The N-terminal domains of NLR immune receptors exhibit structural and functional similarities across divergent plant lineages

Nucleotide-binding domain and leucine-rich repeat (NLR) proteins are a prominent class of intracellular immune receptors in plants. However, our understanding of plant NLR structure and function is limited to the evolutionarily young flowering plant clade. Here, we describe an extended spectrum of NLR diversity across divergent plant lineages and demonstrate the structural and functional similarities of N-terminal domains that trigger immune responses. We show that the broadly distributed coiled-coil (CC) and toll/interleukin-1 receptor (TIR) domain families of non-flowering plants retain immune-related functions through trans-lineage activation of cell death in the angiosperm Nicotiana benthamiana. We further examined a CC subfamily specific to non-flowering lineages and uncovered an essential N-terminal MAEPL motif that is functionally comparable to motifs in resistosome-forming CC-NLRs. Consistent with a conserved role in immunity, the ectopic activation of CCMAEPL in the non-flowering liverwort Marchantia polymorpha led to profound growth inhibition, defense gene activation, and signatures of cell death. Moreover, comparative transcriptomic analyses of CCMAEPL activity delineated a common CC-mediated immune program shared across evolutionarily divergent non-flowering and flowering plants. Collectively, our findings highlight the ancestral nature of NLR-mediated immunity during plant evolution that dates its origin to at least ∼500 million years ago.

Hormonal and genetic control of pluripotency in bryophyte model systems

Land plant meristems are reservoirs of pluripotent stem cells where new tissues emerge, grow and eventually differentiate into specific cell identities. Compared to algae, where cells are produced in two-dimensional tissues via tip or marginal growth, land plants have meristems that allow three-dimensional growth for successful exploration of the terrestrial environment. In land plants, meristem maintenance leads to indeterminate growth and the production of new meristems leads to branching or regeneration via reprogramming of wounded somatic cells. Emerging model systems in the haploid dominant and monophyletic bryophytes are allowing comparative analyses of meristem gene regulatory networks to address whether all plants use common or diverse programs to organise, maintain, and regenerate meristems. In this piece we aim to discuss recent advances in genetic and hormonal control of bryophyte meristems and possible convergence or discrepancies in an exciting and emerging field in plant biology.

The complete chloroplast genome of Porella gracillima Mitt. (Porellaceae) and phylogenetic relationships to other bryophytes

Porella gracillima Mitt. (Jungermanniidae, Porellaceae), a bryophyte is widespread in temperate Asia and North America. In Korea, P. gracillima is mainly observed in shaded and dried rocks or tree trunks on mountains. Here, we determined the complete chloroplast (cp) genome sequence of P. gracillima to provide useful genetic information in the phylogenetic relationship, phylogeographic history, and conservation of the species. The complete cp genome of P. gracillima was assembled using NGS Illumina HiSeqX platform. The cp genome was 121,867 bp in length (GC contents, 33.7%) and showed a typical quadripartite structure, consisting of a large single copy (LSC) of 83,406 bp, a small single copy (SSC) of 19,692 bp, and two inverted repeats (IRs) of 9,385 bp. Phylogenetic analysis shows that Porellaceae was a sister group of Radulaceae, which agrees with the findings of the previous phylogenetic studies. Our cp genome data of P. gracillima may contribute to a better understanding of the evolution of the Porella in Porellaceae and will help to infer its molecular identification, thereby providing a guideline for conservation.

On the configuration and occurrence of 2,6-cyclocuparan-3-ols: Resolving a lasting discrepancy

2,6-Cyclocuparan-3-ols are chemical markers and major volatiles of several liverwort species. Conflicting reports on the structures of these cyclocuparanols can be found in the literature-different research groups assigned the same spectral data to different structures, yet these inconsistencies were never addressed, let alone satisfactorily explained. Following the isolation of all four diastereoisomeric cyclocuparanols from Marchantia polymorpha, their relative and absolute configurations were extensively studied by chemical and spectroscopic methods and definite stereostructures were proposed.

Cembrane-type diterpenoids from the Chinese liverwort Chandonanthus birmensis

A chemical investigation of the Chinese liverwort Chandonanthus birmensis Steph identified five undescribed cembrane-type diterpenoids, together with six known cembrane diterpenes, one fusicoccane-type diterpenoid, and a dolabellane-type diterpenoid. Their structures were established by comprehensive analysis of HRESIMS, NMR spectroscopic data, electronic circular dichroism (ECD) calculations and single-crystal X-ray diffraction analysis. Cytotoxicity tests of the isolated diterpenoids against five cancer cell lines (A2780, A549, H460, H460RT, and HeLa) revealed that several compounds showed moderate inhibitory effects with IC₅₀ values ranging from 11.1 to 36.2 μM.

