Bryophyte diversity and evolution: windows into the early evolution of land plants

Ancient large-scale gene duplications and diversification in bryophytes illuminate the plant terrestrialization

Large-scale gene duplications (LSGDs) are crucial for evolutionary adaptation and recurrent in vascular plants. However, the role of ancient LSGDs in the terrestrialization and diversification of bryophytes, the second most species-rich group of land plants, remains largely elusive due to limited sampling in bryophytes. Employing the most extensive nuclear gene dataset in bryophytes to date, we reconstructed a time-calibrated phylogenetic tree from 209 species, covering virtually all key bryophyte lineages, for phylogenomic analyses of LSGDs and diversification. We newly identified two ancient LSGDs: one in the most recent common ancestor (MRCA) of extant bryophytes and another in the MRCA of the majority of Jungermanniales s. lato. Duplicated genes from these two LSGDs show significant enrichment in photosynthesis-related processes and structures. Rhizoid-responsive ROOTHAIR DEFECTIVE SIX-LIKE (RSL) genes from ancient LSGDs are present in rhizoidless bryophytes, challenging assumptions about rhizoid absence mechanisms. We highlighted four major diversification rate upshifts, two of which slightly postdated LSGDs, potentially linked to the flourishing of gymnosperms and angiosperms and explaining over 80% of bryophyte diversity. Our findings, supported by extensive bryophyte sampling, highlight the significance of LSGDs in the early terrestrialization and diversification of bryophytes, offering new insights into land plant evolution.

From barcodes to genomes: a new era of molecular exploration in bryophyte research

Bryophytes represent a diverse and species-rich group of plants, characterized by a remarkable array of morphological variations. Due to their significant ecological and economic roles worldwide, accurate identification of bryophyte taxa is crucial. However, the variability in morphological traits often complicates their proper identification and subsequent commercial utilization. DNA barcoding has emerged as a valuable tool for the precise identification of bryophyte taxa, facilitating comparisons at both interspecific and intraspecific levels. Recent research involving plastomes, mitogenomes, and transcriptomes of various bryophyte species has provided insights into molecular changes and gene expression in response to environmental stressors. Advances in molecular phylogenetics have shed light on the origin and evolutionary history of bryophytes, thereby clarifying their phylogenetic relationships. Despite these advancements, a comprehensive understanding of the systematic relationships within bryophytes is still lacking. This review synthesizes current molecular studies that have been instrumental in unraveling the complexity of bryophyte taxonomy and systematics. By highlighting key findings from recent genetic and genomic research, we underscore the importance of integrating molecular data with traditional morphological approaches. Such integration is essential for refining the classification systems of bryophytes and for understanding their adaptive strategies in various ecological niches. Future research should focus on expanding the molecular datasets across underrepresented bryophyte lineages and exploring the functional significance of genetic variations under different environmental conditions. This will not only enhance our knowledge of bryophyte evolution, but also inform conservation strategies and potential applications in biotechnology.

Systematic characterization of cinnamyl alcohol dehydrogenase members revealed classification and function divergence in Haplomitrium mnioides

Cinnamyl alcohol dehydrogenase (CAD; EC 1.1.1.195) is considered to be a key enzyme in lignin biosynthesis, which can catalyze cinnamyl aldehyde to produce cinnamyl alcohol. In this study, three putative CADs were characterized from the liverwort Haplomitrium mnioides. The sequence alignment and phylogenetic analysis revealed that HmCADs belonged to a multigene family, with three HmCADs belonging to class II, class III, and class IV, respectively. In vitro enzymatic studies demonstrated that HmCAD2 exhibited high affinity and catalytic activity towards five cinnamyl aldehydes, followed by HmCAD3 with poor catalytic activity, and HmCAD1 catalyzed only the reaction of p-coumaryl aldehyde and coniferyl aldehyde with extremely low catalytic capacity. Protein-substrate binding simulations were performed to investigate the differences in catalytic activity exhibited when proteins catalyzed different substrates. Furthermore, distinct expression patterns of three HmCADs were identified in different plant tissues. Subcellular localization tests confirmed that HmCAD1/2/3 was located in the cytoplasm. The simulated responses of HmCADs to different stresses showed that HmCAD1 played a positive role in coping with each stress, while HmCAD2/3 was weak. These findings demonstrate the diversity of CADs in liverwort, highlight the divergent role of HmCAD1/2/3 in substrate catalysis, and also suggest their possible involvement in stress response, thereby providing new insights into CAD evolution while emphasizing their potential distinctive and collaborative contributions to the normal growth of primitive liverworts.

Unique structural attributes of the PSI-NDH supercomplex in Physcomitrium patens

Cyclic electron transport around photosystem I (PSI) is essential for the protection of the photosynthetic apparatus in plants under diverse light conditions. This process is primarily mediated by Proton Gradient Regulation 5 protein/Proton Gradient Regulation 5-like photosynthetic phenotype 1 protein (PGR5/PGRL1) and NADH dehydrogenase-like complex (NDH). In angiosperms, NDH interacts with two PSI complexes through distinct monomeric antennae, LHCA5 and LHCA6, which is crucial for its higher stability under variable light conditions. This interaction represents an advanced evolutionary stage and offers limited insight into the origin of the PSI-NDH supercomplex in evolutionarily older organisms. In contrast, the moss Physcomitrium patens (Pp), which retains the lhca5 gene but lacks the lhca6, offers a glimpse into an earlier evolutionary stage of the PSI-NDH supercomplex. Here we present structural evidence of the Pp PSI-NDH supercomplex formation by single particle electron microscopy, demonstrating the unique ability of Pp to bind a single PSI in two different configurations. One configuration closely resembles the angiosperm model, whereas the other exhibits a novel PSI orientation, rotated clockwise. This structural flexibility in Pp is presumably enabled by the variable incorporation of LHCA5 within PSI and is indicative of an early evolutionary adaptation that allowed for greater diversity at the PSI-NDH interface. Our findings suggest that this variability was reduced as the structural complexity of the NDH complex increased in vascular plants, primarily angiosperms. This study not only clarifies the evolutionary development of PSI-NDH supercomplexes but also highlights the dynamic nature of the adaptive mechanisms of plant photosynthesis.

Landscape Heterogeneity Drives Genetic Diversity in the Highly Dispersive Moss Funaria hygrometrica Hedw

Funaria hygrometrica, a cosmopolitan moss species known for its remarkable dispersal capacity, was selected as the focal organism to investigate the relationship between landscape features and genetic diversity. Our study encompassed samples collected from two distinct regions: the Spanish Sierra Nevada Mountains (SN), characterized by a diverse landscape with an altitudinal difference of nearly 3500 m within a short distance, and the Murcia Region (MU) in Southeast Spain, characterized by a uniform landscape akin to the lowlands of Sierra Nevada. Genotyping analysis targeted three genetic regions: the nuclear ribosomal internal transcribed spacer (nrITS), the chloroplast rps3-rpl16 region, and the mitochondrial rpl5-rpl16 spacer. Through this analysis, we aimed to assess genetic variability and population structure across these environmentally contrasting regions. The Sierra Nevada populations exhibited significantly higher haplotype diversity (Hd = 0.78 in the highlands and 0.67 overall) and nucleotide diversity (π% = 0.51 for ITS1) compared to the Murcia populations (Hd = 0.35, π% = 0.14). Further investigation unveiled that samples from the lowlands of Sierra Nevada showed a closer genetic affinity to Murcia than to the highlands of Sierra Nevada. Furthermore, the genetic differentiation between highland and lowland populations was significant (ΦST = 0.55), with partial Mantel tests and ResistanceGA analysis revealing a strong correlation between ITS1-based genetic diversity and landscape features, including altitude and bioclimatic variables. Our study elucidated potential explanations for the observed genetic structuring within F. hygrometrica samples' populations. These included factors such as a high selfing rate within restricted habitats, a limited average dispersal distance of spores, hybrid depression affecting partially incompatible genetic lineages, and recent migration facilitated via human activities into formerly unoccupied areas of the dry zones of Southeast Spain.

