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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POLQ plays a key role in repair of CRISPR/Cas9 induced double strand breaks in the moss Physcomitrella patens - Mara - - New Phytologist - Wiley Online Library

Double strand breaks can be repaired by different mechanisms such as homologous recombination (HR), classical non‐homologous end joining (C‐NHEJ) and alternative end joining (Alt‐EJ). The polymerase Q (POLQ) has been proposed to be the main factor involved in Alt‐EJ mediated DNA repair.

•Here we describe the role of POLQ in DNA repair and gene targeting in Physcomitrella patens. The disruption of the POLQ gene does not influence the genetic stability of P. patens nor its development.

•The polq mutant shows the same sensitivity as wild‐type towards most of the genotoxic agents tested (UV, MMS and cisplatin) with the notable exception of bleomycin for which it shows less sensitivity than the wild‐type. Furthermore, we show that POLQ is involved in the repair of CRISPR‐Cas9 induced double strand breaks in P. patens. We also demonstrate that POLQ is a potential competitor and/or inhibitor of the HR repair pathway.

•This has a consequence in terms of genetic engineering as in absence of POLQ the frequency of gene targeting is significantly increased and the number of clean two‐sided HR‐mediated insertions is enhanced. Thus, controlling POLQ activity in plants could be a useful strategy to optimize the tools of genome engineering for plant breeding.
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Abscisic Acid Acts as a Regulator of Molecular Trafficking through Plasmodesmata in the Moss Physcomitrella patens | Plant and Cell Physiology | Oxford Academic

In multi-cellular organisms, cell-to-cell communication is crucial for adapting to changes in the surrounding environment. In plants, plasmodesmata (PD) provide a unique pathway for cell-to-cell communication. PD interconnect most cells and generate a cytoplasmic continuum, allowing the trafficking of various micro- and macromolecules between cells. This molecular trafficking through PD is dynamically regulated by altering PD permeability dependent on environmental changes, thereby leading to an appropriate response to various stresses; however, how PD permeability is dynamically regulated is still largely unknown. Moreover, studies on the regulation of PD permeability have been conducted primarily in a limited number of angiosperms. Here, we studied the regulation of PD permeability in the moss Physcomitrella patens and report that molecular trafficking through PD is rapidly and reversibly restricted by abscisic acid (ABA). Since ABA plays a key role in various stress responses in the moss, PD permeability can be controlled by ABA to adapt to surrounding environmental changes. This ABA-dependent restriction of PD trafficking correlates with a reduction in PD pore size. Furthermore, we also found that the rate of macromolecular trafficking is higher in an ABA-synthesis defective mutant, suggesting that the endogenous level of ABA is also important for PD-mediated macromolecular trafficking. Thus, our study provides compelling evidence that P. patens exploits ABA as one of the key regulators of PD function.
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Algal photoprotection is regulated by the E3 ligase CUL4–DDB1 DET1

Algal photoprotection is regulated by the E3 ligase CUL4–DDB1 DET1 | Early Land Plants | Scoop.it
Light is essential for photosynthesis, but the amounts of light that exceed an organism’s assimilation capacity can cause serious damage1. Photosynthetic organisms minimize such potential harm through protection mechanisms collectively referred to as non-photochemical quenching2. One mechanism of non-photochemical quenching called energy-dependent quenching (qE quenching) is readily activated under high-light conditions and dissipates excess energy as heat. LIGHT-HARVESTING COMPLEX STRESS-RELATED PROTEINS 1 and 3 (LHCSR1 and LHCSR3) have been proposed to mediate qE quenching in the green alga Chlamydomonas reinhardtii when grown under high-light conditions3. LHCSR3 induction requires a blue-light photoreceptor, PHOTOTROPIN (PHOT)4, although the signal transduction pathway between PHOT and LHCSR3 is not yet clear. Here, we identify two phot suppressor loci involved in qE quenching: de-etiolated 1 (det1)5 and damaged DNA-binding 1 (ddb1)6. Using a yeast two-hybrid analysis and an inhibitor assay, we determined that these two genetic elements are part of a protein complex containing CULLIN 4 (CUL4). These findings suggest a photoprotective role for the putative E3 ubiquitin ligase CUL4–DDB1DET1 in unicellular photosynthetic organisms that may mediate blue-light signals to LHCSR1 and LHCSR3 gene expression.
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Paleobotany: Did flowering plants exist in the Jurassic period?