Homogenization of bryophyte species after alpine grassland restoration

The causes of decreasing plant species richness include abandonment of traditional management and the spread of invasive species, even in alpine habitats. Studies on the restoration and management of alpine habitats are predominantly focused on vascular plants, although an important part of alpine vegetation and its diversity is formed by bryophytes. We used bryophytes to indicate changes that occur after the clearcutting of nonindigenous dwarf pine (Pinus mugo Turra) and attempted to reveal the community to which the development of bryophyte species structure was directed. We compared species richness and composition between surveys to test for changes in spatial heterogeneity bryophyte communities. We also tried to reveal the main ecological drivers of the restoration process. The study was performed in the (sub)alpine area of the Eastern High Sudetes Mts. (the Czech Republic). We estimated bryophyte species cover and compared the composition of the bryophyte community in autochthonous grassland areas, areas under the dwarf pine canopy, and clearcut areas to reveal the pattern of shifts 9 years after the treatment. We also measured soil characteristics to reveal the environmental habitat conditions. Evidence of taxonomic homogenization of habitat after dwarf pine removal was found. Light conditions and attributes of litter were the driving factors of successional changes in the bryophyte communities, which led to taxonomic homogenization. This finding explains the slow restoration process due to dwarf pine legacy on the clearcut area. The succession trends were also shaped by unobserved factors, such as climate change and environmental eutrophication. We highly recommended active management and long-term monitoring.

Prenylated bibenzyls from the Chinese liverwort Radula apiculata

Three new prenylated bibenzyls (1-3) and seven known congeners were purified from the Chinese liverwort Radula apiculata. Their structures were identified by the analysis of spectroscopic data and comparison of reported NMR data. All isolated compounds were tested for several human cancer cell lines with adriamycin served as a positive control.

The liverwort Marchantia polymorpha, a model for all ages

The liverwort Marchantia polymorpha has been known to man for millennia due to its inclusion Greek herbals. Perhaps due to its familiarity and association with growth in, often, man-made disturbed habitats, it was readily used to address fundamental biological questions of the day, including elucidation of land plant life cycles in the late 18th century, the formulation of cell theory early in the 19th century and the discovery of the alternation of generations in land plants in the mid-19th century. Subsequently, Marchantia was used as model in botany classes. With the arrival of the molecular era, its organellar genomes, the chloroplast and mitochondrial, were some of the first to be sequenced from any plant. In the past two decades, molecular genetic tools have been applied such that genes may be manipulated seemingly at will. Here, are past, present, and some views to the future of Marchantia as a model.

Something old, something new: Conservation of the ethylene precursor 1-amino-cyclopropane-1-carboxylic acid as a signaling molecule

In seed plants, 1-amino-cyclopropane-1-carboxylic acid (ACC) is the well-known precursor of the plant hormone ethylene. In nonseed plants, the current view is that ACC is produced but is inefficiently converted to ethylene. Distinct responses to ACC that are uncoupled from ethylene biosynthesis have been discovered in diverse aspects of growth and development in liverworts and angiosperms, indicating that ACC itself can function as a signal. Evolutionarily, ACC may have served as a signal before acquiring its role as the ethylene precursor in seed plants. These findings pave the way for unraveling a potentially conserved ACC signaling pathway in plants and have ramifications for the use of ACC as a substitute for ethylene treatment in seed plants.

A plant-specific DYRK kinase DYRKP coordinates cell morphology in Marchantia polymorpha

Dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs) are activated via the auto-phosphorylation of conserved tyrosine residues in their activation loop during protein translation, and they then phosphorylate serine/threonine residues on substrates. The DYRK family is widely conserved in eukaryotes and is composed of six subgroups. In plant lineages, DYRK homologs are classified into four subgroups, DYRK2s, yet another kinase1s, pre-mRNA processing factor 4 kinases, and DYRKPs. Only the DYRKP subgroup is plant-specific and has been identified in a wide array of plant lineages, including land plants and green algae. It has been suggested that in Arabidopsis thaliana DYRKPs are involved in the regulation of centripetal nuclear positioning induced by dark light conditions. However, the molecular functions, such as kinase activity and the developmental and physiological roles of DYRKPs are poorly understood. Here, we focused on a sole DYRKP ortholog in the model bryophyte, Marchantia polymorpha, MpDYRKP. MpDYRKP has a highly conserved kinase domain located in the C-terminal region and shares common sequence motifs in the N-terminal region with other DYRKP members. To identify the roles of MpDYRKP in M. polymorpha, we generated loss-of-function Mpdyrkp mutants via genome editing. Mpdyrkp mutants exhibited abnormal, shrunken morphologies with less flattening in their vegetative plant bodies, thalli, and male reproductive organs, antheridial receptacles. The surfaces of the thalli in the Mpdyrkp mutants appeared uneven and disordered. Moreover, their epidermal cells were drastically altered to a narrower shape when compared to the wild type. These results suggest that MpDYRKP acts as a morphological regulator, which contributes to orderly tissue morphogenesis via the regulation of cell shape.

