Early Land Plants
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Nitrogen deposition drives loss of moss cover in alpine moss–sedge heath via lowered C : N ratio and accelerated decomposition

In alpine ecosystems, nitrogen (N) deposition has been linked to plant community composition change, including loss of bryophytes and increase of graminoids. Since bryophyte growth is stimulated by increased N availability, it has been hypothesized that loss of bryophyte cover is driven by enhanced decomposition. As bryophyte mats are a significant carbon (C) store, their loss may impact C storage in these ecosystems.
We used an N deposition gradient across 15 sites in the UK to examine effects of N deposition on bryophyte litter quality, decomposition and C and N stocks in Racomitrium moss–sedge heath.
Increasing N deposition reduced C : N in bryophyte litter, which in turn enhanced decomposition. Soil N stocks increased significantly in response to increased N deposition, and soil C : N declined. However, depletion of the bryophyte mat and its replacement by graminoids under high N deposition was not associated with a change in total ecosystem C stocks.
We conclude that decomposition processes in Racomitrium heath are very sensitive to N deposition and provide a mechanism by which N deposition drives depletion of the bryophyte mat. Nitrogen deposition did not measurably alter C stocks, but changes in soil N stocks and C : N suggest the ecosystem is becoming N saturated.
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Frontiers | Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales) | Plant Science

Frontiers | Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales) | Plant Science | Early Land Plants | Scoop.it
Ferns are unique among land plants in having sporophyte and gametophyte phases that are both free living and fully independent. Here, we examine patterns of sporophytic and gametophytic gene expression in the fern Polypodium amorphum, a member of the homosporous polypod lineage that comprises 80% of extant fern diversity, to assess how expression of a common genome is partitioned between two morphologically, ecologically, and nutritionally independent phases. Using RNA-sequencing, we generated transcriptome profiles for three replicates of paired samples of sporophyte leaf tissue and whole gametophytes to identify genes with significant differences in expression between the two phases. We found a nearly 90% overlap in the identity and expression levels of the genes expressed in both sporophytes and gametophytes, with less than 3% of genes uniquely expressed in either phase. We compare our results to those from similar studies to establish how phase-specific gene expression varies among major land plant lineages. Notably, despite having greater similarity in the identity of gene families shared between P. amorphum and angiosperms, P. amorphum has phase-specific gene expression profiles that are more like bryophytes and lycophytes than seed plants. Our findings suggest that shared patterns of phase-specific gene expression among seed-free plants likely reflect having relatively large, photosynthetic gametophytes (compared to the gametophytes of seed plants that are highly reduced). Phylogenetic analyses were used to further investigate the evolution of phase-specific expression for the phototropin, terpene synthase, and MADS-box gene families.
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Stepwise evolution of supercomplex formation with photosystem I is required for stabilization of chloroplast NADH dehydrogenase‐like complex: Lhca5‐dependent supercomplex formation in Physcomitrell...

In angiosperms, such as Arabidopsis and barley, the chloroplast NADH dehydrogenase‐like (NDH) complex associates with two copies of photosystem I (PSI) supercomplex to form an NDH−PSI supercomplex for the stabilization of the NDH complex. Two linker proteins, Lhca5 and Lhca6, are members of the light‐harvesting complex I (LHCI) family and mediate this supercomplex formation. The liverwort Marchantia polymorpha has branched from the basal land plant lineage and has neither Lhca5 nor Lhca6. Consequently, the NDH complex does not form a supercomplex with PSI in this plant. The Lhca6 gene does not seem to exist also in the moss Physcomitrella patens (Physcomitrella). Conversely, the Lhca5 gene has been found in Physcomitrella, although experimental evidence is still lacking for its contribution to NDH−PSI supercomplex formation as a linker. Here, we biochemically characterized the Lhca5 knock‐out mutant (lhca5) in Physcomitrella. The NDH−PSI supercomplex observed in wild‐type Physcomitrella was absent in the lhca5 mutant. Lhca5 protein was detected in this NDH−PSI supercomplex. Some PSI and NDH subunits were co‐immunoprecipitated with Lhca5−HA. These results indicate that the Physcomitrella gene is the functional ortholog of Lhca5 reported in Arabidopsis. Between Physcomitrella and Arabidopsis, the stromal loop region is highly conserved in Lhca5 proteins but not in other LHCI members. We found that Lhca5 contributed to the stable accumulation of the NDH complex, but part of the NDH complex was still sensitive to high light intensity, even in the wild‐type. We considered that angiosperms acquired another linker protein, Lhca6, to further stabilize the NDH complex.
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Novel gateway binary vectors for rapid tripartite DNA assembly and promoter analysis with various reporters and tags in the liverwort Marchantia polymorpha