"This shouldn't be here," said Ellie, the paleobotanist in Jurassic Park, as she stared at a leaf. "This species of veriforman has been extinct since... the Cretaceous period." Ellie might have been equally impressed and surprised if she had stumbled across a fossil recently discovered in China that appears to be of a flowering plant that dates to the Jurassic period.
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Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat - Mower - - New Phytologist - Wiley...

Lycophytes are a key group for understanding vascular plant evolution. Lycophyte plastomes are highly distinct, indicating a dynamic evolutionary history, but detailed evaluation is hindered by the limited availability of sequences.

Eight diverse plastomes were sequenced to assess variation in structure and functional content across lycophytes.

Lycopodiaceae plastomes have remained largely unchanged compared with the common ancestor of land plants, whereas plastome evolution in Isoetes and especially Selaginella is highly dynamic. Selaginella plastomes have the highest GC content and fewest genes and introns of any photosynthetic land plant. Uniquely, the canonical inverted repeat was converted into a direct repeat (DR) via large‐scale inversion in some Selaginella species. Ancestral reconstruction identified additional putative transitions between an inverted and DR orientation in Selaginella and Isoetes plastomes. A DR orientation does not disrupt the activity of copy‐dependent repair to suppress substitution rates within repeats.

Lycophyte plastomes include the most archaic among vascular plants and the most reconfigured among land plants. These evolutionary trends correlate with the mitochondrial genome, suggesting shared underlying mechanisms. Copy‐dependent repair for DR‐localized genes indicates that recombination and gene conversion are not inhibited by the DR orientation. Gene relocation in lycophyte plastomes occurs via overlapping inversions rather than transposase/recombinase‐mediated processes.
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The Selaginella rhizophore has a unique transcriptional identity compared to root and shoot meristems - Mello - - New Phytologist - Wiley Online Library

The genus Selaginella resides in an early branch of the land plant lineage that possesses a vasculature and roots. The majority of the Selaginella root system is shoot borne and emerges through a distinctive structure known as the rhizophore, the organ identity of which has been a long‐debated question.

The rhizophore of S. moellendorffii – a model for the lycophytes – shows plasticity to develop into a root or shoot up until 8 d after angle meristem emergence, after which it is committed to root fate. We subsequently use morphology and plasticity to define the stage of rhizophore identity.

Transcriptomic analysis of the rhizophore during its plastic stage reveals that despite some resemblance to the root meristem, rhizophore gene expression patterns are largely distinct from both shoot and root meristems.

Based on this transcriptomic analysis and on historical anatomical work, we conclude that the rhizophore is a distinct organ with unique features.
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ROLE OF CYCLIC AND PSEUDO‐CYCLIC ELECTRON TRANSPORT IN RESPONSE TO DYNAMIC LIGHT CHANGES IN PHYSCOMITRELLA PATENS - Storti - - Plant, Cell & Environment - Wiley Online Library

Photosynthetic organisms support cell metabolism by harvesting sunlight and driving the electron transport chain at the level of thylakoid membranes. Excitation energy and electron flow in the photosynthetic apparatus is continuously modulated in response to dynamic environmental conditions. Alternative electron flow around photosystem I plays a seminal role in this regulation contributing to photo‐protection by mitigating over‐reduction of the electron carriers.

Different pathways of alternative electron flow coexist in the moss Physcomitrella patens, including cyclic electron flow mediated by the PGRL1/PGR5 complex and pseudo‐cyclic electron flow mediated by the flavodiiron proteins FLV. In this work we generated P. patens plants carrying both pgrl1 and flva knock‐out (KO) mutations. A comparative analysis of the WT, pgrl1, flva and pgrl1 flva lines suggests that cyclic and pseudo‐cyclic processes have a synergic role in the regulation of photosynthetic electron transport. However, while both contribute to photosystem I protection from over‐reduction by modulating electron flow following changes in environmental conditions, FLV activity is particularly relevant in the first seconds after a light change while PGRL1 has a major role upon sustained strong illumination.
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Frontiers | Abiotic Stresses: General Defenses of Land Plants and Chances for Engineering Multistress Tolerance | Plant Science