The photo-thermochemical properties and functions of Marchantia phototropin encoded by an unduplicated gene in land plant evolution

Phototropin (phot) is a blue light photoreceptor in plants and possesses two photosensory light‑oxygen-voltage (LOV1 and LOV2) domains with different photo-thermochemical properties. While liverworts contain a single copy of PHOT (e.g., MpPHOT in Marchantia polymorpha), many land plant species contain multicopy PHOT genes (e.g., AtPHOT1 and 2 in Arabidopsis thaliana) due to evolutionary gene duplication. The LOV domains of duplicated phot proteins have been studied in detail, but those of single-copy phot proteins remain to be characterized. As phot has not been duplicated in liverworts, we hypothesized that Mpphot may retain the ancestral function and photo-thermochemical properties. To learn more about the unduplicated phot proteins, we analyzed chloroplast relocation movement and the photo-thermochemical properties of LOV1 and LOV2 in Mpphot (Mpphot-LOV1 and Mpphot-LOV2, respectively). The function of Mpphot-LOV1, which induced a response to move chloroplasts to weak light (the accumulation response) in the absence of photoactive LOV2, differed from that of LOV1 of the duplicated phot proteins of A. thaliana (e.g., Atphot1-LOV1 preventing the accumulation response). On the other hand, the function of Mpphot-LOV2 was similar to that of LOV2 of the duplicated phots. The photo-thermochemical properties of Mpphot were a hybrid of those of the duplicated phots; the photochemical and thermochemical reactions of Mpphot were similar to those of the phot2- and phot1-type proteins, respectively. Our findings reveal conservation and diversification among LOV domains during phot duplication events in land plant evolution.

Fungal-Type Terpene Synthases in Marchantia polymorpha Are Involved in Sesquiterpene Biosynthesis in Oil Body Cells

The liverwort Marchantia polymorpha possesses oil bodies in idioblastic oil body cells scattered in its thallus. Oil bodies are subcellular organelles in which specific sesquiterpenes and bisbibenzyls are accumulated. Therefore, a specialized system for the biosynthesis and accumulation of these defense compounds specifically in oil bodies has been implied. A recent study on M. polymorpha genome sequencing revealed 10 genes that shared high similarities with fungal-type terpene synthases (TPSs). Eight of these fungal-type TPS-like genes in M. polymorpha (MpFTPSL1-6, -9 and -10) are located within a 376-kb stretch on chromosome 6 and share similarities of over 94% at the nucleotide level. Therefore, these genes have likely originated from recent gene duplication events. The expression of a subset of MpFTPSLs was induced under non-axenic growth on vermiculite, which increased the amounts of sesquiterpenes and number of oil bodies. The tdTomato fluorescent protein-based in-fusion reporter assay with MpFTPSL2 promoter revealed fluorescent signals specifically in oil body cells of the thallus, indicating that MpFTPSL2 functions in oil body cells. Recombinant MpFTPSL2 expression in Escherichia coli led to sesquiterpene synthesis from farnesyl pyrophosphate. Moreover, suppression of a subset of MpFTPSLs through RNA interference reduced sesquiterpene accumulation in thalli grown on vermiculite. Taken together, these results suggest that at least a subset of MpFTPSLs is involved in sesquiterpene synthesis in oil body cells.

De novo assembly of the Mylia taylorii transcriptome and identification of sesquiterpene synthases

Mylia taylorii is an ancient nonseed land plant that accumulates various sesquiterpenes with insecticidal and antibacterial activities. Recently, microbial-type sesquiterpene synthases (STSs) with atypical aspartate-rich metal ion binding motifs have been identified in some liverworts. Here, transcriptome analysis of M. taylorii was performed to identify M. taylorii sesquiterpene synthases (MtSTSs) that are potentially involved in sesquiterpene biosynthesis and diversity. A total of 255,669 unigenes were obtained with an average length of 963 bp in the transcriptome data of M. taylorii, among which 148,093 (57.92%) unigenes had BLAST results. Forty-eight unigenes were related to the sesquiterpene backbone biosynthesis according to KEGG annotation. In addition, MtSTS1, MtSTS2 and MtSTS3 identified from putative MtSTSs display sesquiterpene catalytic activities on the basis of functional characterizations in yeast. Interestingly, MtSTSs exhibit a noncanonical metal ion binding motif and the structural composition of a single α-domain, which are features of microbial STSs instead of archetypical plant STSs. This study revealed new microbial-type STS members of nonseed plants, and functionally identified that MtSTSs may contribute to the investigation of the biosynthesis and biological role of sesquiterpenes in M. taylorii.