Contrasting and conserved roles of NPR pathways in diverged land plant lineages

The NPR proteins function as salicylic acid (SA) receptors in Arabidopsis thaliana. AtNPR1 plays a central role in SA-induced transcriptional reprogramming whereby positively regulates SA-mediated defense. NPRs are found in the genomes of nearly all land plants. However, we know little about the molecular functions and physiological roles of NPRs in most plant species. We conducted phylogenetic and alignment analyses of NPRs from 68 species covering the significant lineages of land plants. To investigate NPR functions in bryophyte lineages, we generated and characterized NPR loss-of-function mutants in the liverwort Marchantia polymorpha. Brassicaceae NPR1-like proteins have characteristically gained or lost functional residues identified in AtNPRs, pointing to the possibility of a unique evolutionary trajectory for the Brassicaceae NPR1-like proteins. We find that the only NPR in M. polymorpha, MpNPR, is not the master regulator of SA-induced transcriptional reprogramming and negatively regulates bacterial resistance in this species. The Mpnpr transcriptome suggested roles of MpNPR in heat and far-red light responses. We identify both Mpnpr and Atnpr1-1 display enhanced thermomorphogenesis. Interspecies complementation analysis indicated that the molecular properties of AtNPR1 and MpNPR are partially conserved. We further show that MpNPR has SA-binding activity. NPRs and NPR-associated pathways have evolved distinctively in diverged land plant lineages to cope with different terrestrial environments.

Plant regeneration in the new era: from molecular mechanisms to biotechnology applications

Plants or tissues can be regenerated through various pathways. Like animal regeneration, cell totipotency and pluripotency are the molecular basis of plant regeneration. Detailed systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant regeneration. Specifically, plant hormones, cell division, epigenetic remodeling, and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic cells. Recent research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species, with various plant species using distinct mechanisms and displaying significant differences in regenerative capacity. Conducting multi-omics studies at the single-cell level, tracking plant regeneration processes in real-time, and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration, improve crop regeneration efficiency, and contribute to future crop design.

DWARF27 and CAROTENOID CLEAVAGE DIOXYGENASE 7 genes regulate release, germination and growth of gemma in Marchantia polymorpha

Strigolactones (SLs), a class of carotenoid-derived hormones, play a crucial role in flowering plants by regulating underground communication with symbiotic arbuscular mycorrhizal fungi (AM) and controlling shoot and root architecture. While the functions of core SL genes have been characterized in many plants, their roles in non-tracheophyte plants like liverworts require further investigation. In this study, we employed the model liverwort species Marchantia polymorpha, which lacks detectable SL production and orthologs of key SL biosynthetic genes, including CAROTENOID CLEAVAGE DIOXYGENASE 8 (CCD8) and MORE AXILLARY GROWTH 1 (MAX1). However, it retains some SL pathway components, including DWARF27 (D27) and CCD7. To help elucidate the function of these remaining components in M. polymorpha, knockout mutants were generated for MpD27-1, MpD27-2 and MpCCD7. Phenotypic comparisons of these mutants with the wild-type control revealed a novel role for these genes in regulating the release of gemmae from the gemma cup and the germination and growth of gemmae in the dark. Mpd27-1, Mpd27-2, and Mpccd7 mutants showed lower transcript abundance of genes involved in photosynthesis, such as EARLY LIGHT INDUCED (ELI), and stress responses such as LATE EMBRYOGENESIS ABUNDANT (LEA) but exhibited higher transcript levels of ETHYLENE RESPONSE FACTORS (ERFs) and SL and carotenoid related genes, such as TERPENE SYNTHASE (TS), CCD7 and LECITHIN-RETINAL ACYL TRANSFERASE (LRAT). Furthermore, the mutants of M. polymorpha in the SL pathway exhibited increased contents of carotenoid. This unveils a previously unrecognized role for MpD27-1, MpD27-2 and MpCCD7 in controlling release, germination, and growth of gemmae in response to varying light conditions. These discoveries enhance our comprehension of the regulatory functions of SL biosynthesis genes in non-flowering plants.

Elucidation of arsenic detoxification mechanism in Marchantia polymorpha: The role of ACR3

The arsenic-specific ACR3 transporter plays pivotal roles in As detoxification in yeast and a group of ancient tracheophytes, the ferns. Despite putative ACR3 genes being present in the genomes of bryophytes, whether they have the same relevance also in this lineage is currently unknown. In this study, we characterized the MpACR3 gene from the bryophyte Marchantia polymorpha L. through a multiplicity of functional approaches ranging from phylogenetic reconstruction, expression analysis, loss- and gain-of-function as well as genetic complementation with an MpACR3 gene tagged with a fluorescent protein. Genetic complementation demonstrates that MpACR3 plays a pivotal role in As tolerance in M. polymorpha, with loss-of-function Mpacr3 mutants being hypersensitive and MpACR3 overexpressors more tolerant to As. Additionally, MpACR3 activity regulates intracellular As concentration, affects its speciation and controls the levels of intracellular oxidative stress. The MpACR3::3xCitrine appears to localize at the plasma membrane and possibly in other endomembrane systems. Taken together, these results demonstrate the pivotal function of ACR3 detoxification in both sister lineages of land plants, indicating that it was present in the common ancestor to all embryophytes. We propose that Mpacr3 mutants could be used in developing countries as low-cost and low-technology visual bioindicators to detect As pollution in water.

Molecular and phylogenetic evidence of parallel expansion of anion channels in plants

Aluminum-activated malate transporters (ALMTs) and slow anion channels (SLACs) are important in various physiological processes in plants, including stomatal regulation, nutrient uptake, and in response to abiotic stress such as aluminum toxicity. To understand their evolutionary history and functional divergence, we conducted phylogenetic and expression analyses of ALMTs and SLACs in green plants. Our findings from phylogenetic studies indicate that ALMTs and SLACs may have originated from green algae and red algae, respectively. The ALMTs of early land plants and charophytes formed a monophyletic clade consisting of three subgroups. A single duplication event of ALMTs was identified in vascular plants and subsequent duplications into six clades occurred in angiosperms, including an identified clade, 1-1. The ALMTs experienced gene number losses in clades 1-1 and 2-1 and expansions in clades 1-2 and 2-2b. Interestingly, the expansion of clade 1-2 was also associated with higher expression levels compared to genes in clades that experienced apparent loss. SLACs first diversified in bryophytes, followed by duplication in vascular plants, giving rise to three distinct clades (I, II, and III), and clade II potentially associated with stomatal control in seed plants. SLACs show losses in clades II and III without substantial expansion in clade I. Additionally, ALMT clade 2-2 and SLAC clade III contain genes specifically expressed in reproductive organs and roots in angiosperms, lycophytes, and mosses, indicating neofunctionalization. In summary, our study demonstrates the evolutionary complexity of ALMTs and SLACs, highlighting their crucial role in the adaptation and diversification of vascular plants.