Novel gateway binary vectors for rapid tripartite DNA assembly and promoter analysis with various reporters and tags in the liverwort Marchantia polymorpha | Early Land Plants | Scoop.it
The liverwort Marchantia polymorpha is an emerging model species for basal lineage plant research. In this study, two Gateway cloning-compatible binary vector series, R4pMpGWB and R4L1pMpGWB, were generated to facilitate production of transgenic M. polymorpha. The R4pMpGWB series allows tripartite recombination of any promoter and any coding sequence with a specific reporter or tag. Reporters/tags for the R4pMpGWB series are GUS, ELuc(PEST), FLAG, 3×HA, 4×Myc, mRFP1, Citrine, mCitrine, ER-targeted mCitrine and nucleus-targeted mCitrine. The R4L1pMpGWB series is suitable for promoter analysis. R4L1pMpGWB vector structure is the same as that of R4pMpGWB vectors, except that the attR2 site is replaced with attL1, enabling bipartite recombination of any promoter with a reporter or tag. Reporters/tags for the R4L1pMpGWB series are GUS, G3GFP-GUS, LUC, ELuc(PEST), Citrine, mCitrine, ER-targeted mCitrine and mCitrine-NLS. Both vector series were functional in M. polymorpha cells. These vectors will facilitate the design and assembly of plasmid constructs and generation of transgenic M. polymorpha.
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Biochemical characterization of peroxidases from the moss Dicranum scoparium - ScienceDirect

Mosses are a convenient model to study stress responses of plants because of their remarkable stress tolerance. Peroxidase (EC 1.11.1.7) activities were tested in three moss species, namely Dicranum scoparium, Hylocomium splendens and Pleurozium schreberi growing together in the same location in a boreal forest. Peroxidase activity in D. scoparium was twice as high as in other mosses. Total peroxidase activity in unstressed D. scoparium was constitutively high; furthermore, long-term desiccation caused a significant increase in activity after 48 h of drying. Interestingly, when thalli desiccated for a week were rapidly rehydrated, peroxidase activity initially declined and then increased after 2 h rehydration. Diverse anionic and cationic isoforms were detected by native isoelectric focusing and PAGE of both crude extracts and partially purified peroxidases. The ability of peroxidases from D. scoparium to produce superoxide radical (O2•−) was confirmed using the 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT) reduction assay and in-gel nitroblue tetrazolium chloride (NBT) staining; specific O2•− producing isoforms were revealed using 2D electrophoresis. Given a quinone and chelated Fe3+D. scoparium could produce extracellular hydroxyl radical (•OH), and production was increased by desiccation/rehydration stress. The possible roles of peroxidases and quinone reductases in apoplastic •OH production is discussed. Our data demonstrate that D. scoparium possesses high constitutive peroxidase activity that can be further increased by desiccation stress. Among the diverse moss peroxidases, some anionic isoforms displayed both pro- and antioxidative activities. These findings suggest that the ability of peroxidases to produce and detoxify reactive oxygen species is an evolutionarily ancient characteristic, important for plant stress tolerance.
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Contrasting pectin polymers in guard cell walls of Arabidopsis and the hornwort Phaeoceros reflect physiological differences | Annals of Botany | Oxford Academic

Background and Aims
In seed plants, stomata regulate CO2 acquisition and water relations via transpiration, while minimizing water loss. Walls of guard cells are strong yet flexible because they open and close the pore by changing shape over the substomatal cavity. Pectins are necessary for wall flexibility and proper stomata functioning. This study investigates the differences in pectin composition in guard cells of two taxa that represent key lineages of plants with stomata: Arabidopsis, an angiosperm with diurnal stomatal activity, and Phaeoceros, a bryophyte that lacks active stomatal movement.

Methods
Using immunolocalization techniques in transmission electron microscopy, this study describes and compares the localization of pectin molecule epitopes essential to stomata function in guard cell walls of Arabidopsis and Phaeoceros.