Abiotic stresses, such as low or high temperature, deficient or excessive water, high salinity, heavy metals, and ultraviolet radiation, are hostile to plant growth and development, leading to great crop yield penalty worldwide. It is getting imperative to equip crops with multistress tolerance to relieve the pressure of environmental changes and to meet the demand of population growth, as different abiotic stresses usually arise together in the field. The feasibility is raised as land plants actually have established more generalized defenses against abiotic stresses, including the cuticle outside plants, together with unsaturated fatty acids, reactive species scavengers, molecular chaperones, and compatible solutes inside cells. In stress response, they are orchestrated by a complex regulatory network involving upstream signaling molecules including stress hormones, reactive oxygen species, gasotransmitters, polyamines, phytochromes, and calcium, as well as downstream gene regulation factors, particularly transcription factors. In this review, we aimed at presenting an overview of these defensive systems and the regulatory network, with an eye to their practical potential via genetic engineering and/or exogenous application.
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An Evolutionarily Conserved Abscisic Acid Signaling Pathway Regulates Dormancy in the Liverwort Marchantia polymorpha

Dormancy is a key process allowing land plants to adapt to changing conditions in the terrestrial habitat, allowing the cessation of growth in response to environmental or physiological cues, entrance into a temporary quiescent state, and subsequent reactivation of growth in more favorable environmental conditions [1, 2, 3]. Dormancy may be induced seasonally, sporadically (e.g., in response to drought), or developmentally (e.g., seeds and apical dominance). Asexual propagules, known as gemmae, derived via clonal reproduction in bryophytes, are often dormant until displaced from the parent plant. In the liverwort Marchantia polymorpha, gemmae are produced within specialized receptacles, gemma cups, located on the dorsal side of the vegetative thallus [4]. Mature gemmae are detached from the parent plant but may remain in the cup, with gemma growth suppressed as long as the gemmae remain in the gemma cup and the parental plant is alive [5]. Following dispersal of gemmae from gemma cups by rain, the gemmae germinate in the presence of light and moisture, producing clonal offspring [6]. In land plants, the plant hormone abscisic acid (ABA) regulates many aspects of dormancy and water balance [7]. Here, we demonstrate that ABA plays a central role in the control of gemma dormancy as transgenic M. polymorpha gemmae with reduced sensitivity to ABA fail to establish and/or maintain dormancy. Thus, the common ancestor of land plants used the ABA signaling module to regulate germination of progeny in response to environmental cues, with both gemmae and seeds being derived structures co-opting an ancestral response system.
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Single-cell transcriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation

Background: Next-generation sequencing technologies have made it possible to carry out transcriptome analysis at the single-cell level. Single-cell RNA-sequencing (scRNA-seq) data provide insights into cellular dynamics, including intercellular heterogeneity as well as inter- and intra-cellular fluctuations in gene expression that cannot be studied using populations of cells. The utilization of scRNA-seq is, however, restricted to specific types of cells that can be isolated from their original tissues, and it can be difficult to obtain precise positional information for these cells in situ. Results: Here, we established single cell-digital gene expression (1cell-DGE), a method of scRNA-seq that uses micromanipulation to extract the contents of individual living cells in intact tissue while recording their positional information. Furthermore, we employed a unique molecular identifier to reduce amplification bias in the cDNA libraries. With 1cell-DGE, we could detect differentially expressed genes (DEGs) during the reprogramming of leaf cells into stem cells in excised tissues of the moss Physcomitrella patens, identifying 6,382 DEGs between cells at 0 h and 24 h after excision. We found substantial variations in both the transcript levels of previously reported reprogramming factors and the overall expression profiles between cells, which appeared to be related to their different reprogramming abilities or the estimated states of the cells according to the pseudotime based on the transcript profiles. Conclusions: We developed 1cell-DGE with microcapillary manipulation, a technique that can be used to analyze the gene expression of individual cells without detaching them from their tightly associated tissues, enabling us to retain positional information and investigate cell-cell interactions.
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Convergent recruitment of life cycle regulators to direct sporophyte development in two eukaryotic supergroups

Three amino acid loop extension homeodomain transcription factors (TALE HD TFs) act as life cycle regulators in green algae and land plants. In mosses these regulators are required for the deployment of the sporophyte developmental program. We demonstrate that mutations in either of two TALE HD TF genes, OUROBOROS or SAMSARA, in the brown alga Ectocarpus result in conversion of the sporophyte generation into a gametophyte. The OUROBOROS and SAMSARA proteins heterodimerise in a similar manner to TALE HD TF life cycle regulators in the green lineage. These observations demonstrate that TALE-HD-TF-based life cycle regulation systems have an extremely ancient origin, and that these systems have been independently recruited to regulate sporophyte developmental programs in at least two different complex multicellular eukaryotic supergroups, Archaeplastida and Chromalveolata.
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LEAFY maintains apical stem cell activity during shoot development in the fern Ceratopteris richardii 