Proteome plasticity during Physcomitrium patens spore germination - from the desiccated phase to heterotrophic growth and reconstitution of photoautotrophy

The establishment of moss spores is considered a milestone in plant evolution. They harbor protein networks underpinning desiccation tolerance and accumulation of storage compounds that can be found already in algae and that are also utilized in seeds and pollen. Furthermore, germinating spores must produce proteins that drive the transition through heterotrophic growth to the autotrophic plant. To get insight into the plasticity of this proteome, we investigated it at five timepoints of moss (Physcomitrium patens) spore germination and in protonemata and gametophores. The comparison to previously published Arabidopsis proteome data of seedling establishment showed that not only the proteomes of spores and seeds are functionally related, but also the proteomes of germinating spores and young seedlings. We observed similarities with regard to desiccation tolerance, lipid droplet proteome composition, control of dormancy, and β-oxidation and the glyoxylate cycle. However, there were also striking differences. For example, spores lacked any obvious storage proteins. Furthermore, we did not detect homologs to the main triacylglycerol lipase in Arabidopsis seeds, SUGAR DEPENDENT1. Instead, we discovered a triacylglycerol lipase of the oil body lipase family and a lipoxygenase as being the overall most abundant proteins in spores. This finding indicates an alternative pathway for triacylglycerol degradation via oxylipin intermediates in the moss. The comparison of spores to Nicotiana tabacum pollen indicated similarities for example in regards to resistance to desiccation and hypoxia, but the overall developmental pattern did not align as in the case of seedling establishment and spore germination.

Paternal imprinting in Marchantia polymorpha

We are becoming aware of a growing number of organisms that do not express genetic information equally from both parents as a result of an epigenetic phenomenon called genomic imprinting. Recently, it was shown that the entire paternal genome is repressed during the diploid phase of the life cycle of the liverwort Marchantia polymorpha. The deposition of the repressive epigenetic mark H3K27me3 on the male pronucleus is responsible for the imprinted state, which is reset by the end of meiosis. Here, we put these recent reports in perspective of other forms of imprinting and discuss the potential mechanisms of imprinting in bryophytes and the causes of its evolution.

Effects of Cesium on Physiological Traits of the Catherine's Moss Atrichum undulatum Hedw

Mosses are proven bioindicators of living environments. It is known that mosses accumulate pollutants from precipitates and, to some lesser extent, from the substrate. In this study, the effects of cesium (Cs) on the physiological traits of acrocarp polytrichaceous Catherine's moss (Atrichum undulatum Hedw.) were studied under controlled, in vitro conditions. Cesium can be found in the environment in a stable form (133Cs) and as a radioactive isotope (134Cs and 137Cs). Belonging to the same group of elements, Cs and potassium (K) share various similarities, due to which Cs can interfere with this essential element and thus possibly alter the plant's metabolism. Results have shown that Cs affects the measured physiological characteristics of A. undulatum, although the changes to antioxidative enzyme activities were not drastic following Cs treatments. Therefore, the activities of antioxidative enzymes at lower pH values are more the consequence of pH effects on enzymatic conformation than simply the harmful effects of Cs. Moreover, Cs did not affect the survival of plants grown on the solid substrate nor plants grown in conditions of light and heavy rain simulation using Cs with variable pH, indicating that Cs is not harmful in this form for the studied species A. undulatum.

The trait co-variation regulates the response of bryophytes to nitrogen deposition: A meta-analysis

The nitrogen deposition has the potential to alter the trait composition of plant communities by affecting the fitness and physiological adaptation of species, consequently exerting an influence on ecosystem processes. Despite the importance of bryophytes in nutrient and carbon dynamics across different ecosystems, there is a lack of research examining the relationship between nitrogen deposition and the co-variation of bryophyte traits. To address this gap, a meta-analysis was conducted using data from 27 independent studies to investigate potential associations between trait co-variation of bryophytes and nitrogen deposition. The results revealed that interspecific variability regulates the influence of nitrogen deposition on bryophytes by affecting trait co-variation. Multiple correspondence analysis identified six combinations of closely related traits. For example, species with unbranched main stems frequently exhibit robust leaf midribs, leading to leaf wrinkling and leaf clasping around the stem as a response to water loss. Some weft or mat species tend to obtain resources (nitrogen) through their scale hairs on the main stem. Some species with narrow leaves require leaf teeth to maintain a normal leaf shape. The subgroup analyses indicated that certain traits, including unbranched main stem, changes in leaf morphology, robust leaf midrib, main stem without scale hairs, narrow leaf, leaf margin with teeth, undeveloped apophysis, and erect capsule minimize interaction with pollutants and represent a resource strategy. Conversely, functional traits representing a resource acquisition strategy, such as branched main stem, no changes in leaf morphology, short and weak leaf midrib, main stem with scale hairs, broad leaf, leaf margin without teeth, developed apophysis, and non-erect capsule increase pollutant exposure. Overall, our results suggest that anthropogenic global change may significantly impact bryophytes due to changes in their individual physiology and colony ecological indicators caused by increased nitrogen deposition.

Conserved and non-conserved RNA-target modules in plants: lessons for a better understanding of Marchantia development

A wide variety of functional regulatory non-coding RNAs (ncRNAs) have been identified as essential regulators of plant growth and development. Depending on their category, ncRNAs are not only involved in modulating target gene expression at the transcriptional and post-transcriptional levels but also are involved in processes like RNA splicing and RNA-directed DNA methylation. To fulfill their molecular roles properly, ncRNAs must be precisely processed by multiprotein complexes. In the case of small RNAs, DICER-LIKE (DCL) proteins play critical roles in the production of mature molecules. Land plant genomes contain at least four distinct classes of DCL family proteins (DCL1-DCL4), of which DCL1, DCL3 and DCL4 are also present in the genomes of bryophytes, indicating the early divergence of these genes. The liverwort Marchantia polymorpha has become an attractive model species for investigating the evolutionary history of regulatory ncRNAs and proteins that are responsible for ncRNA biogenesis. Recent studies on Marchantia have started to uncover the similarities and differences in ncRNA production and function between the basal lineage of bryophytes and other land plants. In this review, we summarize findings on the essential role of regulatory ncRNAs in Marchantia development. We provide a comprehensive overview of conserved ncRNA-target modules among M. polymorpha, the moss Physcomitrium patens and the dicot Arabidopsis thaliana, as well as Marchantia-specific modules. Based on functional studies and data from the literature, we propose new connections between regulatory pathways involved in Marchantia's vegetative and reproductive development and emphasize the need for further functional studies to understand the molecular mechanisms that control ncRNA-directed developmental processes.

Stepwise changes in flavonoids in spores/pollen contributed to terrestrial adaptation of plants

Protecting haploid pollen and spores against UV-B light and high temperature, 2 major stresses inherent to the terrestrial environment, is critical for plant reproduction and dispersal. Here, we show flavonoids play an indispensable role in this process. First, we identified the flavanone naringenin, which serves to defend against UV-B damage, in the sporopollenin wall of all vascular plants tested. Second, we found that flavonols are present in the spore/pollen protoplasm of all euphyllophyte plants tested and that these flavonols scavenge reactive oxygen species to protect against environmental stresses, particularly heat. Genetic and biochemical analyses showed that these flavonoids are sequentially synthesized in both the tapetum and microspores during pollen ontogeny in Arabidopsis (Arabidopsis thaliana). We show that stepwise increases in the complexity of flavonoids in spores/pollen during plant evolution mirror their progressive adaptation to terrestrial environments. The close relationship between flavonoid complexity and phylogeny and its strong association with pollen survival phenotypes suggest that flavonoids played a central role in the progression of plants from aquatic environments into progressively dry land habitats.