Key Results
In Arabidopsis, unesterified homogalacturonans very strongly localize throughout guard cell walls and are interspersed with arabinan pectins, while methyl-esterified homogalacturonans are restricted to the exterior of the wall, the ledges and the junction with adjacent epidermal cells. In contrast, arabinans are absent in Phaeoceros, and both unesterified and methyl-esterified homogalacturonans localize throughout guard cell walls.

Conclusions
Arabinans and unesterified homogalacturonans are required for wall flexibility, which is consistent with active regulation of pore opening in Arabidopsis stomata. In contrast, the lack of arabinans and high levels of methyl-esterified homogalacturonans in guard cell walls of Phaeoceros are congruent with the inability of hornwort stomata to open and close with environmental change. Comparisons across groups demonstrate that variations in guard cell wall composition reflect different physiological activity of stomata in land plants.

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Order‐level fern plastome phylogenomics: new insights from Hymenophyllales - Kuo - - American Journal of Botany - Wiley Online Library

Premise of the Study
Filmy ferns (Hymenophyllales) are a highly specialized lineage, having mesophyll one‐cell layer thick and inhabiting particularly shaded and humid environments. The phylogenetic placement of Hymenophyllales has been inconclusive, and while over 87 whole fern plastomes have been published, none was from Hymenophyllales. To better understand the evolutionary history of filmy ferns, we sequenced the first complete plastome for this order.

Methods
We compiled a phylogenomic plastome data set encompassing all 11 fern orders, and reconstructed phylogenies using different data types (nucleotides, codons, and amino acids) and partition schemes (codon positions and loci). To infer the evolution of fern plastome organization, we coded plastome features, including inversions, inverted repeat boundary shifts, gene losses, and tRNA anticodon sequences as characters, and reconstructed the ancestral states for these characters.

Key Results
We discovered a suite of novel, Hymenophyllales‐specific plastome structures that likely resulted from repeated expansions and contractions of the inverted repeat regions. Our phylogenetic analyses reveal that Hymenophyllales is highly supported as either sister to Gleicheniales or to Gleicheniales + the remaining non‐Osmundales leptosporangiates, depending on the data type and partition scheme.

Conclusions
Although our analyses could not confidently resolve the phylogenetic position of Hymenophyalles, the results here highlight the danger of drawing conclusions from “all‐in” phylogenomic data set without exploring potential inconsistencies in the data. Finally, our first order‐level reconstruction of fern plastome structural evolution provides a useful framework for future plastome research.
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Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes

In Eco-Metabolomics interactions are studied of non-model organisms in their natural environment and relations are made between biochemistry and ecological function. Current challenges when processing such metabolomics data involve complex experiment designs which are often carried out in large field campaigns involving multiple study factors, peak detection parameter settings, the high variation of metabolite profiles and the analysis of non-model species with scarcely characterised metabolomes. Here, we present a dataset generated from 108 samples of nine bryophyte species obtained in four seasons using an untargeted liquid chromatography coupled with mass spectrometry acquisition method (LC/MS). Using this dataset we address the current challenges when processing Eco-Metabolomics data. Here, we also present a reproducible and reusable computational workflow implemented in Galaxy focusing on standard formats, data import, technical validation, feature detection, diversity analysis and multivariate statistics. We expect that the representative dataset and the reusable processing pipeline will facilitate future studies in the research field of Eco-Metabolomics.
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Negative regulation of conserved RSL class I bHLH transcription factors evolved independently among land plants

Basic helix-loop-helix transcription factors encoded by RSL class I genes control a gene regulatory network that positively regulates the development of filamentous rooting cells - root hairs and rhizoids - in land plants. The GLABRA2 transcription factor negatively regulates these genes in the angiosperm Arabidopsis thaliana. To find negative regulators of RSL class I genes in early diverging land plants we conducted a mutant screen in the liverwort Marchantia polymorpha. This identified FEW RHIZOIDS1 (MpFRH1) microRNA (miRNA) that negatively regulates the RSL class I gene MpRSL1. The miRNA and its mRNA target constitute a feedback mechanism that controls epidermal cell differentiation. MpFRH1 miRNA target sites are conserved among liverwort RSL class I mRNAs but are not present in RSL class I mRNAs of other land plants. These findings indicate that while RSL class I genes are ancient and conserved, independent negative regulatory mechanisms evolved in different lineages during land plant evolution.
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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 examined the roles of AN homologs in the model bryophyte, M. polymorpha (MpAN). Mpan knock-out 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, while 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.
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Genome-wide organellar analyses from the hornwort Leiosporoceros dussii show low frequency of RNA editing

