Differential expression and co-localization of transcriptional factors during callus transition to differentiation for shoot organogenesis in the water fern Ceratopteris richardii

BACKGROUND AND AIMS

In flowering plants, regeneration can be achieved by a variety of approaches, and different sets of transcriptional factors are involved in these processes. However, regeneration in taxa other than flowering plants remains a mystery. Ceratopteris richardii is a representative fern capable of both direct and indirect organogenesis, and we aimed to investigate the genetics underlying the transition from callus proliferation to differentiation.

METHODS

Morphological and histological analyses were used to determine the type of regeneration involved. RNA sequencing and differential gene expression were used to investigate how the callus switches from proliferation to differentiation. Phylogenetic analysis and RNA in situ hybridization were used to understand whether transcriptional factors are involved in this transition.

KEY RESULTS

The callus formed on nascent leaves and subsequently developed the shoot pro-meristem and shoot meristem, thus completing indirect de novo shoot organogenesis in C. richardii. Genes were differentially expressed during the callus transition from proliferation to differentiation, indicating a role for photosynthesis, stimulus response and transmembrane signalling in this transition and the involvement of almost all cell layers that make up the callus. Transcriptional factors were either downregulated or upregulated, which were generally in many-to-many orthology with genes known to be involved in callus development in flowering plants, suggesting that the genetics of fern callus development are both conserved and divergent. Among them, an STM-like, a PLT-like and an ethylene- and salt-inducible ERF gene3-like gene were expressed simultaneously in the vasculature but not in the other parts of the callus, indicating that the vasculature played a role in the callus transition from proliferation to differentiation.

CONCLUSIONS

Indirect de novo shoot organogenesis could occur in ferns, and the callus transition from proliferation to differentiation required physiological changes, differential expression of transcriptional factors and involvement of the vasculature.

Re-examining meristems through the lens of evo-devo

The concept of the meristem was introduced in 1858 to characterize multicellular, formative, and proliferative tissues that give rise to the entire plant body, based on observations of vascular plants. Although its original definition did not encompass bryophytes, this concept has been used and continuously refined over the past 165 years to describe the diverse apices of all land plants. Here, we re-examine this matter in light of recent evo-devo research and show that, despite displaying high anatomical diversity, land plant meristems are unified by shared genetic control. We also propose a modular view of meristem function and highlight multiple evolutionary mechanisms that are likely to have contributed to the assembly and diversification of the varied meristems during the course of plant evolution.

Fern mycorrhizae do not respond to fertilization in a tropical montane forest

Ferns are known to have a lower incidence of mycorrhization than angiosperms. It has been suggested that this results from carbon being more limiting to fern growth than nutrient availability, but this assertion has not been tested yet. In the present study, we took advantage of a fertilization experiment with nitrogen and phosphorus on cloud forest plots of the Ecuadorean Andes for 15 years. A previous analysis revealed changes in the abundances of fern species in the fertilized plots compared to the control plots and hypothesized that this might be related to the responses of the mycorrhizal relationships to nutrient availability. We revisited the plots to assess the root-associated fungal communities of two epiphytic and two terrestrial fern species that showed shifts in abundance. We sampled and analyzed the roots of 125 individuals following a metabarcoding approach. We recovered 1382 fungal ASVs, with a dominance of members of Tremellales (Basidiomycota) and Heliotales (Ascomycota). The fungal diversity was highly partitioned with little overlap between individuals. We found marked differences between terrestrial and epiphytic species, with the latter fundamentally missing arbuscular mycorrhizal fungi (AMF). We found no effect of fertilization on the diversity or relative abundance of the fungal assemblages. Still, we observed a direct impact of phosphorus fertilization on its concentration in the fern leaves. We conclude that fern-fungi relationships in the study site are not restricted by nutrient availability and suggest the existence of little specificity on the fungal partners relative to the host fern species.

Niche and phenotypic differentiation in fern hybrid speciation, a case study of Pteris fauriei (Pteridaceae)

BACKGROUND AND AIMS

Niche differentiation is a critical issue in speciation. Although it has a well-known role in adaptive processes of hybrid angiosperms, it is less understood in hybrid ferns. Here we investigate whether an intermediate ecological niche of a fern hybrid is a novel adaptation that provides insights into fern hybrid speciation.

METHODS

Pteris fauriei (Pteridaceae) is a natural hybrid fern, occurring environments between its parent species. The maternal P. minor is found in sunny areas, but the habitat of the paternal P. latipinna is shady. We combined data from morphology, leaf anatomy, and photosynthetic traits to explore adaptation and differentiation, along with measuring the environmental features of their niches. We also performed experiments in a common garden to understand ecological plasticity.

KEY RESULTS

The hybrid P. fauriei is intermediate between the parent species in stomatal density, leaf anatomical features, and photosynthetic characteristics in both natural habitats and a common garden. Interestingly, the maternal P. minor showed significant environmental plasticity and was more similar to the hybrid P. fauriei in the common garden, suggesting that the maternal species experiences stress in its natural habitats but thrives in the environments similar to the hybrid's.

CONCLUSIONS

Based on the similar niche preferences of the hybrid and parents, we propose hybrid superiority. Our results indicate that the hybrid P. fauriei exhibits greater fitness and can compete with and occupy the initial niches of the maternal P. minor. Consequently, we suggest that the maternal P. minor has experienced a niche shift, elucidating the pattern of niche differentiation in this hybrid group. These findings offer a potential explanation for the frequent occurrence of hybridization in ferns and provide novel insights into fern hybrid speciation, enhancing our understanding of fern diversity.

Microsatellite Content in 397 Nuclear Exons and Their Flanking Regions in the Fern Family Ophioglossaceae

Microsatellites or SSRs are small tandem repeats that are 1-6 bp long. They are usually highly polymorphic and form important portions of genomes. They have been extensively analyzed in humans, animals and model plants; however, information from non-flowering plants is generally lacking. Here, we examined 29 samples of Ophioglossaceae ferns, mainly from the genera Botrychium and Sceptridium. We analyzed the SSR distribution, density and composition in almost 400 nuclear exons and their flanking regions. We detected 45 SSRs in exons and 1475 SSRs in the flanking regions. In the exons, only di-, tri- and tetranucleotides were found, and all of them were 12 bp long. The annotation of the exons containing SSRs showed that they were related to various processes, such as metabolism, catalysis, transportation or plant growth. The flanking regions contained SSRs from all categories, with the most numerous being dinucleotides, followed by tetranucleotides. More than one-third of all the SSRs in the flanking regions were 12 bp long. The SSR densities in the exons were very low, ranging from 0 to 0.07 SSRs/kb, while those in the flanking regions ranged from 0.24 to 0.81 SSRs/kb; and those in the combined dataset ranged from 0.2 to 0.81 SSRs/kb. The majority of the detected SSRs in the flanking regions were polymorphic and present at the same loci across two or more samples but differing in the number of repeats. The SSRs detected here may serve as a basis for further population genetic, phylogenetic or evolutionary genetic studies, as well as for further studies focusing on SSRs in the genomes and their roles in adaptation, evolution and diseases.

Polyploid goldback and silverback ferns (Pentagramma) occupy a wider, colder, and wetter bioclimatic niche than diploid counterparts

PREMISE

The western North American fern genus Pentagramma (Pteridaceae) is characterized by complex patterns of ploidy variation, an understanding of which is critical to comprehending both the evolutionary processes within the genus and its current diversity.

METHODS

We undertook a cytogeographic study across the range of the genus, using a combination of chromosome counts and flow cytometry to infer ploidy level. Bioclimatic variables and elevation were used to compare niches.

RESULTS

We found that diploids and tetraploids are common and widespread, and triploids are rare and sporadic; in contrast with genome size inferences in earlier studies, no hexaploids were found. Diploids and tetraploids show different geographic ranges: only tetraploids were found in the northernmost portion of the range (Washington, Oregon, and British Columbia) and only diploids were found in the Sierra Nevada of California. Diploid, triploid, and tetraploid cytotypes were found to co-occur in relatively few localities: in the southern (San Diego County, California) and desert Southwest (Arizona) parts of the range, and along the Pacific Coast of California.