The occurrence of 40K and 137Cs radioactivity in mosses during 2015-2019 in the Djerdap National Park (E. Serbia)

The radiation status of the national park (NP) Djerdap (Eastern Serbia) is characterized using bioindicators (mosses). Mosses (16 species, 156 samples) were collected randomly within the area of NP Djerdap during the month of June, periodically from 2015 to 2019. Samples were collected in the regions of Dobra, Donji Milanovac, and Tekija. Within the mosses, the presence of ⁴⁰ K and ¹³⁷Cs is regarded as a good indicator of radionuclides present in the environment due to their easy interchangeability with ³⁹ K highly present in living moss organisms. The activity concentrations of gamma ray-emmiting radionuclides in samples were determined using high-resolution gamma ray spectrometry, an HPGe-ORTEC/Ametek detector. The determining activity concentrations of ⁴⁰ K and ¹³⁷Cs in collected samples were as follows: for ⁴⁰ K from 31.4 to 721 Bq kg^-1and for ¹³⁷Cs varied from 2.6 to 908 Bq kg^-1. The average activity concentrations of ⁴⁰ K and ¹³⁷Cs (Bq kg^-1) in mosses in the period 2015-2019 were the lowest in moss samples collected in the Dobra region, and the highest in the area of Donji Milanovac. The most prevalent collected moss species within the Djerdap National Park was Hypnum cupressiforme. The determined activity concentrations in H. cupressiforme of ¹³⁷Cs for the whole region of NP Djerdap for all 5 years was 78.1 ± 70.3 Bq kg^-1 and of ⁴⁰ K was 181 ± 86.1 Bq kg^-1.

Untargeted Metabolomics for Integrative Taxonomy: Metabolomics, DNA Marker-Based Sequencing, and Phenotype Bioimaging

Integrative taxonomy is a fundamental part of biodiversity and combines traditional morphology with additional methods such as DNA sequencing or biochemistry. Here, we aim to establish untargeted metabolomics for use in chemotaxonomy. We used three thallose liverwort species Riccia glauca, R. sorocarpa, and R. warnstorfii (order Marchantiales, Ricciaceae) with Lunularia cruciata (order Marchantiales, Lunulariacea) as an outgroup. Liquid chromatography high-resolution mass-spectrometry (UPLC/ESI-QTOF-MS) with data-dependent acquisition (DDA-MS) were integrated with DNA marker-based sequencing of the trnL-trnF region and high-resolution bioimaging. Our untargeted chemotaxonomy methodology enables us to distinguish taxa based on chemophenetic markers at different levels of complexity: (1) molecules, (2) compound classes, (3) compound superclasses, and (4) molecular descriptors. For the investigated Riccia species, we identified 71 chemophenetic markers at the molecular level, a characteristic composition in 21 compound classes, and 21 molecular descriptors largely indicating electron state, presence of chemical motifs, and hydrogen bonds. Our untargeted approach revealed many chemophenetic markers at different complexity levels that can provide more mechanistic insight into phylogenetic delimitation of species within a clade than genetic-based methods coupled with traditional morphology-based information. However, analytical and bioinformatics analysis methods still need to be better integrated to link the chemophenetic information at multiple scales.

Ptychostomum schleicheri (Bryophyta) Ekstraktının Yumuşak Çeliğin Korozyonu Üzerine Yeşil Önleyici Etkisi

In present study, the inhibitive impact of Ptychostomum schleicheri extract, a moss species of Bryaceae family, on the mild steel corrosion in 1 M HCl at ambient temperature was firstly analysed by Tafel extrapolation method, electrochemical impedance spectroscopy (EIS) and linear polarization (LPR) techniques. Electrochemical tests were conducted by 1 h immersing mild steels in HCl solutions containing four various concentrations of moss extract. At a concentration of 0.200% (w/v), the moss extract displayed around 90 percent inhibition efficiency by three electrochemical methods, and it was also observed that its protective effect increased depending on the upsurge in the concentration of Ptychostomum schleicheri extract. The morphologies of mild steels surface in 1 M HCl with and without P. schleicheri extract at the end of 1 h immersion time were visualized by a metal microscope. Finally, according to the electrochemical data and surface morphology results, it can be said that the extract molecules adsorbed on the mild steel surface to achieve almost maximal coverage and contact.

Polycomb-mediated repression of paternal chromosomes maintains haploid dosage in diploid embryos of Marchantia

Complex mechanisms regulate gene dosage throughout eukaryotic life cycles. Mechanisms controlling gene dosage have been extensively studied in animals, however it is unknown how generalizable these mechanisms are to diverse eukaryotes. Here, we use the haploid plant Marchantia polymorpha to assess gene dosage control in its short-lived diploid embryo. We show that throughout embryogenesis, paternal chromosomes are repressed resulting in functional haploidy. The paternal genome is targeted for genomic imprinting by the Polycomb mark H3K27me3 starting at fertilization, rendering the maternal genome in control of embryogenesis. Maintaining haploid gene dosage by this new form of imprinting is essential for embryonic development. Our findings illustrate how haploid-dominant species can regulate gene dosage through paternal chromosome inactivation and initiates the exploration of the link between life cycle history and gene dosage in a broader range of organisms.

Diversity, phylogeny, and adaptation of bryophytes: insights from genomic and transcriptomic data

Bryophytes including mosses, liverworts, and hornworts are among the earliest land plants, and occupy a crucial phylogenetic position to aid in the understanding of plant terrestrialization. Despite their small size and simple structure, bryophytes are the second largest group of extant land plants. They live ubiquitously in various habitats and are highly diversified, with adaptive strategies to modern ecosystems on Earth. More and more genomes and transcriptomes have been assembled to address fundamental questions in plant biology. Here, we review recent advances in bryophytes associated with diversity, phylogeny, and ecological adaptation. Phylogenomic studies have provided increasing supports for the monophyly of bryophytes, with hornworts sister to the Setaphyta clade including liverworts and mosses. Further comparative genomic analyses revealed that multiple whole-genome duplications might have contributed to the species richness and morphological diversity in mosses. We highlight that the biological changes through gene gain or neofunctionalization that primarily evolved in bryophytes have facilitated the adaptation to early land environments; among the strategies to adapt to modern ecosystems in bryophytes, desiccation tolerance is the most remarkable. More genomic information for bryophytes would shed light on key mechanisms for the ecological success of these 'dwarfs' in the plant kingdom.

Dependence on clade II bHLH transcription factors for nursing of haploid products by tapetal-like cells is conserved between moss sporangia and angiosperm anthers

Clade II basic helix-loop-helix transcription factors (bHLH TFs) are essential for pollen production and tapetal nursing functions in angiosperm anthers. As pollen has been suggested to be related to bryophyte spores by descent, we characterized two Physcomitrium (Physcomitrella) patens clade II bHLH TFs (PpbHLH092 and PpbHLH098), to test if regulation of sporogenous cells and the nursing cells surrounding them is conserved between angiosperm anthers and bryophyte sporangia. We made CRISPR-Cas9 reporter and loss-of-function lines to address the function of PpbHLH092/098. We sectioned and analyzed WT and mutant sporophytes for a comprehensive stage-by-stage comparison of sporangium development. Spore precursors in the P. patens sporangium are surrounded by nursing cells showing striking similarities to tapetal cells in angiosperms. Moss clade II bHLH TFs are essential for the differentiation of these tapetal-like cells and for the production of functional spores. Clade II bHLH TFs provide a conserved role in controlling the sporophytic somatic cells surrounding and nursing the sporogenous cells in both moss sporangia and angiosperm anthers. This supports the hypothesis that such nursing functions in mosses and angiosperms, lineages separated by c. 450 million years, are related by descent.

