha will serve as a useful model organism in the broader framework of the eukaryotes, where it could readily lend itself to basic cellular studies or subcellular processes compared with other model organisms. We expect that many ambitious studies will appear in the coming decade and we hope that this SFI will serve as an inspiring taster of what is yet to come.
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phylogeny, taxonomy, life cycle and morphology. It describes the phylogenetic position of Marchantia among bryophytes (liverworts, mosses and hornworts) and summarizes the complicated taxonomy of specific and infraspecific taxa of the genus Marchantia. This account will undoubtedly help those who use M. polymorpha as a model organism to understand its phylogeny and taxonomy. Equally useful are the descriptions of its life cycle and morphology, which include original observations that extend earlier reports such as those described by Kny (1890) and Durand (1908), thus serving as an updated reference work for those especially interested in developmental aspects of this plant. To promote consistency and to reduce confusion in the scientific literature, Bowman et al. (2016) present a community proposal for M. polymorpha gene and transgene nomenclature. This nomenclature was built upon the lessons of the past to suit an organism in the genomic era, and we strongly encourage researchers to follow these guidelines. Next, we have five papers (one mini-review and four original papers) reporting tractable methods for M. polymorpha. Ishizaki et al. (2016) review the current molecular tools and techniques developed for researchers including transformation, overexpression, and gene targeting by homologous recombination and genome editing. The haploid-dominating life cycle facilitates genetic analyses, but conversely limits the ability to isolate mutants of essential genes. To circumvent this issue, Nishihama et al. (2016) describe a system that allows conditional gene expression and deletion using the promoter of a heat shock protein gene and the Cre/loxP site-specific recombination system. Concomitantly, Flores-Sandoval et al. (2016) report that amiRs with primary miR hairpin backbones are efficient for silencing genes, and that adaptation of an estrogen-inducible system permits phenotypic analyses at all stages of the life cycle. In addition to nuclear-encoded genes, chloroplast genes are also targets for genetic studies. Boehm et al. (2016) report the development of a fluorescent reporter system expressed from the chloroplast genome. Finally, Tanaka et al. (2016) report a simple cryopreservation protocol for in vitro grown M. polymorpha gemmae, which should allow long-term preservation of transgenic and mutant lines in M. polymorpha. The remaining four research papers featured in this SFI all describe the comprehensive analyses of Marchantia genes: those encoding SNAREs involved in membrane trafficking (Kanazawa et al. 2016); a transcriptome analysis of developing antheridium (male sexual organ) (Higo et al. 2016); and miRs and their targets (Lin et al. 2016, Tsuzuki et al. 2016). The paper by Kanazawa et al. (2016) clearly demonstrates the phylogenetic importance of M. polymorpha to allow a better understanding of basic subcellular processes in land plants. It also shows the potential of M. polymorpha not only as a model organism for plants, but also of use for studying other organisms. The same is also inferred in the paper by Higo et al. (2016)—this transcriptome analysis is the first to report motile gamete formation in basal land plants and will thus serve as a basis for further comparative analyses among angiosperm plants, basal land plants, and animals. Two papers on
Funding This work was supported by the Australian Research Council [DP130100177 to J.L.B.]; the Japan Society for the Promotion of Science (JSPS) [Bilateral Research Program] and the Ministry of Education, Culture, Sports, Science & Technology (MEXT) [Grant-in-Aid for Scientific Research on Innovative Area (25113005 to T.A and 25113009 to T.K.)].
Acknowledgments We thank Professor Tomoyuki Yamaya, Editor-in-Chief, Plant and Cell Physiology, for providing the opportunity for this Special Focus Issue on Marchantia polymorpha. We wish to acknowledge the authors and reviewers who have contributed to this issue.
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