Epiphytic bryophyte biomass estimation on tree trunks and upscaling in tropical montane cloud forests

Epiphytic bryophytes (EB) are some of the most commonly found plant species in tropical montane cloud forests, and they play a disproportionate role in influencing the terrestrial hydrological and nutrient cycles. However, it is difficult to estimate the abundance of EB due to the nature of their "epiphytic" habitat. This study proposes an allometric scaling approach implemented in twenty-one 30 × 30 m plots across an elevation range in 16,773 ha tropical montane cloud forests of northeastern Taiwan to measure EB biomass, a primary metric for indicating plant abundance and productivity. A general allometry was developed to estimate EB biomass of 100 cm² circular-shaped mats (n = 131) with their central depths. We developed a new point-intercept instrument to rapidly measure the depths of EB along tree trunks below 300 cm from the ground level (sampled stem surface area (SSA)) (n = 210). Biomass of EB of each point measure was derived using the general allometry and was aggregated across each SSA, and its performance was evaluated. Total EB biomass of a tree was estimated by referring to an in-situ conversion model and was interpolated for all trees in the plots (n = 1451). Finally, we assessed EB biomass density at the plot scale of the study region. The general EB biomass-depth allometry showed that the depth of an EB mat was a salient variable for biomass estimation (R ² = 0.72, p < 0.001). The performance of upscaling from mats to SSA was satisfactory, which allowed us to further estimate mean (±standard deviation) EB biomass of the 21 plots (272 ± 104 kg ha^-1). Since a significant relationship between tree size and EB abundance is commonly found, regional EB biomass may be mapped by integrating our method and three-dimensional remotely sensed airborne data.

Terpenoids from the Chinese liverwort Heteroscyphus coalitus and their anti-virulence activity against Candida albicans

In this study, 14 previously undescribed terpenoids were isolated from the Chinese liverwort Heteroscyphus coalitus (Hook.) Schiffner, including a rare harziane type diterpenoid, heteroscyphsic acid A; eight ent-clerodane diterpenoids, heteroscyphsic acids B-I; four labdane diterpenoids, heteroscyphins A-D; and one guaiane sesquiterpene, heteroscyphin E; as well as a known ent-junceic acid. Their structures were determined by a combination of MS, NMR spectroscopy, electronic circular dichroism (ECD) and single crystal X-ray diffraction analyses. The anti-virulence activity of the isolated compounds against Candida albicans DSY654 demonstrated that most of them could block hyphal growth at concentrations ranging from 4-32 μg/ml. Further investigation of the most active compound, heteroscyphin D, revealed that it could suppress the ability of C. albicans DSY654 to adhere to A549 cells and form biofilms, and modulate the transcription of related genes in this fungus.

A New Epi-neoverrucosane-type Diterpenoid from the Liverwort Pleurozia subinflata in Borneo

New bioactive 13-epi-neoverrucosane diterpenoid, 5β-acetoxy-13-epi-neoverrucosanic acid (1) along with three known secondary metabolites, 13-epi-neoverrucosan-5β-ol (2), chelodane (3) and (E)-β-farnesene (4) were isolated from the MeOH extract of east Malaysia's liverwort Pleurozia subinflata. The chemical structure of new compound was elucidated by the analyses of its spectroscopic data (FTIR, NMR and HR-ESI-MS). These epi-neoverrucosane-type compounds seem to be notable chemosystematic markers for P. subinflata in Borneo. Compound 3 was widespread in marine sponges however this is the first record for 3 to be found in liverwort. These metabolites were tested for their antifungal potentials against selected fungi from the marine environment. Compound 1 exhibited effective antifungal activity against Lagenidium thermophilum.

Chemotaxonomy and cytotoxicity of the liverwort Porella Viridissima

The first chemotaxonomic study based on volatile components of Porella viridissima (Mitt.) Grolle is reported. The GC-MS analysis of ether extract was performed; ten santalane and five pinguisane-type sesquiterpenes were identified together with perrottetianal A as major diterpene. Most of detected santalane-type sesquiterpenes are reported for the first time in liverwort. P. viridissima was found to belong to the chemotype III (pinguisane/sacculatane) and shared chemical similarities with P. navicularis. Perrotettianal A was isolated and has shown strong cytotoxicity against ovarian cancer.

Phytochrome and Light Signaling in Marchantia

Bryophytes, which comprise liverworts, mosses, and hornworts, are one of the earliest diverging lineages of extant land plants and a key plant group for understanding evolutionary aspects of land plant adaptation. Marchantia polymorpha, a liverwort, has recently been established as a model plant species having molecular genetic tractability. In M. polymorpha, phytochrome is encoded by a single-copy gene, MpPHY, with Mpphy regulating various physiological responses through PHYTOCHROME INTERACTING FACTOR (PIF)-mediated transcriptional regulation. The phytochrome signaling system of M. polymorpha, with its single Mpphy and single PIF (MpPIF), is relatively simple compared with other model plants carrying multiple phytochromes and PIFs. Consequently, investigation of phytochrome signaling using M. polymorpha may provide novel insights into fundamental mechanisms and roles of phytochrome during the course of land plant evolution. This chapter provides a number of basic procedures, along with some tips, for designing and performing experiments with M. polymorpha to study phytochrome signaling.