Need for split: integrative taxonomy reveals unnoticed diversity in the subaquatic species of Pseudohygrohypnum (Pylaisiaceae, Bryophyta)

We present an integrative molecular and morphological study of subaquatic representatives of the genus Pseudohygrohypnum (Pylaisiaceae, Bryophyta), supplemented by distribution modelling of the revealed phylogenetic lineages. Phylogenetic analyses of nuclear and plastid datasets combined with the assemble species by automatic partitioning (ASAP) algorithm revealed eight distinct species within the traditionally circumscribed P. eugyrium and P. subeugyrium. These species are therefore yet another example of seemingly widely distributed taxa that harbour molecularly well-differentiated lineages with narrower distribution ranges. Studied accessions that were previously assigned to P. eugyrium form three clearly allopatric lineages, associated with temperate regions of Europe, eastern North America and eastern Asia. Remarkably, accessions falling under the current morphological concept of P. subeugyrium were shown to be even more diverse, containing five phylogenetic lineages. Three of these lineages occur under harsh Asian continental climates from cool-temperate to Arctic regions, while the remaining two, referred to P. subeugyrium s.str. and P. purpurascens, have more oceanic North Atlantic and East Asian distributions. Niche identity and similarity tests suggested no similarity in the distributions of the phylogenetically related lineages but revealed the identity of two East Asian species and the similarity of two pairs of unrelated species. A morphological survey confirmed the distinctness of all eight phylogenetic lineages, requiring the description of five new species. Pseudohygrohypnum appalachianum and P. orientale are described for North American and East Asian plants of P. eugyrium s.l., while P. sibiricum, P. subarcticum and P. neglectum are described for the three continental, predominantly Asian lineages of P. subeugyrium s.l. Our results highlight the importance of nontropical Asia as a center of bryophyte diversity. Phylogenic dating suggests that the diversification of subaquatic Pseudohygrohypnum lineages appeared in late Miocene, while mesophilous species of the genus split before Miocene cooling, in climatic conditions close to those where the ancestor of Pseudohygrohypnum appeared. We speculate that radiation of the P. subeugyrium complex in temperate Asia might have been driven by progressive cooling, aridification, and increases in seasonality, temperature and humidity gradients. Our results parallel those of several integrative taxonomic studies of North Asian mosses, which have resulted in a number of newly revealed species. These include various endemics from continental areas of Asia suggesting that the so-called Rapoport's rule of low diversity and wide distribution range in subpolar regions might not be applicable to bryophytes. Rather, the strong climatic oscillations in these regions may have served as a driving force of speciation and niche divergence.

The bryophytes Physcomitrium patens and Marchantia polymorpha as model systems for studying evolutionary cell and developmental biology in plants

Bryophytes are nonvascular spore-forming plants. Unlike in flowering plants, the gametophyte (haploid) generation of bryophytes dominates the sporophyte (diploid) generation. A comparison of bryophytes with flowering plants allows us to answer some fundamental questions raised in evolutionary cell and developmental biology. The moss Physcomitrium patens was the first bryophyte with a sequenced genome. Many cell and developmental studies have been conducted in this species using gene targeting by homologous recombination. The liverwort Marchantia polymorpha has recently emerged as an excellent model system with low genomic redundancy in most of its regulatory pathways. With the development of molecular genetic tools such as efficient genome editing, both P. patens and M. polymorpha have provided many valuable insights. Here, we review these advances with a special focus on polarity formation at the cell and tissue levels. We examine current knowledge regarding the cellular mechanisms of polarized cell elongation and cell division, including symmetric and asymmetric cell division. We also examine the role of polar auxin transport in mosses and liverworts. Finally, we discuss the future of evolutionary cell and developmental biological studies in plants.

The evolution of imprinting in plants: beyond the seed

Genomic imprinting results in the biased expression of alleles depending on if the allele was inherited from the mother or the father. Despite the prevalence of sexual reproduction across eukaryotes, imprinting is only found in placental mammals, flowering plants, and some insects, suggesting independent evolutionary origins. Numerous hypotheses have been proposed to explain the selective pressures that favour the innovation of imprinted gene expression and each differs in their experimental support and predictions. Due to the lack of investigation of imprinting in land plants, other than angiosperms with triploid endosperm, we do not know whether imprinting occurs in species lacking endosperm and with embryos developing on maternal plants. Here, we discuss the potential for uncovering additional examples of imprinting in land plants and how these observations may provide additional support for one or more existing imprinting hypotheses.

Cytotoxicity, antimicrobial and antioxidant activities of mosses obtained from open habitats

Mosses are mainly the object of ecological and taxonomic research. This group of plants are still underestimated by scientists in other aspects of research. Recent research has shown that these plants contain remarkable and unique substances with high biological activity. Five species of mosses from a large urban ecosystem were identified for present study. In order to determine their biological potential, multifaceted studies were carried out, including: total phenolics content, antioxidant activity, antimicrobial and antifungal study, cytotoxicity evaluation, and scratch assay to assess pro-regenerative effect in the context of their possible use as the ingredients of biologically active cosmetics. Additionally, determination of individual phenolic compounds in selected extracts of the tested mosses was made. Research showed that Ceratodon purpureus and Dryptodon pulvinatus extracts had the greatest potential as antioxidants and antimicrobial activity. The cytotoxicity assessment indicated that the extracts from Dryptodon pulvinatus and Rhytidiadelphus squarossus exerted the strongest negative effect on mouse fibroblast line L929 viability at higher concentrations. While, the extract from Tortulla muralis best stimulated human foreskin fibroblast line HFF-1 proliferation and wound healing. The research on individual phenolic compounds content in the extracts tested indicated over 20 peaks on UPLC chromatograms. The conducted study has shown that mosses, especially so far unexplored species of open ecosystems, and e.g. epilytic habitats, may be a valuable source of biologically active substances and thus may constitute important medical and cosmetic possibilities.

Biochemical and functional characterization of two microbial type terpene synthases from moss Stereodon subimponens

Terpenes constitute a large class of plant secondary metabolites. Usually, there is only one type of terpene synthase in seed plants, which is called typical plant terpene synthase. Currently, as a new family of plant terpene synthases, microbial terpene synthase-like (MTPSL) is identificated in nonseed plants. However, our knowledge about the biological function of most MTPSLs in nonseed plants is very limited. Here, we investigated the biochemical and functional characterization of the enzymes encoded by two MTPSLs from moss Stereodon subimponens, SsMTPSL1 and SsMTPSL2. A phylogenetic tree analysis showed that SsMTPSL1 and SsMTPSL2 are homologous to AaMTPSL1, AaMTPSL3, ApMTPSL1, and ApMTPSL3 from hornworts. The enzyme activity experiment demonstrated that SsMTPSL1 has monoterpene synthase and sesquiterpene synthase activity, and SsMTPSL2 has monoterpene synthase activity. Next, we selected SsMTPSL1 to study its biochemical functions. Anti-bacterial activity test in vitro showed that the products of SsMTPSL1 have an anti-bacterial effect on Escherichia coli, Pseudomonas syringae pv. Tomato DC3000 (Pst DC3000), and Staphylococcus aureus. To further understand the function of SsMTPSL1, the transgenic Arabidopsis thaliana plant of SsMTPSL1 is inoculated by Pst DC3000, and the result showed that SsMTPSL1 enhances the resistance of A. thaliana to Pst DC3000. All in all, this study provides new information about the functions of moss MTPSLs.