Genome-wide organellar analyses from the hornwort Leiosporoceros dussii show low frequency of RNA editing | Early Land Plants | Scoop.it
Because hornworts occupy a pivotal position in early land colonization as sister to other bryophytes, sister to tracheophytes, or sister to all other land plants, a renewed interest has arisen in their phylogenetic diversity, morphology, and genomes. To date, only five organellar genome sequences are available for hornworts. We sequenced the plastome (155,956 bp) and mitogenome (212,153 bp) of the hornwort Leiosporoceros dussii, the sister taxon to all hornworts. The Leiosporoceros organellar genomes show conserved gene structure and order with respect to the other hornworts and other bryophytes. Additionally, using RNA-seq data we quantified the frequency of RNA-editing events (the canonical C-to-U and the reverse editing U-to-C) in both organellar genomes. In total, 109 sites were found in the plastome and 108 in the mitogenome, respectively. The proportion of edited sites corresponds to 0.06% of the plastome and 0.05% of the mitogenome (in reference to the total genome size), in contrast to 0.58% of edited sites in the plastome of Anthoceros angustus (161,162 bp). All edited sites in the plastome and 88 of 108 sites in the mitogenome are C-to-U conversions. Twenty reverse edited sites (U-to-C conversions) were found in the mitogenome (17.8%) and none in the plastome. The low frequency of RNA editing in Leiosporoceros, which is nearly 88% less than in the plastome of Anthoceros and the mitogenome of Nothoceros, indicates that the frequency of RNA editing has fluctuated during hornwort diversification. Hornworts are a pivotal land plant group to unravel the genomic implications of RNA editing and its maintenance despite the evident evolutionary disadvantages.
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Functional diversity and convergence in the evolution of plant reproductive structures | Annals of Botany | Oxford Academic

Background and Aims
Structures that simultaneously perform many functional roles are likely to show a variety of morphological solutions to these demands, and thus probably exhibit high morphological disparity. In contrast, specialization for a few simple functions should result in a more limited suite of morphologies. We explore this idea using lycopsid reproductive structures, which, throughout their history, have performed a limited set of functional roles compared with the reproductive structures of other plant groups such as seed plants.

Methods
We scored living and fossil lycopsid taxa for 18 discrete character measurements and several continuous traits, including sporangium size, supporting axis diameter, and strobilus length and width. We used the discrete characters to construct a multivariate morphospace for lycopsid reproductive morphology through time, and the continuous characters to test whether fossil and extant lycopsids show similar patterns of tissue allocation within reproductive structures.

Results
Lycopsids occupy similar areas of reproductive morphospace and show similar patterns of tissue allocation over most of their history, alternating between diffuse fertile zones with leaf-like sporophylls and compact strobili with specialized sporophylls that allow sporangia to be closely packed while also protected during their development. Growth habit also plays an important role in lycopsid reproductive evolution, broadly influencing the size and shape of reproductive structures.

Conclusions
Lycopsid reproductive structures are primarily specialized for densely packaging sporangia, and are consistent with the idea that performing limited functional roles is associated with reduced morphological disparity. Morphologies similar to lycopsid strobili are also found in other groups with simple, wind-dispersed propagules, suggesting that the same processes occur across plant lineages.
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Mode of action and specificity of a chitinase from unicellular microalgae, Euglena gracilis

The unicellular alga, E. gracilis, produces a chitinase consisting of two GH18 catalytic domains (Cat1 and Cat2) and two CBM18 chitin-binding domains (CBD1 and CBD2). Here, we produced a recombinant protein of the Cat2 domain to examine its mode of action as well as specificity. Cat2 hydrolyzed N-acetylglucosamine (A) oligomers (An, n = 4, 5, and 6) and partially N-acetylated chitosans with a non-processive/endo-splitting mode of action. NMR analysis of the product mixture from the enzymatic digestion of chitosan revealed that the reducing ends were exclusively A-unit, and the nearest neighbors of the reducing ends were mostly A-unit but not exclusively. Both A-unit and D-unit were found at the non-reducing ends and the nearest neighbors. These results indicated strong and absolute specificities for subsites − 2 and − 1, respectively, and no preference for A-unit at subsites + 1 and + 2. The same results were obtained from sugar sequence analysis of the individual enzymatic products from the chitosans. The subsite specificities of Cat2 are similar to those of GH18 human chitotriosidase, but differ from those of plant GH18 chitinases. Since the structures of Cat1 and Cat2 resemble to each other (99% similarity in amino acid sequences), Cat1 may hydrolyze the substrate with the same mode of action. Thus, the E. gracilis chitinase appears to act toward chitin polysaccharide chain through a cooperative action of the two endo-splitting catalytic domains, recognizing two contiguous A-units at subsites − 2 and − 1.
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Balancing protection and efficiency in the regulation of photosynthetic electron transport across plant evolution - Alboresi - - New Phytologist - Wiley Online Library