CONCLUSIONS

Tetraploids occupy a wider bioclimatic niche than diploids both within P. triangularis and at the genus-wide scale. It is unknown whether the wider niche of tetraploids is due to their expansion upon the diploid niche, if diploids have contracted their niche due to competition or changing abiotic conditions, or if this wider niche occupancy is due to multiple origins of tetraploids.

A new approach to an old problem: how to categorize the habit of ferns and lycophytes

BACKGROUND AND AIMS

Substrate preferences are often treated as species traits and are used to distinguish different habits, i.e. an epiphytic, lithophytic or terrestrial habit. Such a categorization, however, ignores substantial intraspecific variation. An approach that takes biological variability within a species into account is needed.

METHODS

We focused on four large genera of ferns and lycophytes and found relevant information in >500 sources, such as online databases, checklists, floras and species descriptions. Translating textual information into a quantitative index, we quantified the propensity to grow on either substrate as a continuous trait for 1475 species.

KEY RESULTS

Only a minority of species exhibited strict substrate fidelity, but a majority of them showed clear habitat preferences. The relative frequencies of intermediates between strict lithophytes, epiphytes and terrestrials does not support the frequent notion of ecological similarity of the lithophytic and epiphytic habitat.

CONCLUSIONS

The compiled data are useful immediately for ecological and evolutionary studies with the focal taxa. More importantly, we propose the replacement of the concept of distinct habits with one of gradual differences. This should have a profound impact on any such study with plants in general.

Global patterns and climatic determinants of phylogenetic structure of regional fern floras

Knowledge of relationships between phylogenetic structure of a biological assemblage and ecological factors that drive the variation of phylogenetic structure among regions is crucial for understanding the causes of variation in taxonomic composition and richness among regions, but this knowledge is lacking for the global flora of ferns. Here, we fill this critical knowledge gap. We divided the globe into 392 geographic units on land, collated species lists of ferns for each geographic unit, and used different phylogenetic metrics (tip- vs basal-weighted) reflecting different evolutionary depths to quantify phylogenetic structure. We then related taxonomic and phylogenetic structure metrics to six climatic variables for ferns as a whole and for two groups of ferns (old clades vs polypods) reflecting different evolutionary histories across the globe and within each continental region. We found that when old clades and polypods were considered separately, temperature-related variables explained more variation in these metrics than did precipitation-related variables in both groups. When analyses were conducted for continental regions separately, this pattern holds in most cases. Climate extremes have a stronger relationship with phylogenetic structure of ferns than does climate seasonality. Climatic variables explained more variation in phylogenetic structure at deeper evolutionary depths.

"Diminishing returns" and leaf area-biomass scaling of ferns in subtropical ecosystems

Foliage leaves are the primary photosynthetic organ of the majority of vascular plants, and their area vs. biomass scaling relationships provide valuable insights into the capacity and investment in light interception, which is critical to plant growth and performance. The "diminishing returns" hypothesis (DRH), which is based primarily on data from gymnosperms and angiosperms, posits that leaf (lamina) area scales with leaf dry mass. on average with a scaling exponent less than 1.0. However, it remains uncertain whether DRH applies to ferns or whether ecological factors affect the scaling exponents governing fern leaf morphometrics. To address this issue, 182 individuals of 28 subtropical ferns species were studied at low, medium, and high elevations (i.e., 600 m, 900 m, and 1200 m, respectively) in Mount Wuyi National Park, Jiangxi Province, China. The scaling relationships between leaf area and leaf biomass for individual and total leaf of ferns at different elevations were examined by using standardized major axis regression protocols. Analyses of the 28 fern species (using Blomberg K-value protocols) indicated no phylogenetic biases among the species compositions of the three different elevations. In addition, at the individual plant level, individual leaf area (ILA) did not differ significantly among the three different elevations (P > 0.05). However, individual leaf mass (ILM) was significantly higher at 900m than at 1200m (P < 0.05), resulting in a significantly higher leaf mass per area (LMA) at the 900m elevation than at the 600m and 1200m elevations (P < 0.05). The ILA and ILM at the 900m elevation were significantly higher than at the 600m elevation (P < 0.05). At the species level, ILA and ILM did not differ significantly among the three elevations (P > 0.05). The total leaf area per individual (TLA) did not differ significantly across the different elevations (P > 0.05). However, total leaf mass per individual (TLM) did differ significantly (P < 0.05). At the individual plant level, the scaling exponents for ILA vs. ILM and TLA vs. TLM at the three different elevations were all significantly less than 1.0 (P < 0.05), which was consistent with the DRH. At the species level, the scaling exponents for the ILA vs. ILM were significantly less than 1.0 at the middle and high elevations, but not at the low elevation. The scaling exponents of the TLA and TLM were numerically highest in the middle elevation, and all were less than 1.0 for the three elevations. These results indicate that the scaling relationships of leaf area versus mass of subtropical ferns at different elevations support the DRH hypothesis. The study further informs our understanding of the resource allocation strategies of an ancient and diverse plant lineage.

A New Species of Ultratenuipalpus (Acari: Tenuipalpidae) from Brazil and Re-Description of Ultratenuipalpus meekeri (De Leon), the Type Species of the Genus, with DNA Barcodes

Species of the genus Ultratenuipalpus bear a broad subquadrate propodosoma with many large, flattened, lanceolate to ovate dorsal setae. They also bear some plesiomorphic character states, such as the presence of three pairs of ventral ps setae. Here, we describe Ultratenuipalpus parameekeri Castro, Ochoa & Feres sp. nov. based on adult females, males, and immatures, collected on ferns from Brazil. We also re-describe Ultratenuipalpus meekeri (De Leon), the type species of the genus, based on types and newly collected material from Mexico, and include additional novel data (e.g., dorsal and ventral ornamentation, leg chaetotaxy, and setal measurements) in a standardized form. We include highly detailed images obtained using LT-SEM, accompanied by DNA barcodes, for both species. The ontogenetic additions of leg chaetotaxy are presented and discussed.

Distribution patterns of fern species richness along elevations the Tibetan Plateau in China: regional differences and effects of climate change variables

Because of its distinct geological history, frigid temperature, and rich biodiversity, the Tibetan Plateau gives an excellent opportunity to assess the effect of climate change on determining species richness. The distribution patterns of fern species richness and their underlying processes have long been a matter of debate in ecology research, with various hypotheses suggested over the years. Here, we explore richness patterns of fern species in Xizang on the southern and western Tibetan Plateau along an elevational gradient (100-5300 m a.s.l.) and evaluate climatic factors causing the spatial decrease and increase of fern species richness. We used regression and correlation analyses to relate the species richness with elevation and climatic variables. Throughout our research, we identified 441 fern species from 97 genera and 30 families. The Dryopteridaceae family (S = 97) has the highest number of species. All energy-temperature and moisture variables except drought index (DI) had a significant correlation with elevation. The altitude has a unimodal relationship with fern species, and the species richness is the largest at an altitude of 2500 m. The horizontal richness pattern of fern species on the Tibetan Plateau also showed that areas of extremely high species richness are mainly distributed in Zayü and Mêdog County, with an average elevation of 2800 m and 2500 m, respectively. The richness of fern species has a log-linear relationship with moisture-related factors such as moisture index (MI), mean annual precipitation (MAP), and drought index (DI). Because the peak corresponds spatially with the MI index, the unimodal patterns confirm the significance of moisture on fern distributions. Our results showed that mid-altitudes have the highest species richness (high MI), but high elevations have lower richness due to high solar radiation, and low elevations have lower richness due to high temperatures and low precipitation. Twenty-two of the total species are classified as nearly threatened, vulnerable or critically endangered, and varied in elevation from 800 m to 4200 m. Such relationships between the distribution and richness of fern species and climates on the Tibetan Plateau can provide data support for future predictions of the impacts of climate change scenarios on fern species, the ecological protection of representative fern species, and references for the planning and construction of nature reserves in the future.