Exploring the response of Marchantia polymorpha: Growth, morphology and chlorophyll content in the presence of anthracene

Polycyclic aromatic hydrocarbons (PAHs) were identified as hazardous contaminants that are ubiquitous and persistent in aquatic environments, where bryophytes sensu lato (mosses, liverworts and hornworts) are frequently present. Marchantia polymorpha (Class Hepaticae; thalloid liverwort) is known to respond fast to changes in the environment; it accumulates toxic substances in its tissues due to the lack of vascular and radicular systems and a reduced or absent cuticle. The objective of the present study was to quantify the effects of increasing concentrations of anthracene (0, 50 100, 280 μM) on the germination of propagules, plant morphology and chlorophyll content index (CCI) in M. polymorpha under in vitro cultures. The results show that anthracene had no statistical effect on germination or propagula formation. However, plants exposed to anthracene for 30 days showed significantly lowered the content of chlorophyll (measured as CCI), irregular growth patterns and the induction of thalli asexual reproduction as evidenced by the production of multicellular viable propagules in gemmae cups. Results of epifluorescence microscopy also showed concomitant accumulation of anthracene in the cell walls. All of these distinctive morphological and physiological adaptive responses indicators, clearly suggest that M. polymorpha are capable of resisting high (coal tar) anthracene concentrations.

Observation of Phototropic Responses in the Liverwort Marchantia polymorpha

The liverwort species, Marchantia polymorpha, shows environment-dependent morphological plasticity throughout its life cycle. Thalli, representing the predominant body form throughout most of this bryophyte's life cycle, grow with repeated dichotomous branching at the apex and develop horizontally under sufficient light intensity. Spores, after germination, produce a mass of cells, called sporelings, which then grow into thalli. Both thalli and sporelings, if grown under weak light conditions, form narrow shapes, and their apices grow toward the light source. These phototropic responses are specific to blue light and dependent on the blue-light receptor phototropin. This chapter provides several basic procedures, along with some tips, for designing and performing experiments with M. polymorpha to observe their phototropic responses, as well as methods for observing the localization of the phototropin "Mpphot" with a fluorescent protein tag.

Direct and indirect effects of land use on bryophytes in grasslands

Land-use intensification is the major threat for biodiversity in agricultural grasslands, and fertilization has been suggested as the most important driver. A common explanation for the decline of bryophyte diversity with higher land-use intensity is an indirect negative effect via the increase in vascular plant productivity, which reduces light levels for bryophytes. However, direct negative effects of land-use intensification may also be important. Here, we disentangle direct and vascular plant biomass mediated indirect effects of land use on bryophytes. We analyzed two complementary datasets from agricultural grasslands, an observational study across 144 differently managed grasslands in Germany and an experimental fertilization and irrigation study of eleven grasslands in the Swiss Alps. We found that bryophyte richness and cover strongly declined with land-use intensity and in particular with fertilization. However, structural equation modelling revealed that although both direct and indirect effects were important, the direct negative effect of fertilization was even stronger than the indirect effect mediated by increased plant biomass. Thus, our results challenge the widespread view that the negative effects of fertilization are mostly indirect and mediated via increased light competition with vascular plants. Our study shows that land use intensification reduces bryophyte diversity through several different mechanisms. Therefore, only low-intensity management with limited fertilizer inputs will allow the maintenance of bryophyte-rich grasslands.

ANGUSTIFOLIA contributes to the regulation of three-dimensional morphogenesis in the liverwort Marchantia polymorpha

Arabidopsis thaliana mutants deficient in ANGUSTIFOLIA (AN) exhibit several phenotypes at the sporophyte stage, such as narrow and thicker leaves, trichomes with two branches, and twisted fruits. It is thought that these phenotypes are caused by abnormal arrangement of cortical microtubules (MTs). AN homologs are present in the genomes of diverse land plants, including the basal land plant Marchantia polymorpha, and their molecular functions have been shown to be evolutionarily conserved in terms of the ability to complement the A. thaliana an-1 mutation. However, the roles of ANs in bryophytes, the life cycle of which includes a dominant haploid gametophyte generation, remain unknown. Here, we have examined the roles of AN homologs in the model bryophyte M. polymorpha (MpAN). Mpan knockout mutants showed abnormal twisted thalli and suppressed thallus growth along the growth axis. Under weak blue light conditions, elongated thallus growth was observed in wild-type plants, whereas it was suppressed in the mutants. Moreover, disordered cortical MT orientations were observed. Our findings suggest that MpAN contributes to three-dimensional morphogenesis by regulating cortical MT arrangement in the gametophytes of bryophytes.