Photosynthetic electron transport requires continuous modulation to maintain the balance between light availability and metabolic demands. Multiple mechanisms for the regulation of electron transport have been identified and are unevenly distributed among photosynthetic organisms. Flavodiiron proteins (FLVs) influence photosynthetic electron transport by accepting electrons downstream of photosystem I to reduce oxygen to water. FLV activity has been demonstrated in cyanobacteria, green algae and mosses to be important in avoiding photosystem I overreduction upon changes in light intensity. FLV‐encoding sequences were nevertheless lost during evolution by angiosperms, suggesting that these plants increased the efficiency of other mechanisms capable of accepting electrons from photosystem I, making the FLV activity for protection from overreduction superfluous or even detrimental for photosynthetic efficiency.
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Sphagnum Species Modulate their Phenolic Profiles and Mycorrhizal Colonization of Surrounding Andromeda polifolia along Peatland Microhabitats

Sphagnum mosses mediate long-term carbon accumulation in peatlands. Given their functional role as keystone species, it is important to consider their responses to ecological gradients and environmental changes through the production of phenolics. We compared the extent to which Sphagnum phenolic production was dependent on species, microhabitats and season, and how surrounding dwarf shrubs responded to Sphagnum phenolics. We evaluated the phenolic profiles of aqueous extracts of Sphagnum fallax and Sphagnum magellanicum over a 6-month period in two microhabitats (wet lawns versus dry hummocks) in a French peatland. Phenolic profiles of water-soluble extracts were measured by UHPLC-QTOF-MS. Andromeda polifolia mycorrhizal colonization was quantified by assessing the intensity of global root cortex colonization. Phenolic profiles of both Sphagnum mosses were species-, season- and microhabitat- dependant. Sphagnum-derived acids were the phenolics mostly recovered; relative quantities were 2.5-fold higher in S. fallax than in S. magellanicum. Microtopography and vascular plant cover strongly influenced phenolic profiles, especially for minor metabolites present in low abundance. Higher mycorrhizal colonization of A. polifolia was found in lawns as compared to hummocks. Mycorrhizal abundance, in contrast to environmental parameters, was correlated with production of minor phenolics in S. fallax. Our results highlight the close interaction between mycorrhizae such as those colonizing A. polifolia and the release of Sphagnum phenolic metabolites and suggest that Sphagnum-derived acids and minor phenolics play different roles in this interaction. This work provides new insight into the ecological role of Sphagnum phenolics by proposing a strong association with mycorrhizal colonization of shrubs.


Via Jean-Michel Ané
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Ancient plants with ancient fungi

Arbuscular mycorrhizas are widespread in land plants including liverworts, some of the closest living relatives of the first plants to colonize land 500 million years ago (MYA). Previous investigations reported near-exclusive colonization of liverworts by the most recently evolved arbuscular mycorrhizal fungi, the Glomeraceae, indicating a recent acquisition from flowering plants at odds with the widely held notion that arbuscular mycorrhizal-like associations in liverworts represent the ancestral symbiotic condition in land plants. We performed an analysis of symbiotic fungi in 674 globally collected liverworts using molecular phylogenetics and electron microscopy. Here, we show every order of arbuscular mycorrhizal fungi colonizes early-diverging liverworts, with non-Glomeraceae being at least 10 times more common than in flowering plants. Arbuscular mycorrhizal fungi in liverworts and other ancient plant lineages (hornworts, lycopods, and ferns) were delimited into 58 taxa and 36 singletons, of which at least 43 are novel and specific to liverworts. The discovery that early plant lineages are colonized by early-diverging fungi supports the hypothesis that arbuscular mycorrhizas are an ancestral symbiosis for all land plants
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Frontiers | Co-expression and Transcriptome Analysis of Marchantia polymorpha Transcription Factors Supports Class C ARFs as Independent Actors of an Ancient Auxin Regulatory Module | Plant Science