The Pioneering Role of Bryophytes in Ecological Restoration of Manganese Waste Residue Areas, Southwestern China

The mining of manganese brings excellent wealth to humankind. However, it destroys the ecological environment, mainly manifested as heavy metal pollution and vegetation destruction. The restoration of ecological vegetation in manganese mining areas has become an important work after mineral exploitation. The effect of bryophytes on ecological restoration in mining areas is irreplaceable. The bryophytes diversity and its pioneering role in two types of manganese waste residue areas were investigated in Guizhou province, China. The results showed that there were 24 species of mosses in mine waste slag areas, and all of them belonged to 6 families and 15 genera; the species Gymnostomum subrigidulum, Pohlia gedeana, and Bryum atrovirens were the dominant mosses. There were 6 species of mosses in electrolytic manganese slag areas, and all of them belonged to 5 families and 5 genera. The dominant moss was B. atrovirens. The bryophytes diversity in the electrolytic manganese slag areas with lower pH was poorer than that in mine slag areas. The accumulation of heavy metals in mosses showed that B. atrovirens collected from two types of areas had a strong ability to accumulate Mn with the cumulants 5588.00 μg/g and 4283.41 μg/g, respectively. All mosses had a strong enrichment ability to Cd. It indicated that mosses had strong tolerance to heavy metals. Bryophytes increased the available nutrients and bacterial community diversity of mosses growth substrates in two types of areas. Besides, we studied the relationships between bacterial community structure and soil factors. The main soil factor affecting the bacterial community structure was available nitrogen (AN) in mine waste slag areas, while it was pH in the electrolytic manganese residue areas. The systematic study suggested that bryophytes increased the available nutrients and the microbial community diversity of the growth substrates in manganese waste residue areas, which provided the basic conditions for the growth of vascular plants.

Large-Scale Phylogenomic Analyses Reveal the Monophyly of Bryophytes and Neoproterozoic Origin of Land Plants

The relationships among the four major embryophyte lineages (mosses, liverworts, hornworts, vascular plants) and the timing of the origin of land plants are enigmatic problems in plant evolution. Here, we resolve the monophyly of bryophytes by improving taxon sampling of hornworts and eliminating the effect of synonymous substitutions. We then estimate the divergence time of crown embryophytes based on three fossil calibration strategies, and reveal that maximum calibration constraints have a major effect on estimating the time of origin of land plants. Moreover, comparison of priors and posteriors provides a guide for evaluating the optimal calibration strategy. By considering the reliability of fossil calibrations and the influences of molecular data, we estimate that land plants originated in the Precambrian (980–682 Ma), much older than widely recognized. Our study highlights the important contribution of molecular data when faced with contentious fossil evidence, and that fossil calibrations used in estimating the timescale of plant evolution require critical scrutiny.

Bryophytes are predicted to lag behind future climate change despite their high dispersal capacities

The extent to which species can balance out the loss of suitable habitats due to climate warming by shifting their ranges is an area of controversy. Here, we assess whether highly efficient wind-dispersed organisms like bryophytes can keep-up with projected shifts in their areas of suitable climate. Using a hybrid statistical-mechanistic approach accounting for spatial and temporal variations in both climatic and wind conditions, we simulate future migrations across Europe for 40 bryophyte species until 2050. The median ratios between predicted range loss vs expansion by 2050 across species and climate change scenarios range from 1.6 to 3.3 when only shifts in climatic suitability were considered, but increase to 34.7–96.8 when species dispersal abilities are added to our models. This highlights the importance of accounting for dispersal restrictions when projecting future distribution ranges and suggests that even highly dispersive organisms like bryophytes are not equipped to fully track the rates of ongoing climate change in the course of the next decades.

Bryophytes tend to be sensitive to warming, but their high dispersal ability could help them track climate change. Here the authors combine correlative niche models and mechanistic dispersal models for 40 European bryophyte species under RCP4.5 and RCP8.5, finding that most of these species are unlikely to track climate change over the coming decades.

A Comprehensive Toolkit for Quick and Easy Visualization of Marker Proteins, Protein-Protein Interactions and Cell Morphology in Marchantia polymorpha

Even though stable genomic transformation of sporelings and thalli of Marchantia polymorpha is straightforward and efficient, numerous problems can arise during critical phases of the process such as efficient spore production, poor selection capacity of antibiotics or low transformation efficiency. It is therefore also desirable to establish quick methods not relying on stable transgenics to analyze the localization, interactions and functions of proteins of interest. The introduction of foreign DNA into living cells via biolistic mechanisms has been first reported roughly 30 years ago and has been commonly exploited in established plant model species such as Arabidopsis thaliana or Nicotiana benthamiana. Here, we report the fast and reliable transient biolistic transformation of Marchantia thallus epidermal cells using fluorescent protein fusions. We present a catalog of fluorescent markers which can be readily used for tagging of a variety of subcellular compartments. Moreover, we report the functionality of the bimolecular fluorescence complementation (BiFC) in M. polymorpha with the example of the p-body markers MpDCP1/2. Finally, we provide standard staining procedures for live cell imaging in M. polymorpha, applicable to visualize cell boundaries or cellular structures, to complement or support protein localizations and to understand how results gained by transient transformations can be embedded in cell architecture and dynamics. Taken together, we offer a set of easy and quick tools for experiments that aim at understanding subcellular localization, protein-protein interactions and thus functions of proteins of interest in the emerging early diverging land plant model M. polymorpha.

The wave of gene advance under diverse systems of mating

Mating systems will influence gene spread across the natural distribution of a plant species. Existing theories have not fully explored the role of mating systems on the wave of advance of an advantageous gene. Here, we develop a theory to account for the rate of spread of both advantageous and neutral genes under different mating systems, based on migration-selection processes. We show that a complex relationship exists between selfing rate and the speed of gene spread. The interaction of selfing with gametophytic selection shapes the traveling wave of the advantageous gene. Selfing can impede (or enhance) the spread of an advantageous gene in the presence (or absence) of gametophytic selection. The interaction of selfing with recombination shapes the spread of a neutral gene. Linkage disequilibrium, mainly generated by selfing, enhances the traveling wave of the neutral gene that is tightly linked with the selective gene. Recombination gradually breaks down the genetic hitchhiking effects along the direction of advantageous gene spread, yielding decreasing waves of advance of neutral genes. The stochastic process does not alter the pattern of selfing effects except for increasing the uncertainty of the waves of advance of both advantageous and neutral genes. This theory helps us to explain how mating systems act as a barrier to spread of adaptive and neutral genes, and to interpret species cohesion maintained by a low level of adaptive gene flow.