Extensive epigenetic reprogramming during the life cycle of Marchantia polymorpha

Background

In plants, the existence and possible role of epigenetic reprogramming has been questioned because of the occurrence of stably inherited epialleles. Evidence suggests that epigenetic reprogramming does occur during land plant reproduction, but there is little consensus on the generality and extent of epigenetic reprogramming in plants. We studied DNA methylation dynamics during the life cycle of the liverwort Marchantia polymorpha. We isolated thalli and meristems from male and female gametophytes, archegonia, antherozoids, as well as sporophytes at early and late developmental stages, and compared their DNA methylation profiles.

Results

Of all cytosines tested for differential DNA methylation, 42% vary significantly in their methylation pattern throughout the life cycle. However, the differences are limited to few comparisons between specific stages of the life cycle and suggest four major epigenetic states specific to sporophytes, vegetative gametophytes, antherozoids, and archegonia. Further analyses indicated clear differences in the mechanisms underlying reprogramming in the gametophytic and sporophytic generations, which are paralleled by differences in the expression of genes involved in DNA methylation. Differentially methylated cytosines with a gain in methylation in antherozoids and archegonia are enriched in the CG and CHG contexts, as well as in gene bodies and gene flanking regions. In contrast, gain of DNA methylation during sporophyte development is mostly limited to the CHH context, LTR retrotransposons, DNA transposons, and repeats.

Conclusion

We conclude that epigenetic reprogramming occurs at least twice during the life cycle of M. polymorpha and that the underlying mechanisms are likely different between the two events.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-017-1383-z) contains supplementary material, which is available to authorized users.

The isolation and functional characterization of three liverwort genes encoding cinnamate 4-hydroxylase

The plant phenylpropanoid pathway is responsible for the synthesis of a wide variety of secondary metabolites. The second step in phenylpropanoid synthesis is carried out by the cytochrome P450 monooxygenase enzyme cinnamate 4-hydroxylase (C4H), which catalyzes the p-hydroxylation of trans-cinnamic acid to p-coumarate. Genes encoding C4H have been characterized in many vascular plant species, but as yet not in any bryophyte species. Here, a survey of the transcriptome sequences of four liverwort species was able to identify eight putative C4Hs. The three liverwort C4H genes taken forward for isolation and functional characterization were harbored by Plagiochasma appendiculatum (PaC4H) and Marchantia paleacea (MpC4H1 and MpC4H2). When the genes were heterologously expressed in yeast culture, an assay of enzyme activity indicated that PaC4H and MpC4H1 had a higher level of activity than MpC4H2. The favored substrate (trans-cinnamic acid) of all three liverwort C4Hs was the same as that of higher plant C4Hs. The co-expression of PaC4H in yeast cells harboring PaPAL (a P. appendiculatum ene encoding phenylalanine ammonia lyase) allowed the conversion of L-phenylalanine to p-coumaric acid. Furthermore, the expression level of PaC4H was enhanced after treatment with abiotic stress inducers UV irradiation or salicylic acid in the thallus of P. appendiculatum. The likelihood is that high activity C4Hs evolved in the liverworts and have remained highly conserved across the plant kingdom.

Cloning and functional characterization of a phenolic acid decarboxylase from the liverwort Conocephalum japonicum

Some commercially important vinyl derivatives are produced by the decarboxylation of phenolic acids. Enzymatically, this process can be achieved by phenolic acid decarboxylases (PADs), which are able to act on phenolic acid substrates such as ferulic and p-coumaric acid. Although many microbial PADs have been characterized, little is known regarding their plant homologs. Transcriptome sequencing in the liverworts has identified seven putative PADs, which share a measure of sequence identity with microbial PADs, but are typically much longer proteins. Here, a PAD-encoding gene was isolated from the liverwort species Conocephalum japonicum. The 1197 nt CjPAD cDNA sequence was predicted to be translated into a 398 residue protein. When the gene was heterologously expressed in Escherichia coli, its product exhibited a high level of PAD activity when provided with either p-coumaric or ferulic acid as substrate, along with the conversion of caffeic acid and sinapic acid to their corresponding decarboxylated products. Both N- and C-terminal truncation derivatives were non-functional. The transient expression in tobacco of a GFP/CjPAD fusion gene demonstrated that the CjPAD protein is expressed in the cytoplasm. It is first time a PAD was characterized from plants and the present investigation provided a candidate gene for catalyzing the formation of volatile phenols.