Frontiers | Co-expression and Transcriptome Analysis of Marchantia polymorpha Transcription Factors Supports Class C ARFs as Independent Actors of an Ancient Auxin Regulatory Module | Plant Science | Early Land Plants | Scoop.it
We performed differential gene expression (DGE) and co-expression analyses with genes encoding components of hormonal signaling pathways and the ∼400 annotated transcription factors (TFs) of M. polymorpha across multiple developmental stages of the life cycle. We identify a putative auxin-related co-expression module that has significant overlap with transcripts induced in auxin-treated tissues. Consistent with phylogenetic and functional studies, the class C ARF, MpARF3, is not part of the auxin-related co-expression module and instead is associated with transcripts enriched in gamete-producing gametangiophores. We analyze the Mparf3 and MpmiR160 mutant transcriptomes in the context of coexpression to suggest that MpARF3 may antagonize the reproductive transition via activating the MpMIR11671 and MpMIR529c precursors whose encoded microRNAs target SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcripts of MpSPL1 and MpSPL2. Both MpSPL genes are part of the MpARF3 co-expression group corroborating their functional significance. We provide evidence of the independence of MpARF3 from the auxin-signaling module and provide new testable hypotheses on the role of auxin-related genes in patterning meristems and differentiation events in liverworts.

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Growth of Sphagnum riparium is strongly rhythmic: Contribution of the seasonal, circalunar and third rhythmic components

Continuous high-resolution monitoring of Sphagnum growth can provide insights into the biological rhythms of moss growth. Moss Sphagnum riparium is a convenient model for growth monitoring. Application of the method of geotropic curvatures has enabled a three-year monitoring with two to five-day intervals. We measured the increment in ca. 85000 shoots and produced ca. 3500 growth rate estimates, making this study a champion in precision compared to previous efforts. The zeitgeber for seasonal growth rhythms is the temperature seasonal cycle (R2=0.21-0.52). When the temperature changes by 10 C, moss growth rate is modified by 0.10-0.17cm/day according to the linear model, and 1.47-2.06-fold in the exponential model. The zeitgeber for circalunar rhythms is the lunar synodic cycle (R2=0.14-0.26). The average amplitude of the fluctuations it induces in the growth rate is 0.0425-0.0572cm/day, which is equivalent to the effect of a 3.43-4.53 C change in temperature. The third rhythm can be distinguished in periodograms. Its period ranges from 10 to 16 days, but we did not detect the zeitgeber. In total, three rhythms explain 51-78% of the growth rate. We believe that the strong rhythmicity in Sphagnum growth is associated with shoot growth synchronization.
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Evolution of root apical meristem structures in vascular plants: plasmodesmatal networks - Imaichi - - American Journal of Botany - Wiley Online Library

Abstract
Premise of the study
The apical meristem generates indeterminate apical growth of the stem and root of vascular plants. Our previous examination showed that shoot apical meristems (SAMs) can be classified into two types based on plasmodesmatal networks (PNs), which are important elements in symplasmic signaling pathways within the apical meristem. Here, we examined the PNs of root apical meristems (RAMs) in comparison with those of SAMs.

Methods
Root apical meristems of 18 families and 22 species of lycophytes and euphyllophytes were analyzed. Plasmodesmata (PD) in cell walls in median longitudinal sections of RAMs were enumerated using transmission electron micrographs, and the PD density per 1 μm2 of each cell wall was calculated.

Key results
Root apical meristems with prominent apical cells of monilophytes (euphyllophytes) and Selaginellaceae (lycophytes) had high PD densities, while RAMs with plural initial cells of gymnosperms and angiosperms (euphyllophytes), and of Lycopodiaceae and Isoetaceae (lycophytes) had low PD densities. This correlation between structures of apical meristems and PD densities is identical to that in SAMs already described.

Conclusions
Irrespective of their diversified structures, the RAMs of vascular plants can be classified into two types with respect to PNs: the fern (monilophyte) type, which has a lineage‐specific PN with only primary PD, and the seed‐plant type, which has an interspecific PN with secondary PD in addition to primary PD. PNs may have played a key role in the evolution of apical meristems in vascular plants.
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Stepwise evolution of supercomplex formation with photosystem I is required for stabilization of chloroplast NADH dehydrogenase‐like complex: Lhca5‐dependent supercomplex formation in Physcomitrell...