Fern cell walls and the evolution of arabinogalactan proteins in streptophytes

Significant changes have occurred in plant cell wall composition during evolution and diversification of tracheophytes. As the sister lineage to seed plants, knowledge on the cell wall of ferns is key to track evolutionary changes across tracheophytes and to understand seed plant-specific evolutionary innovations. Fern cell wall composition is not fully understood, including limited knowledge of glycoproteins such as the fern arabinogalactan proteins (AGPs). Here, we characterize the AGPs from the leptosporangiate fern genera Azolla, Salvinia, and Ceratopteris. The carbohydrate moiety of seed plant AGPs consists of a galactan backbone including mainly 1,3- and 1,3,6-linked pyranosidic galactose, which is conserved across the investigated fern AGPs. Yet, unlike AGPs of angiosperms, those of ferns contained the unusual sugar 3-O-methylrhamnose. Besides terminal furanosidic arabinose, Ara (Araf), the main linkage type of Araf in the ferns was 1,2-linked Araf, whereas in seed plants 1,5-linked Araf is often dominating. Antibodies directed against carbohydrate epitopes of AGPs supported the structural differences between AGPs of ferns and seed plants. Comparison of AGP linkage types across the streptophyte lineage showed that angiosperms have rather conserved monosaccharide linkage types; by contrast bryophytes, ferns, and gymnosperms showed more variability. Phylogenetic analyses of glycosyltransferases involved in AGP biosynthesis and bioinformatic search for AGP protein backbones revealed a versatile genetic toolkit for AGP complexity in ferns. Our data reveal important differences across AGP diversity of which the functional significance is unknown. This diversity sheds light on the evolution of the hallmark feature of tracheophytes: their elaborate cell walls.

A metabarcoding protocol targeting two DNA regions to analyze root-associated fungal communities in ferns and lycophytes

Premise

Detailed studies of the fungi associated with lycophytes and ferns provide crucial insights into the early evolution of land plants. However, most investigations to date have assessed fern-fungus interactions based only on visual root inspection. In the present research, we establish and evaluate a metabarcoding protocol to analyze the fungal communities associated with fern and lycophyte roots.

Methods

We used two primer pairs focused on the ITS rRNA region to screen the general fungal communities, and the 18S rRNA to target Glomeromycota fungi (i.e., arbuscular mycorrhizal fungi). To test these approaches, we collected and processed roots from 12 phylogenetically distant fern and lycophyte species.

Results

We found marked compositional differences between the ITS and 18S data sets. While the ITS data set demonstrated the dominance of orders Glomerales (phylum Glomeromycota), Pleosporales, and Helotiales (both in phylum Ascomycota), the 18S data set revealed the greatest diversity of Glomeromycota. Non-metric multidimensional scaling (NMDS) ordination suggested an important geographical effect in sample similarities.

Discussion

The ITS-based approach is a reliable and effective method to analyze the fungal communities associated with fern and lycophyte roots. The 18S approach is more appropriate for studies focused on the detailed screening of arbuscular mycorrhizal fungi.

Phylogenomic evolutionary insights in the fern family Gleicheniaceae

The pantropical fern family Gleicheniaceae comprises approximately 157 species. Seven genera are currently recognized in the family, although their monophyly is still uncertain due to low sampling in phylogenetic studies. We examined the monophyly of the genera through extended sampling, using the first phylogenomic inference of the family including data from both nuclear and plastid genomes. Seventy-six samples were sequenced (70 Gleicheniaceae species and six outgroups) using high throughput sequencing, including all seven currently recognized genera. Plastid and nuclear data were recovered and assembled; the nuclear data was phased to reduce paralogy as well as hybrid noise in the final recovered topology. Maximum likelihood trees were built for each locus, and a concatenated dataset was built for both datasets. A species tree based on a multispecies coalescent model was generated, and divergence time analyses performed. We here present the first genomic phylogenetic inferences concerning Gleicheniaceae, confirming the monophyly of most genera except Sticherus, which we recovered as paraphyletic. Although most of the extant genera of Gleicheniaceae originated during the Mesozoic, several genera show Neogene and even Quaternary diversifications, and our results suggest that reticulation and polyploidy may have played significant roles during this diversification. However, some genera, such as Rouxopteris and Stromatopteris, appear to represent evolutionary relicts.

Bioaccumulation of Per- and Polyfluoroalkyl Substances (PFAS) in Ferns: Effect of PFAS Molecular Structure and Plant Root Characteristics

The present study assessed the bioaccumulation potential of per- and polyfluoroalkyl substances (PFAS) in ferns and linked root uptake behaviors to root characteristics and PFAS molecular structure. Tissue and subcellular-level behavioral differences between alternative and legacy PFAS were compared via an electron probe microanalyzer with energy dispersive spectroscopy (EPMA-EDS) and differential centrifugation. Our results show that ferns can accumulate PFAS from water, immobilize them in roots, and store them in harvestable tissue. The PFAS loading in roots was dominated by PFOS; however, a substantial amount of associated PFOS could be rinsed off by methanol. Correlation analyses indicated that root length, surface and project area, surface area per unit length of the root system, and molecular size and hydrophobicity of PFAS were the most significant factors affecting the magnitude of root uptake and upward translocation. EPMA-EDS images together with exposure experiments suggested that long-chain hydrophobic compounds tend to be adsorbed and retained on the root epidermis, while short-chain compounds are absorbed and quickly translocated upward. Our findings demonstrated the feasibility of using ferns in phytostabilization and phytoextraction initiatives of PFAS in the future.

Revisiting ancient polyploidy in leptosporangiate ferns

Ferns, and particularly homosporous ferns, have long been assumed to have experienced recurrent whole-genome duplication (WGD) events because of their substantially large genome sizes, surprisingly high chromosome numbers, and high degrees of polyploidy among many extant members. As the number of sequenced fern genomes is limited, recent studies have employed transcriptome data to find evidence for WGDs in ferns. However, they have reached conflicting results concerning the occurrence of ancient polyploidy, for instance, in the lineage of leptosporangiate ferns. Because identifying WGDs in a phylogenetic context is the foremost step in studying the contribution of ancient polyploidy to evolution, we here revisited earlier identified WGDs in leptosporangiate ferns, mainly the core leptosporangiate ferns, by building K_S -age distributions and applying substitution rate corrections and by conducting statistical gene tree-species tree reconciliation analyses. Our integrative analyses not only identified four ancient WGDs in the sampled core leptosporangiate ferns but also identified false positives and false negatives for WGDs that recent studies have reported earlier. In conclusion, we underscore the significance of substitution rate corrections and uncertainties in gene tree-species tree reconciliations in calling WGD events and advance an exemplar workflow to overcome such often-overlooked issues.

Comparison between the Gametophyte and the Sporophyte Transcriptomes of the Endangered Fern Vandenboschia speciosa

Genomic resources are essential to understanding the evolution and functional biology of organisms. Nevertheless, generating genomic resources from endangered species may be challenging due to the scarcity of available specimens and sampling difficulties. In this study, we compare the transcriptomes of the sporophyte and the gametophyte of the endangered fern Vandenboschia speciosa. After Illumina sequencing and de novo transcriptome assembly of the gametophyte, annotation proved the existence of cross-species contamination in the gametophyte sample. Thus, we developed an in silico decontamination step for the gametophyte sequences. Once the quality check of the decontaminated reads passed, we produced a de novo assembly with the decontaminated gametophyte reads (with 43,139 contigs) and another combining the sporophyte and in silico decontaminated gametophyte reads (with 42,918 contigs). A comparison of the enriched GO terms from the top 1000 most expressed transcripts from both tissues showed that the gametophyte GO term set was enriched in sequences involved in development, response to stress, and plastid organization, while the sporophyte GO term set had a larger representation of more general metabolic functions. This study complements the available genomic resources on the life cycle of the endangered fern Vandenboschia speciosa.

Early land plants: Plentiful but neglected nutritional resources for herbivores?