Profiling and Characterization of Small RNAs in the Liverwort, Marchantia polymorpha, Belonging to the First Diverged Land Plants

MicroRNAs (miRNAs) have important roles in gene regulation during plant development. Previous studies revealed that some miRNAs are highly shared by most land plants. Recently, the liverwort, Marchantia polymorpha, has been studied by molecular genetic approaches, and sequencing of its genome is currently underway. The expression pattern and the detailed functions of miRNAs during Marchantia development are unknown. Here, we profiled the small RNAs expressed in thalli, antheridiophores and archegoniophores of M. polymorpha using high-throughput RNA sequencing. We revealed that a limited number of miRNAs are shared between M. polymorpha and the moss, Physcomitrella patens, and that a number of miRNAs are M. polymorpha specific. Like other land plants, cognate target genes corresponding to conserved miRNAs could be found in the genome database and were experimentally confirmed to guide cleavage of target mRNAs. The results suggested that two genes in the SPL (SQUAMOSA PROMOTER BINDING-LIKE) transcription factor family, which are regulated by miR156 in most land plants, were instead targeted by two distinct miRNAs in M. polymorpha. In order to demonstrate the physiological roles of miRNAs in M. polymorpha, we constructed an miRNA ectopic expression system to establish overexpression transformants for conserved miRNAs, miR166 and miR319. Ectopic expression of these miRNAs induced abnormal development of the thallus and gemma cups, suggesting that balanced expression of miRNA/target mRNAs has a crucial role in developmental regulation in M. polymorpha. Profiling data on miRNA together with the ectopic expression system would provide new information on the liverwort small RNA world and evolutionary divergence/conservation of small RNA function among land plants.

The Naming of Names: Guidelines for Gene Nomenclature in Marchantia

While Marchantia polymorpha has been utilized as a model system to investigate fundamental biological questions for over almost two centuries, there is renewed interest in M. polymorpha as a model genetic organism in the genomics era. Here we outline community guidelines for M. polymorpha gene and transgene nomenclature, and we anticipate that these guidelines will promote consistency and reduce both redundancy and confusion in the scientific literature.

Marchantia polymorpha: Taxonomy, Phylogeny and Morphology of a Model System

One of the classical research plants in plant biology, Marchantia polymorpha, is drawing attention as a new model system. Its ease of genetic transformation and a genome sequencing project have attracted attention to the species. Here I present a thorough assessment of the taxonomic status, anatomy and developmental morphology of each organ and tissue of the gametophyte and sporophyte on the basis of a thorough review of the literature and my own observations. Marchantia polymorpha has been a subject of intensive study for nearly 200 years, and the information summarized here offers an invaluable resource for future studies on this model plant.

SNARE Molecules in Marchantia polymorpha: Unique and Conserved Features of the Membrane Fusion Machinery

The membrane trafficking pathway has been diversified in a specific way for each eukaryotic lineage, probably to fulfill specific functions in the organisms. In green plants, comparative genomics has supported the possibility that terrestrialization and/or multicellularization could be associated with the elaboration and diversification of membrane trafficking pathways, which have been accomplished by an expansion of the numbers of genes required for machinery components of membrane trafficking, including soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. However, information regarding membrane trafficking pathways in basal land plant lineages remains limited. In the present study, we conducted extensive analyses of SNARE molecules, which mediate membrane fusion between target membranes and transport vesicles or donor organelles, in the liverwort, Marchantia polymorpha. The M. polymorpha genome contained at least 34 genes for 36 SNARE proteins, comprising fundamental sets of SNARE proteins that are shared among land plant lineages with low degrees of redundancy. We examined the subcellular distribution of a major portion of these SNARE proteins by expressing Citrine-tagged SNARE proteins in M. polymorpha, and the results showed that some of the SNARE proteins were targeted to different compartments from their orthologous products in Arabidopsis thaliana. For example, MpSYP12B was localized to the surface of the oil body, which is a unique organelle in liverworts. Furthermore, we identified three VAMP72 members with distinctive structural characteristics, whose N-terminal extensions contain consensus sequences for N-myristoylation. These results suggest that M. polymorpha has acquired unique membrane trafficking pathways associated with newly acquired machinery components during evolution.

Conditional Gene Expression/Deletion Systems for Marchantia polymorpha Using its Own Heat-Shock Promoter and Cre/loxP-Mediated Site-Specific Recombination

The liverwort Marchantia polymorpha is an emerging model plant suitable for addressing, using genetic approaches, various evolutionary questions in the land plant lineage. Haploid dominancy in its life cycle facilitates genetic analyses, but conversely limits the ability to isolate mutants of essential genes. To overcome this issue and to be employed in cell lineage, mosaic and cell autonomy analyses, we developed a system that allows conditional gene expression and deletion using a promoter of a heat-shock protein (HSP) gene and the Cre/loxP site-specific recombination system. Because the widely used promoter of the Arabidopsis HSP18.2 gene did not operate in M. polymorpha, we identified a promoter of an endogenous HSP gene, MpHSP17.8A1, which exhibited a highly inducible transient expression level upon heat shock with a low basal activity level. Reporter genes fused to this promoter were induced globally in thalli under whole-plant heat treatment and also locally using a laser-assisted targeted heating technique. By expressing Cre fused to the glucocorticoid receptor under the control of the MpHSP17.8A1 promoter, a low background, sufficiently inducible control for loxP-mediated recombination could be achieved in M. polymorpha. Based on these findings, we developed a Gateway technology-based binary vector for the conditional induction of gene deletions.