During land plant evolution, determinate spore-bearing axes (retained in extant bryophytes such as mosses) were progressively transformed into indeterminate branching shoots with specialized reproductive axes that form flowers. The LEAFY transcription factor, which is required for the first zygotic cell division in mosses and primarily for floral meristem identity in flowering plants, may have facilitated developmental innovations during these transitions. Mapping the LEAFY evolutionary trajectory has been challenging, however, because there is no functional overlap between mosses and flowering plants, and no functional data from intervening lineages. Here, we report a transgenic analysis in the fern Ceratopteris richardii that reveals a role for LEAFY in maintaining cell divisions in the apical stem cells of both haploid and diploid phases of the lifecycle. These results support an evolutionary trajectory in which an ancestral LEAFY module that promotes cell proliferation was progressively co-opted, adapted and specialized as novel shoot developmental contexts emerged.
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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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Anatomical constraints to non‐stomatal diffusion conductance and photosynthesis in lycophytes and bryophytes - Carriquí - - New Phytologist - Wiley Online Library

Photosynthesis in bryophytes and lycophytes has received less attention than terrestrial plant groups. In particular, few studies have addressed the non‐stomatal diffusion conductance to CO2 (gnsd) of these plant groups.

Their lower photosynthetic rate per leaf mass area at any given nitrogen concentration as compared to vascular plants suggested a stronger limitation by CO2 diffusion. We hypothesized that bryophyte and lycophyte photosynthesis is largely limited by low gnsd. Here we studied CO2 diffusion inside the photosynthetic tissues and its relationships with photosynthesis and anatomical parameters in bryophyte and lycophyte species in Antarctica, Australia, Estonia, Hawaii and Spain.

On average, lycophytes and, specially, bryophytes had the lowest photosynthetic rates and non‐stomatal diffusion conductance reported for terrestrial plants. These low values are related to their very thick cell walls and their low exposure of chloroplasts to cell perimeter.

We conclude that the reason why bryophytes lie at the lower end of the leaf economics spectrum is their strong non‐stomatal diffusion conductance limitation to photosynthesis, which is driven by their specific anatomical characteristics.
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A cis‐acting bidirectional transcription switch controls sexual dimorphism in the liverwort

Plant life cycles alternate between haploid gametophytes and diploid sporophytes. While regulatory factors determining male and female sexual morphologies have been identified for sporophytic reproductive organs, such as stamens and pistils of angiosperms, those regulating sex‐specific traits in the haploid gametophytes that produce male and female gametes and hence are central to plant sexual reproduction are poorly understood. Here, we identified a MYB‐type transcription factor, MpFGMYB, as a key regulator of female sexual differentiation in the haploid‐dominant dioicous liverwort, Marchantia polymorpha. MpFGMYB is specifically expressed in females and its loss resulted in female‐to‐male sex conversion. Strikingly, MpFGMYB expression is suppressed in males by a cis‐acting antisense gene SUF at the same locus, and loss‐of‐function suf mutations resulted in male‐to‐female sex conversion. Thus, the bidirectional transcription module at the MpFGMYB/SUF locus acts as a toggle between female and male sexual differentiation in M. polymorpha gametophytes. Arabidopsis thaliana MpFGMYB orthologs are known to be expressed in embryo sacs and promote their development. Thus, phylogenetically related MYB transcription factors regulate female gametophyte development across land plants.
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Massive tandem proliferation of ELIPs supports convergent evolution of desiccation tolerance across land plants

Desiccation tolerance was a critical adaptation for the colonization of land by early non-vascular plants. Resurrection plants have maintained or rewired these ancestral protective mechanisms and desiccation-tolerant species are dispersed across the land plant phylogeny. Though common physiological, biochemical, and molecular signatures are observed across resurrection plant lineages, features underlying the recurrent evolution of desiccation tolerance are unknown. Here we used a comparative approach to identify patterns of genome evolution and gene duplication associated with desiccation tolerance. We identified a single gene family with dramatic expansion in all sequenced resurrection plant genomes and no expansion in desiccation-sensitive species. This gene family of early light-induced proteins (ELIPs) expanded in resurrection plants convergent through repeated tandem gene duplication. ELIPS are universally highly expressed during desiccation in all surveyed resurrection plants and may play a role in protecting against photooxidative damage of the photosynthetic apparatus during prolonged dehydration. Photosynthesis is particularly sensitive to dehydration and the increased abundance of ELIPs may help facilitate the rapid recovery observed for most resurrection plants. Together, these observations support convergent evolution of desiccation tolerance in land plants through tandem gene duplication.
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An unexpected noncarpellate epigynous flower from the Jurassic of China