Bryophyte flora of two Natural Parks in Amapá: richness, composition and new records

The aim of this study is to investigate the richness and composition of the bryophytes of two Municipal Natural Parks in Amapá, eastern Amazon. Bryophytes were collected in the Arivaldo Gomes Barreto Municipal Natural Park (AGBMNP), Macapá municipality, and Cancão Municipal Natural Park (CMNP), Serra do Navio municipality, in October 2010 and October 2012, respectively. Ten plots of 10 x 10 m were established in each park for sampling, and, in addition, random collections were made, in order to maximize the knowledge on the local bryophyte flora. In total, 53 species were identified in AGBMNP, and 110 species in CMNP. The results shown a lower richness in AGBMNP than in CMNP, which may be related to the own size of each park, the level of conservation, and its localization. In terms of abundance, the neotropical pattern and the species locally rare were most representative in both parks, however, the floristic composition diverged. The AGBMNP is composed mostly by generalist species, while the CMNP by both generalists and shade specialists. The present study recorded 54% of the known bryophyte flora of Amapá, 63 new records for the state and, in addition, three new records for the North region of Brazil.

Cell Division Patterns in the Peristomial Layers of the Moss Genus Costesia: Two Hypotheses and a Third Solution

The Chilean endemic genus Costesia belongs to the Gigaspermaceae, one of the most basal groups of arthrodontous mosses. While none of the species in this family has a peristome, earlier stages of sporophyte development often disclose its basic structure. The study of Costesia sporophytes at the early stages of development was conducted to identify possible similarities with Diphyscium, the genus sister to Gigaspermaceae plus all other arthrodontous mosses in the moss phylogenetic tree. Diphyscium shares a strongly unequal cell division pattern with the Dicranidae. In groups more closely related to Diphyscium, as it is the case of Costesia, this pattern is not known. Our study of Costesia found only irregular presence of slightly unequal cell divisions that may then be considered as a plesiomorphic state in peristomate mosses. The most frequently present pattern revealed in Costesia is common with the Polytrichaceae, a more basal moss group with nematodontous peristomes.

Tradeoffs between phenotypic plasticity and local adaptation influence the ecophysiology of the moss, Sphagnum magellanicum

Bryophytes are a diverse plant group and are functionally different from vascular plants. Yet, their peculiarities are rarely considered in the theoretical frameworks for plants. Currently, we lack information about the magnitude and the importance of intraspecific variability in the ecophysiology of bryophytes and how these might translate to local adaptation-a prerequisite for adaptive evolution. Capitalizing on two ecologically distinct (hummock and hollow) phenotypes of Sphagnum magellanicum, we explored the magnitude and pattern of intraspecific variability in this species and asked whether the environmental-mediated changes in shoot and physiological traits are due to phenotypic plasticity or local adaptation. Size, pigmentation, and habitat type that distinguished the phenotypes in the field did not influence the trait responses under a transplant and factorial experiment. In addition, the magnitude and pattern of trait variability (e.g., branch, stem and capitulum mass) changed with the treatments, which suggest that trait responses were due largely to phenotypic plasticity. The trait responses also suggest that the ecophysiological needs for mosses to grow in clumps, where they maintain a uniform growth may have an overriding effect over the potential for a fixed adaptive response to environmental heterogeneity, which would constrain local adaptation. We conclude that extending the trait-based framework to mosses or making comparisons between mosses and vascular plants under any theoretical framework would only be meaningful to the extent that growth form and dispersal strategies are considered.

Mosses: Versatile plants for biotechnological applications

Mosses have long been recognized as powerful experimental tools for the elucidation of complex processes in plant biology. Recent increases in the availability of sequenced genomes and mutant collections, the establishment of novel technologies for targeted mutagenesis, and the development of viable protocols for large-scale production in bioreactors are now transforming mosses into one of the most versatile tools for biotechnological applications. In the present review, we highlight the astonishing biotechnological potential of mosses and how these plants are being exploited for industrial, pharmaceutical, and environmental applications. We focus on the biological features that support their use as model organisms for basic and applied research, and how these are being leveraged to explore the biotechnological potential in an increasing number of species. Finally, we also provide an overview of the available moss cultivation protocols from an industrial perspective, offering insights into batch operations that are not yet well established or do not even exist in the literature. Our goal is to bolster the use of mosses as factories for the biosynthesis of molecules of interest and to show how these species can be harnessed for the generation of novel and commercially useful bioproducts.

An endocannabinoid catabolic enzyme FAAH and its paralogs in an early land plant reveal evolutionary and functional relationship with eukaryotic orthologs

Endocannabinoids were known to exist only among Animalia but recent report of their occurrence in early land plants prompted us to study its function and metabolism. In mammals, anandamide, as an endocannabinoid ligand, mediates several neurological and physiological processes, which are terminated by fatty acid amide hydrolase (FAAH). We identified nine orthologs of FAAH in the moss Physcomitrella patens (PpFAAH1 to PpFAAH9) with amidase signature and catalytic triad. The optimal amidase activity for PpFAAH1 was at 37 °C and pH 8.0, with higher specificity to anandamide. Further, the phylogeny and predicted structural analyses of the nine paralogs revealed that PpFAAH1 to PpFAAH4 were closely related to plant FAAH while PpFAAH6 to PpFAAH9 were to the rat FAAH, categorized based on the membrane binding cap, membrane access channel and substrate binding pocket. We also identified that a true 'dynamic paddle' that is responsible for tighter regulation of FAAH is recent in vertebrates and absent or not fully emerged in plants and non-vertebrates. These data reveal evolutionary and functional relationship among eukaryotic FAAH orthologs and features that contribute to versatility and tighter regulation of FAAH. Future studies will utilize FAAH mutants of moss to elucidate the role of anandamide in early land plants.

Water Extract of Cryphaea heteromalla (Hedw.) D. Mohr Bryophyte as a Natural Powerful Source of Biologically Active Compounds

Bryophytes comprise of the mosses, liverworts, and hornworts. Cryphaea heteromalla, (Hedw.) D. Mohr, is a non-vascular lower plant belonging to mosses group. To the date, the most chemically characterized species belong to the liverworts, while only 3.2% and 8.8% of the species belonging to the mosses and hornworts, respectively, have been investigated. In this work, we present Folin-Ciocalteu and oxygen radical absorbance capacity (ORAC) data related to crude extracts of C. heteromalla obtained by three different extraction solvents: pure water (WT), methanol:water (80:20 v/v) (MET), and ethanol:water (80:20 v/v) (ETH). The water extract proved to be the best solvent showing the highest content of biophenols and the highest ORAC value. The C. heteromalla-WT extract was investigated by HPLC-TOF/MS (High Performance Liquid Chromatography-Time of Flight/Mass Spectrometry) allowing for the detection of 14 compounds, five of which were phenolic compounds, derivatives of benzoic, caffeic, and coumaric acids. Moreover, the C. heteromalla WT extract showed a protective effect against reactive oxygen species (ROS) generation induced by tert-butyl hydroperoxide (TBH) on the murine NIH-3T3 fibroblast cell line.

Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species

The central aim in ecometabolomics and chemical ecology is to pinpoint chemical features that explain molecular functioning. The greatest challenge is the identification of compounds due to the lack of constitutive reference spectra, the large number of completely unknown compounds, and bioinformatic methods to analyze the big data. In this study we present an interdisciplinary methodological framework that extends ultra-performance liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC/ESI-QTOF-MS) with data-dependent acquisition (DDA-MS) and the automated in silico classification of fragment peaks into compound classes. We synthesize findings from a prior study that explored the influence of seasonal variations on the chemodiversity of secondary metabolites in nine bryophyte species. Here we reuse and extend the representative dataset with DDA-MS data. Hierarchical clustering, heatmaps, dbRDA, and ANOVA with post-hoc Tukey HSD were used to determine relationships of the study factors species, seasons, and ecological characteristics. The tested bryophytes showed species-specific metabolic responses to seasonal variations (50% vs. 5% of explained variation). Marchantia polymorpha, Plagiomnium undulatum, and Polytrichum strictum were biochemically most diverse and unique. Flavonoids and sesquiterpenoids were upregulated in all bryophytes in the growing seasons. We identified ecological functioning of compound classes indicating light protection (flavonoids), biotic and pathogen interactions (sesquiterpenoids, flavonoids), low temperature and desiccation tolerance (glycosides, sesquiterpenoids, anthocyanins, lactones), and moss growth supporting anatomic structures (few methoxyphenols and cinnamic acids as part of proto-lignin constituents). The reusable bioinformatic framework of this study can differentiate species based on automated compound classification. Our study allows detailed insights into the ecological roles of biochemical constituents of bryophytes with regard to seasonal variations. We demonstrate that compound classification can be improved with adding constitutive reference spectra to existing spectral libraries. We also show that generalization on compound classes improves our understanding of molecular ecological functioning and can be used to generate new research hypotheses.

One thousand plant transcriptomes and the phylogenomics of green plants

Green plants (Viridiplantae) include around 450,000-500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

Building new insights in plant gametogenesis from an evolutionary perspective

Extant bryophytes are thought to preserve characteristics of ancestral land plants, with a life cycle dominated by the haploid gametophyte. The gametophyte produces gametes in specialized organs that differentiate after an extensive phase of vegetative development. During land plant evolution, these organs became extremely reduced. As a result, in flowers of angiosperms the haploid phase of the life cycle is reduced to few-celled gametophytes, namely the embryo sac (female) and pollen (male). Although many factors contributing to gametogenesis have been identified in flowering plants, the extreme reduction of the gametophytes has prevented a clear molecular dissection of key processes of gametogenesis. Recent studies in the model bryophyte Marchantia polymorpha have identified conserved transcription factors regulating the equivalent steps in the sexual reproduction of land plants. These include FEMALE GAMETOPHYTE MYB for female gametophyte development, BONOBO for gamete progenitor cell specification, DUO POLLEN1 for sperm differentiation and members of the RWP-RK domain family for female gamete formation. These studies demonstrate that M. polymorpha is a powerful model to untangle the core processes of gametogenesis in land plants. We anticipate that a deeper understanding of gametogenesis in bryophytes will circumscribe the origin of plant germ cells and define the differentiation programmes of sperm and eggs.

Ancient duplications and grass-specific transposition influenced the evolution of LEAFY transcription factor genes

The LFY transcription factor gene family are important in the promotion of cell proliferation and floral development. Understanding their evolution offers an insight into floral development in plant evolution. Though a promiscuous transition intermediate and a gene duplication event within the LFY family had been identified previously, the early evolutionary path of this family remained elusive. Here, we reconstructed the LFY family phylogeny using maximum-likelihood and Bayesian inference methods incorporating LFY genes from all major lineages of streptophytes. The well-resolved phylogeny unveiled a high-confidence duplication event before the functional divergence of types I and II LFY genes in the ancestry of liverworts, mosses and tracheophytes, supporting sub-functionalization of an ancestral promiscuous gene. The identification of promiscuous genes in Osmunda suggested promiscuous LFY genes experienced an ancient transient duplication. Genomic synteny comparisons demonstrated a deep genomic positional conservation of LFY genes and an ancestral lineage-specific transposition activity in grasses.

Rapid turnover of life-cycle-related genes in the brown algae

BACKGROUND

Sexual life cycles in eukaryotes involve a cyclic alternation between haploid and diploid phases. While most animals possess a diploid life cycle, many plants and algae alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. In many algae, gametophytes and sporophytes are independent and free-living and may present dramatic phenotypic differences. The same shared genome can therefore be subject to different, even conflicting, selection pressures during each of the life cycle generations. Here, we analyze the nature and extent of genome-wide, generation-biased gene expression in four species of brown algae with contrasting levels of dimorphism between life cycle generations.

RESULTS

We show that the proportion of the transcriptome that is generation-specific is broadly associated with the level of phenotypic dimorphism between the life cycle stages. Importantly, our data reveals a remarkably high turnover rate for life-cycle-related gene sets across the brown algae and highlights the importance not only of co-option of regulatory programs from one generation to the other but also of a role for newly emerged, lineage-specific gene expression patterns in the evolution of the gametophyte and sporophyte developmental programs in this major eukaryotic group. Moreover, we show that generation-biased genes display distinct evolutionary modes, with gametophyte-biased genes evolving rapidly at the coding sequence level whereas sporophyte-biased genes tend to exhibit changes in their patterns of expression.

CONCLUSION

Our analysis uncovers the characteristics, expression patterns, and evolution of generation-biased genes and underlines the selective forces that shape this previously underappreciated source of phenotypic diversity.

Mosses in Low Earth Orbit: Implications for the Limits of Life and the Habitability of Mars

As a part of the European Space Agency mission "EXPOSE-R2" on the International Space Station (ISS), the BIOMEX (Biology and Mars Experiment) experiment investigates the habitability of Mars and the limits of life. In preparation for the mission, experimental verification tests and scientific verification tests simulating different combinations of abiotic space- and Mars-like conditions were performed to analyze the resistance of a range of model organisms. The simulated abiotic space- and Mars-stressors were extreme temperatures, vacuum, and Mars-like surface ultraviolet (UV) irradiation in different atmospheres. We present for the first time simulated space exposure data of mosses using plantlets of the bryophyte genus Grimmia, which is adapted to high altitudinal extreme abiotic conditions at the Swiss Alps. Our preflight tests showed that severe UVR_200-400nm irradiation with the maximal dose of 5 and 6.8 × 10⁵ kJ·m^-2, respectively, was the only stressor with a negative impact on the vitality with a 37% (terrestrial atmosphere) or 36% reduction (space- and Mars-like atmospheres) in photosynthetic activity. With every exposure to UVR_200-400nm 10⁵ kJ·m^-2, the vitality of the bryophytes dropped by 6%. No effect was found, however, by any other stressor. As the mosses were still vital after doses of ultraviolet radiation (UVR) expected during the EXPOSE-R2 mission on ISS, we show that this earliest extant lineage of land plants is highly resistant to extreme abiotic conditions.

Mating system shifts a species' range

Understanding the ecological and evolutionary mechanisms that shape a species' range is an important goal in evolutionary biology. Evidence indicates that mating system is an effective predictor of the global range of native species or naturalized alien plants, but the mechanisms underlying this predictability are not elaborated. Here, we develop a theoretical model to account for the ranges of plants under different mating systems based on migration-selection processes (an idea proposed by Haldane). The model includes alternation of gametophyte and sporophyte generations in one life cycle and the dispersal of haploid pollen and diploid seeds as vectors for gene flow. We show that the interaction between selfing rates and gametophytic selection determines the role of mating system in shaping a species' range. Selfing restricts the species' range under gametophytic selection in nonrandom mating systems, but expands the species' range under the absence of gametophytic selection in any mating system. Gametophytic selection slightly restricts the species' range in random mating. Both logarithmic and logistic models of population demography yield similar conclusions in the case of fixed or evolving genetic variance. The theory also helps to explain a broader relationship between mating system and range size following biological invasion or plant naturalization.