Scapaundulin C, a novel labdane diterpenoid isolated from Chinese liverwort Scapania undulate, inhibits acetylcholinesterase activity

In the present study, scapaundulin C (1), a new labdane diterpenoid, and four related known compounds scapaundulin A (2), 5α, 8α, 9α-trihydroxy-13E-labden-12-one (3), 5α, 8α-dihydroxy-13E-labden-12-one (4), and (13S)-15-hydroxylabd-8 (17)-en-19-oic acid (5), were isolated from the Chinese liverwort Scapania undulate (L.) Dum., using column chromatography. The structures of these compounds were determined on the basis of 1D- and 2D-NMR analyses. The acetylcholinesterase (AchE) inhibitory activity was evaluated using a bioautographic TLC assay and the cytotoxic activity was evaluated by the MTT method. All the compounds were reported for the first time to exhibit moderate AchE inhibitory activity with minimal inhibitory quantities ranging from 250 to 500 ng. All the compounds were tested for their cytotoxicity against five human tumor cell lines, A549, K562, A2780, Hela, and HT29, and compounds 3 and 4 exhibited moderate inhibitory effects on the growth of A2780 cells.

Cloning and functional characterization of a 4-coumarate CoA ligase from liverwort Plagiochasma appendiculatum

Plant phenylpropanoids represent a large group of secondary metabolites which have played an important role in terrestrial plant life, beginning with the evolution of land plants from primitive green algae. 4-Coumarate: coenzyme A ligase (4CL) is a provider of activated thioester substrates within the phenylpropanoid synthesis pathway. Although 4CLs have been extensively characterized in angiosperm, gymnosperm and moss species, little is known of their functions in liverworts. Here, a 4CL homolog (designated as Pa4CL1) was isolated from the liverwort species Plagiochasma appendiculatum. The full-length cDNA sequence of Pa4CL1 contains 1644bp and is predicted to encode a protein with 547amino acids. The gene products were 40-50% identical with 4CL sequences reported in public databases. The recombinant protein was heterologously expressed in Escherichia coli and exhibited a high level of 4CL activity, catalyzing formation of hydroxycinnamate-CoA thioesters by a two-step reaction mechanism from corresponding hydroxycinnamic acids. Kinetic analysis indicated that the most favorable substrate for Pa4CL1 is p-coumaric acid. The transcription of Pa4CL1 was induced when P. appendiculatum thallus was treated with either salicylic acid or methyl jasmonate.

Abscisic acid-induced rearrangement of intracellular structures associated with freezing and desiccation stress tolerance in the liverwort Marchantia polymorpha

The plant growth regulator abscisic acid (ABA) is known to be involved in triggering responses to various environmental stresses such as freezing and desiccation in angiosperms, but little is known about its role in basal land plants, especially in liverworts, representing the earliest land plant lineage. We show here that survival rate after freezing and desiccation of Marchantia polymorpha gemmalings was increased by pretreatment with ABA in the presence of increasing concentrations of sucrose. ABA treatment increased accumulation of soluble sugars in gemmalings, and sugar accumulation was further increased by addition of sucrose to the culture medium. ABA treatment of gemmalings also induced accumulation of transcripts for proteins with similarity to late embryogenesis abundant (LEA) proteins, which accumulate in association with acquisition of desiccation tolerance in maturing seeds. Observation by light and electron microscopy indicated that the ABA treatment caused fragmentation of vacuoles with increased cytosolic volume, which was more prominent in the presence of a high concentration of external sucrose. ABA treatment also increased the density of chloroplast distribution and remarkably enlarged their volume. These results demonstrate that ABA induces drastic physiological changes in liverwort cells for stress tolerance, accompanied by accumulation of protectants against dehydration and rearrangement and morphological alterations of cellular organelles.

Dominance of Paris-type morphology on mycothallus of Lunularia cruciata colonised by Glomus proliferum

Microscopic evidence confirms that L. cruciata hosting G. proliferum shows major anatomical traits (arbuscules, coils, arbusculate coils and vesicles) generally associated arbuscular mycorrhizal roots and the anatomical morphology of intra-thalli mycelium is predominantly of the Paris-type. Colonised L. cruciata showed a reduction of biomass when compared with axenic plants suggesting a drain of resources towards the fungus and depletion of nutrients required for optimum plant growth. The behaviour of mycothalli regarding available KH2PO4 indicates that the nutritional stress threshold for phosphorus (P) is above the residual amount of P already present in Phytagel(TM) and in plant inoculum. These raise the possibility that in certain circumstances the relationship between L. cruciata and G. proliferum be parasitic rather than symbiotic and open the door for future studies to ascertain the nature of liverwort-AM fungi relationships.