The origin of angiosperms has been a long-standing botanical debate. The great diversity of angiosperms in the Early Cretaceous makes the Jurassic a promising period in which to anticipate the origins of the angiosperms. Here, based on observations of 264 specimens of 198 individual flowers preserved on 34 slabs in various states and orientations, from the South Xiangshan Formation (Early Jurassic) of China, we describe a fossil flower, Nanjinganthus dendrostyla gen. et sp. nov.. The large number of specimens and various preservations allow for an evidence-based reconstruction of the flower. From the evidence of the combination of an invaginated receptacle and ovarian roof, we infer that the seeds of Nanjinganthus were completely enclosed. Evidence of an actinomorphic flower with a dendroid style, cup-form receptacle, and angiospermy, is consistent with Nanjinganthus being a bona fide angiosperm from the Jurassic, an inference that we hope will re-invigorate research into angiosperm origins
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Mechanistic insights into the evolution of DUF26-containing proteins in land plants

Large protein families are a prominent feature of plant genomes and their size variation is a key element for adaptation in plants. Here we infer the evolutionary history of a representative protein family, the DOMAIN OF UNKNOWN FUNCTION (DUF) 26-containing proteins. The DUF26 first appeared in secreted proteins. Domain duplications and rearrangements led to the emergence of CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASES (CRKs) and PLASMODESMATA-LOCALIZED PROTEINS (PDLPs). While the DUF26 itself is specific to land plants, structural analyses of Arabidopsis PDLP5 and PDLP8 ectodomains revealed strong similarity to fungal lectins. Therefore, we propose that DUF26-containing proteins constitute a novel group of plant carbohydrate-binding proteins. Following their appearance, CRKs expanded both through tandem duplications and preferential retention of duplicates in whole genome duplication events, whereas PDLPs evolved according to the dosage balance hypothesis. Based on our findings, we suggest that the main mechanism of expansion in new gene families is small-scale duplication, whereas genome fractionation and genetic drift after whole genome multiplications drive families towards dosage balance.
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Hydraulics regulates stomatal responses to changes in leaf water status in Athyrium filix-femina

Stomatal responses to changes in leaf water status are important for the diurnal regulation of gas exchange and the survival of plants during drought. These stomatal responses in angiosperm species are well characterized, yet an ongoing debate surrounds the role of metabolism, particularly the role of the hormone abscisic acid (ABA), in functionally regulating stomatal responses to changes in leaf water status in species of non-seed plants. Here we measured the stomatal response to changes in vapour pressure deficit (VPD) in two natural forms of the fern species Athyrium filix-femina, recently suggested to have stomata that are regulated by ABA. The two forms measured had considerable differences in key hydraulic traits, including leaf hydraulic conductance and capacitance, as well as the kinetics of stomatal response to changes in VPD. In both forms the stomatal responses to VPD could be accurately predicted by a dynamic, mechanistic model that assumes guard cell turgor changes in concert with leaf turgor in the light, and not via metabolic processes including the level of ABA. During drought, endogenous ABA was found to play no role in closing stomata, while exogenous ABA applied to live and intact leaves did not close stomata. Our results indicate that functional stomatal responses to changes in leaf water status in ferns are regulated by leaf hydraulics and not metabolism. With ferns being sister to seed plants, this result has implications for the evolutionary reconstruction of functional stomatal responses across vascular land plants lineages.
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Evolutionary and ecological functional genomics, from lab to the wild - Zaidem - - The Plant Journal - Wiley Online Library

Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the least few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.
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Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.) - de Sousa - - New Phytologist - Wiley Online Library

Unraveling the phylogenetic relationships between the four major lineages of terrestrial plants (mosses, liverworts, hornworts, and vascular plants) is essential for an understanding of the evolution of traits specific to land plants, such as their complex life cycles, and the evolutionary development of stomata and vascular tissue.

Well supported phylogenetic hypotheses resulting from different data and methods are often incongruent due to processes of nucleotide evolution, which are difficult to model: for example, substitutional saturation and composition heterogeneity. We reanalyse a large published dataset of nuclear data and model these processes using degenerate codon recoding and tree‐heterogeneous composition substitution models.

Our analyses resolve bryophytes as a monophyletic group and show that the non‐monophyly of the clade, that is supported by the analysis of nuclear nucleotide data, is due solely to fast‐evolving synonymous substitutions.