Plants and herbivores have been engaged in a co-evolutionary arms race for millions of years, during which plants evolved various defenses and other traits to cope with herbivores, whereas herbivores evolved traits to overcome the plants' resistance strategies. Herbivores may also avoid certain plants merely because these lack suitable nutrients for their development. Interestingly, the number of herbivores that attack individual early land plants like mosses and ferns is quite low. Among others, poor nutrient quality has been hypothesized to explain the apparent low herbivory pressure on such plants but still waits for scientific evidences. Here, the nutritive suitability of representative mosses and liverworts (bryophytes) and ferns (pteridophytes) for herbivores was investigated using feeding assays combined with quantifications of nutrients (proteins, amino acids, and sugars). Growth and survival of two polyphagous herbivores, a caterpillar and a snail, were monitored when fed on 15 species of bryophytes and pteridophytes, as well as on maize (Zea mays, angiosperm) used as an external indicative nutritional resource. Overall, our results show that the poor performance of the herbivores on the studied early land plants is not correlated with nutritional quality. The growth and performance of snails and caterpillars fed with these plants were highly variable and independent of nutrient content. These findings arguably dismiss the poor nutrient quality hypothesis as the cause of herbivory deficit in bryophytes and pteridophytes. They suggest the possible presence of early resistance traits that have persisted all through the long evolutionary history of plant-herbivore interactions.

Ecotoxicological Risk Assessment of Actellic 50 EC Insecticide on Non-Target Organisms in Parallel with the Application of Standardized Tests

This paper contributes to the ecotoxicological risk assessment of the Actellic 50 EC insecticide (with 50% pirimiphos-methyl as the active substance) tested on non-target organisms. The insecticide concentrations tested were the same for all organisms (0.1, 0.01, and 0.001 mg L^-1 of Actellic 50 EC), with an exposure of 3-5-21 days for plants and 4-5-14 days for animals. The non-target organisms tested were both plants (wheat and two ferns) and animals (the Prussian carp and marsh frog tadpoles). The tested insecticide significantly inhibited the growth of roots in wheat, a result that was also confirmed by a microbiotest application (62% root growth inhibition in sorghum and 100% germination inhibition in white mustard and garden cress). In ferns, even for the lowest concentration, the percentage of germinated spores was inhibited by 40% for Asplenium scolopendrium. The recorded toxicological effects of Actellic 50 EC upon the Prussian carp included a decrease in the respiratory rate and oxygen consumption, an increase in the number of erythrocytes and leukocytes, and an increase in blood glucose levels. The highest concentration (0.1 mg L^-1 of Actellic 50 EC) caused a 50% decrease in the survival rate of marsh frog tadpoles after 5 days of exposure, negatively affecting body volume and length. Given the high degree of toxicity of the insecticide Actellic 50 EC, we recommend continuing investigations on non-target species, including both plants and animals, as the sub-chronic effects are quite little known in the scientific literature.

Filmy Ferns (Hymenophyllaceae) and Associated Spike-Mosses (Selaginellaceae) from the Mid-Cretaceous Kachin Amber, Myanmar

Filmy ferns (Hymenophyllaceae) are the most diverse lineage of the early-diverging leptosporangiate ferns with ca. 430 species widely distributed around the world but with the highest diversity in the humid tropics. However, their fossil record is scarce because of the low preservation potential of the delicate, membranous laminae. So far, no Hymenophyllaceae fossils have been reported from tropical Asia. Here, we describe some fern remains and their syninclusions (spike-mosses) in four pieces of Kachin amber from the mid-Cretaceous of Hukawng Valley, Northern Myanmar, as Hymenophyllites angustus sp. nov., H. kachinensis sp. nov., H. setosus sp. nov. (Hymenophyllaceae) and Selaginella alata sp. nov. (Selaginellaceae), respectively. These fern remains are assigned to Hymenophyllaceae based on the filmy, one-cell thick, decompound pinnatifid laminae and dichotomous venation. They represent the first fossil record of Hymenophyllaceae in tropical Asia. The growth habits of these ferns and associated spike-mosses and their implication for paleoenvironment are discussed. Our study expands the diversity of the cryptogams in mid-Cretaceous Kachin amber. Together with other contemporaneous findings, the present fossils indicate that Hymenophyllaceae have already accumulated some notable diversity in the Cretaceous.

Deep vicariance and frequent transoceanic dispersal shape the evolutionary history of a globally distributed fern family

PREMISE

The historical biogeography of ferns is typically expected to be dominated by long-distance dispersal due to their minuscule spores. However, few studies have inferred the historical biogeography of a large and widely distributed group of ferns to test this hypothesis. Our aims were to determine the extent to which long-distance dispersal vs. vicariance have shaped the history of the fern family Blechnaceae, to explore ecological correlates of dispersal and diversification, and to determine whether these patterns differ between the northern and southern hemispheres.

METHODS

We used sequence data for three chloroplast loci to infer a time-calibrated phylogeny for 154 of 265 species of Blechnaceae, including representatives of all genera in the family. This tree was used to conduct ancestral range reconstruction and stochastic character mapping, estimate diversification rates, and identify ecological correlates of diversification.

RESULTS

Blechnaceae originated in Eurasia and began diversifying in the late Cretaceous. A lineage comprising most extant diversity diversified principally in the austral Pacific region around the Paleocene-Eocene Thermal Maximum. Land connections that existed near the poles during periods of warm climates likely facilitated migration of several lineages, with subsequent climate-mediated vicariance shaping current distributions. Long-distance dispersal is frequent and asymmetrical, with New Zealand/Pacific Islands, Australia, and tropical America being major source areas.

CONCLUSIONS

Ancient vicariance and extensive long-distance dispersal have shaped the history of Blechnaceae in both the northern and southern hemispheres. The exceptional diversity in austral regions appears to reflect rapid speciation in these areas; mechanisms underlying this evolutionary success remain uncertain.

Hydathodes in ferns: their phylogenetic distribution, structure and function

BACKGROUND AND AIMS

Ferns are the second largest group of vascular plants and are distributed nearly worldwide. Although ferns have been integrated into some comparative ecological studies focusing on hydathodes, there is a considerable gap in our understanding of the functional anatomy of these secretory tissues that are found on the vein endings of many fern leaves. In this study, we aimed to investigate the phylogenetic distribution, structure and function of fern hydathodes.

METHODS

We performed a global review on fern hydathodes and their phylogenetic distribution, carried out an ancestral character state reconstruction, and studied the structure, guttation and elemental composition of salt residues of eight species, and the diurnal patterns of xylem pressure of two species.

KEY RESULTS

Hydathodes are known from 1189 fern species, 92 genera and 19 families of 2 orders, Equisetales and Polypodiales. Stochastic character mapping indicated multiple gains and losses of hydathodes at the genus level, occurring especially during the last 50 million years of fern evolution. Hydathodes were located on the adaxial leaf surface and characterized by a cytoplasm-rich, pore-free epidermis, and became functional for several weeks after nearly complete leaf expansion. In two species, positive xylem pressure built up at night, potentially facilitating guttation. Guttation fluid was rich in Ca and often Si, but also contained P, Mg, Na and Al.

CONCLUSIONS

Stochastic character mapping and the structural and functional diversity of hydathodes indicate multiple origins, and their presence/absence in closely related taxa implies secondary losses during fern evolution. Positive xylem pressure and high air humidity play an important role as drivers of guttation. Hydathodes may contribute to the regulation of leaf nutrient stoichiometry by the release of excessive compounds and minerals other than waste products, but the presence of essential chemical elements in salt residues also indicates possible leakage.

The Dynamic Changes of Alternative Electron Flows upon Transition from Low to High Light in the Fern Cyrtomium fortune and the Gymnosperm Nageia nagi

In photosynthetic organisms except angiosperms, an alternative electron sink that is mediated by flavodiiron proteins (FLVs) plays the major role in preventing PSI photoinhibition while cyclic electron flow (CEF) is also essential for normal growth under fluctuating light. However, the dynamic changes of FLVs and CEF has not yet been well clarified. In this study, we measured the P700 signal, chlorophyll fluorescence, and electrochromic shift spectra in the fern Cyrtomium fortune and the gymnosperm Nageia nagi. We found that both species could not build up a sufficient proton gradient (∆pH) within the first 30 s after light abruptly increased. During this period, FLVs-dependent alternative electron flow was functional to avoid PSI over-reduction. This functional time of FLVs was much longer than previously thought. By comparison, CEF was highly activated within the first 10 s after transition from low to high light, which favored energy balancing rather than the regulation of a PSI redox state. When FLVs were inactivated during steady-state photosynthesis, CEF was re-activated to favor photoprotection and to sustain photosynthesis. These results provide new insight into how FLVs and CEF interact to regulate photosynthesis in non-angiosperms.