In angiosperms, such as Arabidopsis and barley, the chloroplast NADH dehydrogenase‐like (NDH) complex associates with two copies of photosystem I (PSI) supercomplex to form an NDH‐PSI supercomplex for the stabilization of the NDH complex. Two linker proteins, Lhca5 and Lhca6, are members of the light‐harvesting complex I (LHCI) family and mediate this supercomplex formation. The liverwort Marchantia polymorpha has branched from the basal land plant lineage and has neither Lhca5 nor Lhca6. Consequently, NDH complex does not form a supercomplex with PSI in this plant. The Lhca6 gene does not seem to exist also in the moss Physcomitrella patens (Physcomitrella). On the other hand, the Lhca5 gene has been found in Physcomitrella, although experimental evidence is still lacking for its contribution to NDH‐PSI supercomplex formation as a linker. Here, we biochemically characterized the Lhca5 knockout mutant (lhca5) in Physcomitrella. The NDH‐PSI supercomplex observed in wild‐type Physcomitrella was absent in the lhca5 mutant. Lhca5 protein was detected in this NDH‐PSI supercomplex. Some PSI and NDH subunits were co‐immunoprecipitated with Lhca5‐HA. These results indicate that the Physcomitrella gene is the functional ortholog of Lhca5 reported in Arabidopsis. Between Physcomitrella and Arabidopsis, the stromal loop region is highly conserved in Lhca5 proteins but not in other LHCI members. We found that Lhca5 contributed to the stable accumulation of the NDH complex, but part of the NDH complex was still sensitive to high light, even in the wild type. We considered that angiosperms acquired another linker protein, Lhca6, to further stabilize the NDH complex.
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Frontiers | Co-expression and transcriptome analysis of Marchantia polymorpha transcription factors supports class C ARFs as independent actors of an ancient auxin regulatory module | Plant Science

We performed differential gene expression (DGE) and co-expression analyses with genes encoding components of hormonal signaling pathways and the ~400 annotated transcription factors (TFs) of M. polymorpha across multiple developmental stages of the life cycle. We identify a putative auxin-related co-expression module that has significant overlap with transcripts induced in auxin-treated tissues. Consistent with phylogenetic and functional studies, the class C ARF, MpARF3, is not part of the auxin-related co-expression module and instead is associated with transcripts enriched in gamete-producing gametangiophores. We analyse the Mparf3 and MpmiR160 mutant transcriptomes in the context of coexpression to suggest that MpARF3 antagonizes the reproductive transition via activating the MpMIR11671 and MpMIR529c precursors whose encoded microRNAs target SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcripts of MpSPL1 and MpSPL2. Both MpSPL genes are part of the MpARF3 co-expression group corroborating their functional significance. We provide evidence of the independence of MpARF3 from the auxin-signalling module and provide new testable hypotheses on the role of auxin-related genes in patterning meristems and differentiation events in liverworts.
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Marchantia liverworts as a proxy to plants’ basal microbiomes

Marchantia liverworts as a proxy to plants’ basal microbiomes | Early Land Plants | Scoop.it
Microbiomes influence plant establishment, development, nutrient acquisition, pathogen defense, and health. Plant microbiomes are shaped by interactions between the microbes and a selection process of host plants that distinguishes between pathogens, commensals, symbionts and transient bacteria. In this work, we explore the microbiomes through massive sequencing of the 16S rRNA genes of microbiomes two Marchantia species of liverworts. We compared microbiomes from M. polymorpha and M. paleacea plants collected in the wild relative to their soils substrates and from plants grown in vitro that were established from gemmae obtained from the same populations of wild plants. Our experimental setup allowed identification of microbes found in both native and in vitro Marchantia species. The main OTUs (97% identity) in Marchantia microbiomes were assigned to the following genera: Methylobacterium, Rhizobium, Paenibacillus, Lysobacter, Pirellula, Steroidobacter, and Bryobacter. The assigned genera correspond to bacteria capable of plant-growth promotion, complex exudate degradation, nitrogen fixation, methylotrophs, and disease-suppressive bacteria, all hosted in the relatively simple anatomy of the plant. Based on their long evolutionary history Marchantia is a promising model to study not only long-term relationships between plants and their microbes but also the transgenerational contribution of microbiomes to plant development and their response to environmental changes.
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Tree of death: The role of fossils in resolving the overall pattern of plant phylogeny - Rothwell - - American Journal of Botany - Wiley Online Library

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Assessing the evolutionary history of the fern family Dipteridaceae (Gleicheniales) by incorporating both extant and extinct members in a combined phylogenetic study - Choo - - American Journal of ...