The current congruence among phylogenies of both nuclear and chloroplast analyses lend considerable support to the conclusion that the bryophytes are a monophyletic group. An initial split between bryophytes and vascular plants implies that the bryophyte life cycle (with a dominant gametophyte nurturing an unbranched sporophyte) may not be ancestral to all land plants and that stomata are likely a symplesiomorphy among embryophytes.
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Longevity of Preserved Germplasm: The Temperature Dependency of Aging Reactions in Glassy Matrices of Dried Fern Spores | Plant and Cell Physiology | Oxford Academic

This study explores temperature dependency of aging rate in dry cells over a broad temperature range encompassing the fluid to solid transition (Tg) and well below. Spores from diverse species of eight families of ferns were stored at temperatures ranging from +45oC to c. -176oC (vapor phase above liquid nitrogen), and viability was monitored periodically for up to 4300 days (ca. 12 years). Accompanying measurements using differential scanning calorimetry (DSC) provide insights into structural changes that occur such as Tg, between +45 and -20oC (depending on moisture), and triacylglycerol (TAG) crystallization, between -5 and -35oC (depending on species). We detected aging even at cryogenic temperatures, which we consider analogous to unscheduled degradation of pharmaceuticals stored well below Tg caused by a shift in the nature of molecular motions that dominate chemical reactivity. We occasionally observed faster aging of spores stored at -18oC (conventional freezer) compared to 5oC (refrigerator), and linked this with mobility and crystallization within TAG, which likely influences molecular motion of dried cytoplasm in a narrow temperature range. Temperature dependency of longevity was remarkably similar among diverse fern spores, despite widely disparate aging rates; this provides a powerful tool to predict deterioration of germplasm preserved in the solid state. Future work will increase our understanding of molecular organization and composition contributing to differences in longevity.
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Frontiers | Evolution of the Symbiosis-Specific GRAS Regulatory Network in Bryophytes | Plant Science

Frontiers | Evolution of the Symbiosis-Specific GRAS Regulatory Network in Bryophytes | Plant Science | Early Land Plants | Scoop.it
Arbuscular mycorrhiza is one of the most common plant symbiotic interactions observed today. Due to their nearly ubiquitous occurrence and their beneficial impact on both partners it was suggested that this mutualistic interaction was crucial for plants to colonize the terrestrial habitat approximately 500 Ma ago. On the plant side the association is established via the common symbiotic pathway (CSP). This pathway allows the recognition of the fungal symbiotic partner, subsequent signaling to the nucleus, and initiation of the symbiotic program with respect to specific gene expression and cellular re-organization. The downstream part of the CSP is a regulatory network that coordinates the transcription of genes necessary to establish the symbiosis, comprising multiple GRAS transcription factors (TFs). These regulate their own expression as an intricate transcriptional network. Deduced from non-host genome data the loss of genes encoding CSP components coincides with the loss of the interaction itself. Here, we analyzed bryophyte species with special emphasis on the moss Physcomitrella patens, supposed to be a non-host, for the composition of the GRAS regulatory network components. We show lineage specific losses and expansions of several of these factors in bryophytes, potentially coinciding with the proposed host/non-host status of the lineages. We evaluate losses and expansions and infer clade-specific evolution of GRAS TFs.
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A unique supramolecular organization of photosystem I in the moss Physcomitrella patens

A unique supramolecular organization of photosystem I in the moss Physcomitrella patens | Early Land Plants | Scoop.it
The photosynthesis machinery in chloroplast thylakoid membranes is comprised of multiple protein complexes and supercomplexes1,2. Here, we show a novel supramolecular organization of photosystem I (PSI) in the moss Physcomitrella patens by single-particle cryo-electron microscopy. The moss-specific light-harvesting complex (LHC) protein Lhcb9 is involved in this PSI supercomplex, which has been shown to have a molecular density similar to that of the green alga Chlamydomonas reinhardtii3. Our results show that the structural organization is unexpectedly different—two rows of the LHCI belt exist as in C. reinhardtii4, but the outer one is shifted toward the PsaK side. Furthermore, one trimeric LHC protein and one monomeric LHC protein position alongside PsaL/K, filling the gap between these subunits and the outer LHCI belt. We provide evidence showing that Lhcb9 is a key factor, acting as a linkage between the PSI core and the outer LHCI belt to form the unique supramolecular organization of the PSI supercomplex in P. patens.
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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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