Bacterial Microbiome in the Phyllo-Endosphere of Highly Specialized Rock Spleenwort

Bacteria communities associated with plants have been given increasing consideration because they are arguably beneficial to their host plants. To understand the ecological and evolutionary impact of these mutualistic associations, it is important to explore the vast unknown territory of bacterial genomic diversity and their functional contributions associated with the major branches of the tree-of-life. Arguably, this aim can be achieved by profiling bacterial communities by applying high throughput sequencing approaches, besides establishing model plant organisms to test key predictions. This study utilized the Illumina Miseq reads of bacterial 16S rRNA sequences to determine the bacterial diversity associated with the endosphere of the leaves of the highly specialized rock spleenwort Asplenium delavayi (Aspleniaceae). By documenting the bacterial communities associated with ferns collected in natural occurrence and cultivation, this study discovered the most species-rich bacterial communities associated with terrestrial ferns reported until now. Despite the substantial variations of species diversity and composition among accessions, a set of 28 bacterial OTUs was found to be shared among all accessions. Functional analyses recovered evidence to support the predictions that changes in bacterial community compositions correspond to functional differentiation. Given the ease of cultivating this species, Asplenium delavayi is introduced here as a model organism to explore the ecological and evolutionary benefits created by mutualistic associations between bacteria and ferns.

Cell growth dynamics in two types of apical meristems in fern gametophytes

In contrast to seed plants, the gametophytes of seed-free plants develop pluripotent meristems, which promote and sustain their independent growth and development. To date, the cellular basis of meristem development in gametophytes of seed-free ferns remains largely unknown. In this study, we used Woodsia obtusa, the blunt-lobe cliff fern, to quantitatively determine cell growth dynamics in two different types of apical meristems - the apical initial centered meristem and the multicellular apical meristem in gametophytes. Through confocal time-lapse live imaging and computational image analysis and quantification, we determined unique patterns of cell division and growth that sustain or terminate apical initials, dictate the transition from apical initials to multicellular apical meristems, and drive proliferation of apical meristems in ferns. Quantitative results showed that small cells correlated to active cell division in fern gametophytes. The marginal cells of multicellular apical meristems in fern gametophytes undergo division in both anticlinal and periclinal orientations, not only increasing cell numbers but also playing a dominant role in increasing cell layers during gametophyte development. All these findings provide insights into the function and regulation of meristems in gametophytes of seed-free vascular plants, suggesting both conserved and diversified mechanisms underlying meristem cell proliferation across land plants.

Excavation of Genes Responsive to Brassinosteroids by Transcriptome Sequencing in Adiantum flabellulatum Gametophytes

Brassinosteroids (BRs) are a class of polyhydroxysteroid plant hormones; they play important roles in the development and stress resistance of plants. The research on BRs has mainly been carried out in angiosperms, but in ferns-research is still limited to the physiological level and is not in-depth. In this study, Adiantum flabellulatum gametophytes were used as materials and treated with 10^-6 M brassinolide (BL). The differentially expressed genes (DEGs) responsive to BRs were identified by transcriptome sequencing, GO, KEGG analysis, as well as a quantitative real-time polymerase chain reaction. From this, a total of 8394 DEGs were screened. We found that the expressions of photosynthetic genes were widely inhibited by high concentrations of BL in A. flabellulatum gametophytes. Moreover, we detected many BR synthase genes, except BR6ox2, which may be why castasterone (CS) rather than BL was detected in ferns. Additionally, we identified (for the first time) that the expressions of BR synthase genes (CYP90B1, CYP90C1, CYP90D1, CPD, and BR6ox1) were negatively regulated by BL in fern gametophytes, which indicated that ferns, including gametophytes, also needed the regulatory mechanism for maintaining BR homeostasis. Based on transcriptome sequencing, this study can provide a large number of gene expression data for BRs regulating the development of fern gametophytes.

Phylogenomic Analysis Reconstructed the Order Matoniales from Paleopolyploidy Veil

Phylogenetic conflicts limit our understanding of the evolution of terrestrial life under multiple whole genome duplication events, and the phylogeny of early terrestrial plants remains full of controversy. Although much incongruence has been solved with so-called robust topology based on single or lower copy genes, the evolutionary mechanisms behind phylogenetic conflicts such as polyploidization remain poorly understood. Here, through decreasing the effects of polyploidization and increasing the samples of species, which represent all four orders and eight families that comprise early leptosporangiate ferns, we have reconstructed a robust phylogenetic tree and network with 1125 1-to-1 orthologs based on both coalescent and concatenation methods. Our data consistently suggest that Matoniales, as a monophyletic lineage including Matoniaceae and Dipteridaceae, should be redefined as an ordinal rank. Furthermore, we have identified and located at least 11 whole-genome duplication events within the evolutionary history of four leptosporangiates lineages, and associated polyploidization with higher speciation rates and mass extinction events. We hypothesize that paleopolyploidization may have enabled leptosporangiate ferns to survive during mass extinction events at the end Permian period and then flourish throughout the Mesozoic era, which is supported by extensive fossil records. Our results highlight how ancient polyploidy can result in rapid species radiation, thus causing phylogenetic conflicts yet allowing plants to survive and thrive during mass extinction events.

Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation

PREMISE

Biodiversity is often only measured with species richness; however, this metric ignores evolutionary history and is not sufficient for making conservation decisions. Here, we characterize multiple facets and drivers of biodiversity to understand how these relate to bioregions and conservation status in the ferns of Japan.

METHODS

We compiled a community data set of 1239 grid cells (20 × 20 km each) including 672 taxa based on >300,000 specimen records. We combined the community data with a phylogeny and functional traits to analyze taxonomic, phylogenetic, and functional diversity and modeled biodiversity metrics in response to environmental factors and reproductive mode. Hierarchical clustering was used to delimit bioregions. Conservation status and threats were assessed by comparing the overlap of significantly diverse grid cells with conservation zones and range maps of native Japanese deer.

RESULTS

Taxonomic richness was highest at mid-latitudes. Phylogenetic and functional diversity and phylogenetic endemism were highest in small southern islands. Relative phylogenetic and functional diversity were high at high and low latitudes, and low at mid-latitudes. Grid cells were grouped into three (phylogenetic) or four (taxonomic) major bioregions. Temperature and apomixis were identified as drivers of biodiversity patterns. Conservation status was generally high for grid cells with significantly high biodiversity, but the threat due to herbivory by deer was greater for taxonomic richness than other metrics.

CONCLUSIONS

Our integrative approach reveals previously undetected patterns and drivers of biodiversity in the ferns of Japan. Future conservation efforts should recognize that threats can vary by biodiversity metric and consider multiple metrics when establishing conservation priorities.

Once more unto the breach, dear friends: Resolving the origins and relationships of the Pellaea wrightiana hybrid complex

PREMISE

The taxonomic status of Wright's cliff brake fern, Pellaea wrightiana, has been in dispute ever since it was first described by Hooker in 1858. Previously published evidence suggested that this "taxon" may represent a polyploid complex rather than a single discrete species, a hypothesis tested here using a multifaceted analytical approach.

METHODS

Data derived from cytogenetics, spore analyses, leaf morphometrics, enzyme electrophoresis, and phylogenetic analyses of plastid and nuclear DNA sequences are used to elucidate the origin, relationships, and taxonomic circumscription of P. wrightiana.