Premise of the Study
Dipteridaceae is a lineage of ferns that has existed from the early Mesozoic and is known for its extensive fossil record. By integrating information from all described extant and extinct genera into a single phylogenetic study, this paper aims to examine the taxonomy of the group on a whole and explore character evolution within the lineage across time.

Methods
A morphological matrix of 51 characters was developed for 72 species (43 extinct and 29 extant) based on published information. Morphological characters were combined with nucleotide sequences for four chloroplast genes (rbcL, atpA, atpB, and rps4) for extant taxa, and combined parsimony analyses were conducted to infer evolutionary trends in the group.

Key Results
Dipteridaceae was found to be monophyletic and characterized by highly anastomosing minor veins forming a meshwork of areoles with free‐included veinlets. Based on our analyses, we recognize six previously described genera (i.e., Goeppertella, Thaumatopteris, Clathropteris, Digitopteris, Dipteris, and Cheiropleuria) and one new genus (i.e., Sewardalea). Fossils currently described as Dictyophyllum, Kenderlykia, Hausmannia, and Protorhipis are ambiguously placed on the tree and are recognized as possibly unnatural morphogenera.

Conclusions
Overall, the evolutionary trend in Dipteridaceae has been toward increasing complexity in the venation pattern and laminal fusion. Only the Hausmannia‐type frond with dichotomizing primary veins and relatively fused lamina persisted in the later part of the Mesozoic to the present. Within the crown group, we see evidence of re‐radiation of frond forms in Dipteris and Cheiropleuria.
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Loss of CG methylation in Marchantia polymorpha causes disorganization of cell division and reveals unique DNA methylation regulatory mechanisms of non-CG methylation | Plant and Cell Physiology | ...

DNA methylation is an epigenetic mark that ensures silencing of transposable elements (TEs) and affects gene expression in many organisms. The function of different DNA methylation regulatory pathways has been largely characterized in the model plant Arabidopsis thaliana. However, far less is known about DNA methylation regulation and functions in basal land plants. Here we focus on the liverwort Marchantia polymorpha, an emerging model species that represents a basal lineage of land plants. We identified MpMET, the M. polymorpha orthologue of the METHYLTRANSFERASE 1 (MET1) gene required for maintenance of methylation at CG sites in angiosperms. We generated Mpmet mutants using the CRISPR/Cas9 system, which showed a significant loss of CG methylation and severe morphological changes and developmental defects. The mutants developed many adventitious shoot-like structures, suggesting that MpMET is required for maintaining differentiated cellular identities in the gametophyte. Even though numerous TEs were up-regulated, non-CG methylation was generally highly increased at TEs in the Mpmet mutants. Closer inspection of CHG methylation revealed features unique to M. polymorpha. Methylation of CCG sites in M. polymorpha does not depend on MET1, unlike in A. thaliana and Physcomitrella patens. Furthermore, unlike A. thaliana, M. polymorpha shows higher methylation level at CAG sites than at other CHG contexts and CAG/CTG sites are mostly methylated asymmetrically. Interestingly, CAG and CTG methylation reached comparable levels and symmetry upon loss of CG methylation. Our results highlight the diversity of non-CG methylation regulatory mechanisms in plants.
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Quantitative moss cell biology - ScienceDirect

Quantitative moss cell biology - ScienceDirect | Early Land Plants | Scoop.it
Research on mosses has provided answers to many fundamental questions in the life sciences, with the model moss Physcomitrella patens spearheading the field. Recent breakthroughs in cell biology were obtained in the quantification of chlorophyll fluorescence, signalling via calcium waves, the creation of designer organelles, gene identification in cellular reprogramming, reproduction via motile sperm and egg cells, asymmetric cell division, visualization of the actin cytoskeleton, identification of genes responsible for the shift from 2D to 3D growth, the structure and importance of the cell wall, and in the live imaging and modelling of protein networks in general. Highly standardized growth conditions, simplicity of most moss tissues, and an outstandingly efficient gene editing facilitate quantitative moss cell biology.
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