RESULTS

Plants traditionally assigned to this taxon represent three distinct polyploids. The most widespread, P. wrightiana, is a fertile allotetraploid that arose through hybridization between two divergent diploid species, P. truncata and P. ternifolia. Sterile triploids commonly identified as P. wrightiana, were found to be backcross hybrids between this fertile tetraploid and diploid P. truncata. Relatively common across Arizona and New Mexico, they are here assigned to P. ×wagneri hyb. nov. In addition, occasional sterile tetraploid plants assigned to P. wrightiana are shown here to be hybrids between the fertile allotetraploid and the tetraploid P. ternifolia subsp. arizonica. These tetraploid hybrids originated independently in two regions of parental sympatry (southern Arizona and west Texas) and are here assigned to P. ×gooddingii hyb. nov.

CONCLUSIONS

Weaving together data from a diversity of taxonomic approaches, we show that plants identified as P. wrightiana represent three morphologically distinguishable polyploids that have arisen through repeated hybridization events involving the divergent sexual taxa P. ternifolia and P. truncata.

Rapid diversification of vascular architecture underlies the Carboniferous fern radiation

Vascular plants account for 93% of Earth's terrestrial flora. Xylem and phloem, vital for transporting water and nutrients through the plant, unite this diverse clade. Three-dimensional arrangements of these tissues (vascular architecture) are manifold across living and extinct species. However, the evolutionary processes underlying this variation remain elusive. Using ferns, a diverse clade with multiple radiations over their ca 400-million-year history, we synthesized data across 3339 species to explore the tempo and mode of vascular evolution and to contextualize dynamics of phenotypic innovation during major fern diversification events. Our results reveal three paradigm shifts in our understanding of fern vascular evolution. (i) The canonical theory on the stepwise and unidirectional evolution of vascular architecture does not capture the complexities of character evolution among ferns. Rather, a new model permitting additional transitions, rate heterogeneity and multiple reversions is more likely. (ii) Major shifts in vascular architecture correspond to developmental changes in body size, not regional water availability. (iii) The early Carboniferous radiation of crown-group ferns was characterized by an explosion of phenotypic innovation. By contrast, during the Cretaceous and Cenozoic rise of eupolypods, rates of vascular evolution were dramatically low and seemingly decoupled from lineage diversification.

The biology of C. richardii as a tool to understand plant evolution

The fern Ceratopteris richardii has been studied as a model organism for over 50 years because it is easy to grow and has a short life cycle. In particular, as the first homosporous vascular plant for which genomic resources were developed, C. richardii has been an important system for studying plant evolution. However, we know relatively little about the natural history of C. richardii. In this article, we summarize what is known about this aspect of C. richardii, and discuss how learning more about its natural history could greatly increase our understanding of the evolution of land plants.

The ecology and physiology of fern gametophytes: A methodological synthesis

All green plants alternate between the gametophyte and sporophyte life stages, but only seed-free vascular plants (ferns and lycophytes) have independent, free-living gametophytes. Fern and lycophyte gametophytes are significantly reduced in size and morphological complexity relative to their sporophytic counterparts and have often been overlooked in ecological and physiological studies. Understanding the ecological and physiological factors that directly impact this life stage is of critical importance because the ultimate existence of a sporophyte is dependent upon successful fertilization in the gametophyte generation. Furthermore, previous research has shown that the dual nature of the life cycle and the high dispersibility of spores can result in different geographic patterns between gametophytes and their respective sporophytes. This variation in distribution patterns likely exacerbates the separation of selective pressures acting on gametophyte and sporophyte generations, and can uniquely impact a species' ecology and physiology. Here, we provide a review of historical and contemporary methodologies used to examine ecological and physiological aspects of fern gametophytes, as well as those that allow for comparisons between the two generations. We conclude by suggesting methodological approaches to answer currently outstanding questions. We hope that the information covered herein will serve as a guide to current researchers and stimulate future discoveries in fern gametophyte ecology and physiology.

Why Do Heterosporous Plants Have So Few Chromosomes?

The mechanisms controlling chromosome number, size, and shape, and the relationship of these traits to genome size, remain some of the least understood aspects of genome evolution. Across vascular plants, there is a striking disparity in chromosome number between homosporous and heterosporous lineages. Homosporous plants (comprising most ferns and some lycophytes) have high chromosome numbers compared to heterosporous lineages (some ferns and lycophytes and all seed plants). Many studies have investigated why homosporous plants have so many chromosomes. However, homospory is the ancestral condition from which heterospory has been derived several times. Following this phylogenetic perspective, a more appropriate question to ask is why heterosporous plants have so few chromosomes. Here, we review life history differences between heterosporous and homosporous plants, previous work on chromosome number and genome size in each lineage, known mechanisms of genome downsizing and chromosomal rearrangements, and conclude with future prospects for comparative research.

Quantitative live-imaging reveals the dynamics of apical cells during gametophyte development in ferns

Meristems in land plants share conserved functions but develop highly variable structures. Meristems in seed-free plants, including ferns, usually contain one or a few pyramid-/wedge-shaped apical cells (ACs) as initials, which are lacking in seed plants. It remained unclear how ACs promote cell proliferation in fern gametophytes and whether any persistent AC exists to sustain fern gametophyte development continuously. Here, we uncovered previously undefined ACs maintained even at late developmental stages in fern gametophytes. Through quantitative live-imaging, we determined division patterns and growth dynamics that maintain the persistent AC in Sphenomeris chinensis, a representative fern. The AC and its immediate progenies form a conserved cell packet, driving cell proliferation and prothallus expansion. At the apical centre of gametophytes, the AC and its adjacent progenies display small dimensions resulting from active cell division instead of reduced cell expansion. These findings provide insight into diversified meristem development in land plants.

Edaphic heterogeneity and the evolutionary trajectory of Amazonian plant communities

We investigated how the phylogenetic structure of Amazonian plant communities varies along an edaphic gradient within the non-inundated forests. Forty localities were sampled on three terrain types representing two kinds of soil: clayey soils of a high base cation concentration derived from the Solimões formation, and loamy soils with lower base cation concentration derived from the Içá formation and alluvial terraces. Phylogenetic community metrics were calculated for each locality for ferns and palms both with ferns as one group and for each of three fern clades with a crown group age comparable to that of palms. Palm and fern communities showed significant and contrasting phylogenetic signals along the soil gradient. Fern species richness increased but standard effect size of mean pairwise distance (SES.MPD) and variation of pairwise distances (VPD) decreased with increasing soil base cation concentration. In contrast, palm communities were more species rich on less cation-rich soils and their SES.MPD increased with soil base cation concentration. Species turnover between the communities reflected the soil gradient slightly better when based on species occurrences than when phylogenetic distances between the species were considered. Each of the three fern subclades behaved differently from each other and from the entire fern clade. The fern clade whose phylogenetic patterns were most similar to those of palms also resembled palms in being most species-rich on cation-poor soils. The phylogenetic structuring of local plant communities varies along a soil base cation concentration gradient within non-inundated Amazonian rain forests. Lineages can show either similar or different phylogenetic community structure patterns and evolutionary trajectories, and we suggest this to be linked to their environmental adaptations. Consequently, geological heterogeneity can be expected to translate into a potentially highly diverse set of evolutionarily distinct community assembly pathways in Amazonia and elsewhere.

Polypodium vulgare L. (Polypodiaceae) as a Source of Bioactive Compounds: Polyphenolic Profile, Cytotoxicity and Cytoprotective Properties in Different Cell Lines

Pteridophytes, represented by ferns and allies, are an important phytogenetic bridge between lower and higher plants. Ferns have evolved independently of any other species in the plant kingdom being its secondary metabolism a reservoir of phytochemicals characteristic of this taxon. The study of the potential uses of Polypodium vulgare L. (Polypodiaceae) as medicinal plant has increased in recent years particularly when in 2008 the European Medicines Agency published a monograph about the rhizome of this species. Our objective is to provide scientific knowledge on the polar constituents extracted from the fronds of P. vulgare, one of the main ferns of European distribution, to contribute to the validation of certain traditional uses. Specifically, we have characterized the methanolic extract of P. vulgare fronds (PVM) by HPLC-DAD and investigated its potential cytotoxicity, phototoxicity, ROS production and protective effects against oxidative stress by using in vitro methods. The 3T3, HaCaT, HeLa, HepG2, MCF-7 and A549 were the cell lines used to evaluate the possible cytotoxic behaviour of the PVM. HPLC-DAD was utilized to validate the polyphenolic profile of the extract. H₂O₂ and UVA were the prooxidant agents to induce oxidative stress by different conditions in 3T3 and HaCaT cell lines. Antioxidant activity of in vitro PVM in 3T3 and HaCaT cell lines was evaluated by ROS assay. Our results demonstrate that PVM contains significant amounts of shikimic acid together with caffeoylquinic acid derivatives and flavonoids such as epicatechin and catechin; PVM is not cytotoxic at physiological concentrations against the different cell lines, showing cytoprotective and cellular repair activity in 3T3 fibroblast cells. This biological activity could be attributed to the high content of polyphenolic compounds. The fronds of the P. vulgare are a source of polyphenolic compounds, which can be responsible for certain traditional uses like wound healing properties. In the present work, fronds of the common polypody are positioned as a candidate for pharmaceutical applications based on traditional medicine uses but also as potential food ingredients due to lack of toxicity at physiological concentrations.

Receptor-mediated biological effects of extracts obtained from three Asplenium species

This study reports the effects of aqueous extracts obtained from three fern species of Bulgarian origin: Asplenium ceterach L., Asplenium scolopendrium L., and Asplenium trichomanes L. on the contractility and bioelectrogenesis of rat gastric smooth muscle tissues. In the concentration range 0.015-0.150 mg/mL the three extracts contracted smooth muscle tissues in a concentration-dependent manner. The contractions caused by A. ceterach L. and A. scolopendrium L. extracts (0.150 mg/mL) were reduced by ketanserin (5 × 10^-7 and 5 × 10^-6 mol/L), an antagonist of serotonin 5-HT2 receptor. The contraction evoked by A. trichomanes L. (0.150 mg/mL) was significantly reduced by 1 × 10^-6 mol/L atropine, an antagonist of muscarinic receptors, and turned into relaxation against the background of 3 × 10^-7 mol/L galantamine. After combined pretreatment with galantamine and l-arginine (5 × 10^-4 mol/L), this relaxation become more pronounced. The study demonstrates that constituents of A. ceterach L. and A. scolopendrium L. extracts act as agonists of 5-HT2 receptors and cause contraction by activating serotonergic signaling system. A. trichomanes L.-induced reaction is an additive result of two opposite-in-character effects. The dominant contraction is initiated by inhibition of acetylcholinesterase activity. The relaxation develops with pre-inhibited acetylcholinesterase, it is significantly potentiated by l-arginine, and therefore associated with nitrergic signaling pathway.

Transposable element landscapes illuminate past evolutionary events in the endangered fern Vandenboschia speciosa

Vandenboschia speciosa is an endangered tetraploid fern species with a large genome (10.5 Gb). Its geographical distribution is characterized by disjoined tertiary flora refuges, with relict populations that survived past climate crises. Here, we analyzed the transposable elements (TEs) and found that they comprise approximately 76% of the V. speciosa genome, thus being the most abundant type of DNA sequence in this gigantic genome. The V. speciosa genome is composed of 51% and 5.6% of Class I and Class II elements, respectively. LTR retrotransposons were the most abundant TEs in this species (at least 42% of the genome), followed by non-LTR retrotransposons, which constituted at least 8.7% of the genome of this species. We introduce an additional analysis to identify the nature of non-annotated elements (19% of the genome). A BLAST search of the non-annotated contigs against the V. speciosa TE database allowed for the identification of almost half of them, which were most likely diverged sequence variants of the annotated TEs. In general, the TE composition in V. speciosa resembles the TE composition in seed plants. In addition, repeat landscapes revealed three episodes of amplification for all TEs, most likely due to demographic changes associated with past climate crises.

Phylogenetic comparative morphological analysis of fern spores in subfamily Pteridoideae (Pteridaceae, Pteridophyta)

Scanning electron microscopy (SEM) was used to characterize spore morphology of 24 taxa of the subfamily Pteridoideae C. Chr. ex Crabbe, Jermy & Mickel of the family Pteridaceae E.D.M. Kirchn. The family is considered to be one of the most taxonomically confusing families due to its high level of polymorphism. The standardized data on spore morphology of the subfamily Pteridoideae were projected onto the final phylogenetic tree in the Mesquite program. This approach made it possible to carry out a comprehensive interdisciplinary analysis of the evolution of spore morphology characters of the subfamily Pteridoideae, as well as to assess the relationships in the family Pteridaceae. The equatorial ridge (cingulum, "flange") has been proven as one of the key spore morphology features, which confirms the close relationship of "Onychium clade" with Pteris. The species-specific characters of the subfamily are fold and tubercle along laesura, equatorial ridge on proximal and distal side, tubercle, and folds on proximal and distal side. The knowledge will help to solve the problems of taxonomy in the family Preridaceae and to supplement the information on the natural classification of the subfamily Pteridoideae.

Transcriptome-wide SNPs for Botrychium lunaria ferns enable fine-grained analysis of ploidy and population structure

Ferns are the second most diverse group of land plants after angiosperms. Extant species occupy a wide range of habitats and contribute significantly to ecosystem functioning. Despite the importance of ferns, most taxa are poorly covered by genomic resources and within‐species studies based on high‐resolution markers are entirely lacking. The genus Botrychium belongs to the family Ophioglossaceae, which includes species with very large genomes and chromosome numbers (e.g., Ophioglossum reticulatum 2n = 1520). The genus has a cosmopolitan distribution with 35 species, half of which are polyploids. Here, we establish a transcriptome for Botrychium lunaria (L.) Sw., a diploid species with an extremely large genome of about ~19.0–23.7 Gb. We assembled 25,677 high‐quality transcripts with an average length of 1,333 bp based on deep RNA‐sequencing of a single individual. We sequenced 11 additional transcriptomes of individuals from two populations in Switzerland, including the population of the reference individual. Based on read mapping to reference transcript sequences, we identified 374,463 single nucleotide polymorphisms (SNPs) segregating among individuals for an average density of 14 SNPs per kilobase. We found that all 12 transcriptomes were most likely from diploid individuals. The transcriptome‐wide markers provided unprecedented resolution of the population genetic structure, revealing substantial variation in heterozygosity among individuals. We also constructed a phylogenomic tree of 92 taxa representing all fern orders to ascertain the placement of the genus Botrychium. High‐quality transcriptomic resources and SNP sets constitute powerful population genomic resources to investigate the ecology, and evolution of fern populations.

De Novo Sporophyte Transcriptome Assembly and Functional Annotation in the Endangered Fern Species Vandenboschia speciosa (Willd.) G. Kunkel

We sequenced the sporophyte transcriptome of Killarney fern (Vandenboschia speciosa (Willd.) G. Kunkel). In addition to being a rare endangered Macaronesian-European endemism, this species has a huge genome (10.52 Gb) as well as particular biological features and extreme ecological requirements. These characteristics, together with the systematic position of ferns among vascular plants, make it of high interest for evolutionary, conservation and functional genomics studies. The transcriptome was constructed de novo and contained 36,430 transcripts, of which 17,706 had valid BLAST hits. A total of 19,539 transcripts showed at least one of the 7362 GO terms assigned to the transcriptome, whereas 6547 transcripts showed at least one of the 1359 KEGG assigned terms. A prospective analysis of functional annotation results provided relevant insights on genes involved in important functions such as growth and development as well as physiological adaptations. In this context, a catalogue of genes involved in the genetic control of plant development, during the vegetative to reproductive transition, in stress response as well as genes coding for transcription factors is given. Altogether, this study provides a first step towards understanding the gene expression of a significant fern species and the in silico functional and comparative analyses reported here provide important data and insights for further comparative evolutionary studies in ferns and land plants in general.

Variation in frequency of plastid RNA editing within Adiantum implies rapid evolution in fern plastomes

PREMISE

Recent studies of plant RNA editing have demonstrated that the number of editing sites can vary widely among large taxonomic groups (orders, families). Yet, very little is known about intrageneric variation in frequency of plant RNA editing, and no study has been conducted in ferns.

METHODS

We determined plastid RNA-editing counts for two species of Adiantum (Pteridaceae), A. shastense and A. aleuticum, by implementing a pipeline that integrated read-mapping and SNP-calling software to identify RNA-editing sites. We then compared the edits found in A. aleuticum and A. shastense with previously published edits from A. capillus-veneris by generating alignments for each plastid gene.

RESULTS

We found direct evidence for 505 plastid RNA-editing sites in A. aleuticum and 509 in A. shastense, compared with 350 sites in A. capillus-veneris. We observed striking variation in the number and location of the RNA-editing sites among the three species, with reverse (U-to-C) editing sites showing a higher degree of conservation than forward (C-to-U) sites. Additionally, sites involving start and stop codons were highly conserved.

CONCLUSIONS

Variation in the frequency of RNA editing within Adiantum implies that RNA-editing sites can be rapidly gained or lost throughout evolution. However, varying degrees of conservation between both C-to-U and U-to-C sites and sites in start or stop codons, versus other codons, hints at the likely independent origin of both types of edits and a potential selective advantage conferred by RNA editing.

Partial mycoheterotrophy is common among chlorophyllous plants with Paris-type arbuscular mycorrhiza

BACKGROUND AND AIMS

An arbuscular mycorrhiza is a mutualistic symbiosis with plants as carbon providers for fungi. However, achlorophyllous arbuscular mycorrhizal species are known to obtain carbon from fungi, i.e. they are mycoheterotrophic. These species all have the Paris type of arbuscular mycorrhiza. Recently, two chlorophyllous Paris-type species proved to be partially mycoheterotrophic. In this study, we explore the frequency of this condition and its association with Paris-type arbuscular mycorrhiza.

METHODS

We searched for evidence of mycoheterotrophy in all currently published 13C, 2H and 15N stable isotope abundance patterns suited for calculations of enrichment factors, i.e. isotopic differences between neighbouring Paris- and Arum-type species. We found suitable data for 135 plant species classified into the two arbuscular mycorrhizal morphotypes.

KEY RESULTS

About half of the chlorophyllous Paris-type species tested were significantly enriched in 13C and often also enriched in 2H and 15N, compared with co-occurring Arum-type species. Based on a two-source linear mixing model, the carbon gain from the fungal source ranged between 7 and 93 % with ferns > horsetails > seed plants. The seed plants represented 13 families, many without a previous record of mycoheterotrophy. The 13C-enriched chlorophyllous Paris-type species were exclusively herbaceous perennials, with a majority of them thriving on shady forest ground.

CONCLUSIONS

Significant carbon acquisition from fungi appears quite common and widespread among Paris-type species, this arbuscular mycorrhizal morphotype probably being a pre-condition for developing varying degrees of mycoheterotrophy.

Biogeography and genome size evolution of the oldest extant vascular plant genus, Equisetum (Equisetaceae)

BACKGROUND AND AIMS

Extant plant groups with a long fossil history are key elements in understanding vascular plant evolution. Horsetails (Equisetum, Equisetaceae) have a nearly continuous fossil record dating back to the Carboniferous, but their phylogenetic and biogeographic patterns are still poorly understood. We use here the most extensive phylogenetic analysis to date as a framework to evaluate their age, biogeography and genome size evolution.

METHODS

DNA sequences of four plastid loci were used to estimate divergence times and investigate the biogeographic history of all extant species of Equisetum. Flow cytometry was used to study genome size evolution against the framework of phylogenetic relationships in Equisetum.

KEY RESULTS

On a well-supported phylogenetic tree including all extant Equisetum species, a molecular clock calibrated with multiple fossils places the node at which the outgroup and Equisetum diverged at 343 Mya (Early Carboniferous), with the first major split among extant species occurring 170 Mya (Middle Jurassic). These dates are older than those reported in some other recent molecular clock studies but are largely in agreement with a timeline established by fossil appearance in the geological record. Representatives of evergreen subgenus Hippochaete have much larger genome sizes than those of deciduous subgenus Equisetum, despite their shared conserved chromosome number. Subgenus Paramochaete has an intermediate genome size and maintains the same number of chromosomes.

CONCLUSIONS

The first divergences among extant members of the genus coincided with the break-up of Pangaea and the resulting more humid, warmer climate. Subsequent tectonic activity most likely involved vicariance events that led to species divergences combined with some more recent, long-distance dispersal events. We hypothesize that differences in genome size between subgenera may be related to the number of sperm flagellae.

A De Novo Transcriptome Assembly of Ceratopteris richardii Provides Insights into the Evolutionary Dynamics of Complex Gene Families in Land Plants

As the closest extant sister group to seed plants, ferns are an important reference point to study the origin and evolution of plant genes and traits. One bottleneck to the use of ferns in phylogenetic and genetic studies is the fact that genome-level sequence information of this group is limited, due to the extreme genome sizes of most ferns. Ceratopteris richardii (hereafter Ceratopteris) has been widely used as a model system for ferns. In this study, we generated a transcriptome of Ceratopteris, through the de novo assembly of the RNA-seq data from 17 sequencing libraries that are derived from two sexual types of gametophytes and five different sporophyte tissues. The Ceratopteris transcriptome, together with 38 genomes and transcriptomes from other species across the Viridiplantae, were used to uncover the evolutionary dynamics of orthogroups (predicted gene families using OrthoFinder) within the euphyllophytes and identify proteins associated with the major shifts in plant morphology and physiology that occurred in the last common ancestors of euphyllophytes, ferns, and seed plants. Furthermore, this resource was used to identify and classify the GRAS domain transcriptional regulators of many developmental processes in plants. Through the phylogenetic analysis within each of the 15 GRAS orthogroups, we uncovered which GRAS family members are conserved or have diversified in ferns and seed plants. Taken together, the transcriptome database and analyses reported here provide an important platform for exploring the evolution of gene families in land plants and for studying gene function in seed-free vascular plants.

Functional Diversity in Ferns Is Driven by Species Richness Rather Than by Environmental Constraints

Functional traits determine how species interact with their abiotic and biotic environment. In turn, functional diversity describes how assemblages of species as a whole are adapted to their environment, which also determines how they might react to changing conditions. To fully understand functional diversity, it is fundamental to (a) disentangle the influences of environmental filtering and species richness from each other, (b) assess if the trait space saturates at high levels of species richness, and (c) understand how changes in species numbers affect the relative importance of the trait niche expansion and packing. In the present study, we determined functional diversity of fern assemblages by describing morphological traits related to resource acquisition along four tropical elevational transects with different environmental conditions and species richness. We used several functional diversity indices and their standardized effect size to consider different aspects of functional diversity. We contrasted these aspects of functional diversity with climate data and species richness using linear models and linear mixed models. Our results show that functional morphological trait diversity was primarily driven by species richness and only marginally by environmental conditions. Moreover, increasing species richness contributed progressively to packing of the morphological niche space, while at the same time decreasing morphological expansion until a saturation point was reached. Overall, our findings suggest that the density of co-occurring species is the fundamental driving force of morphological niche structure, and environmental conditions have only an indirect influence on fern resource acquisition strategies.

Insights into the evolutionary history and widespread occurrence of antheridiogen systems in ferns

Sex expression of homosporous ferns is controlled by multiple factors, one being the antheridiogen system. Antheridiogens are pheromones released by sexually mature female fern gametophytes, turning nearby asexual gametophytes precociously male. Nevertheless, not all species respond. It is still unknown how many fern species use antheridiogens, how the antheridiogen system evolved, and whether it is affected by polyploidy and/or apomixis. We tested the response of 68 fern species to antheridiogens in cultivation. These results were combined with a comprehensive review of literature to form the largest dataset of antheridiogen interactions to date. Analyzed species also were coded as apomictic or sexual and diploid or polyploid. Our final dataset contains a total of 498 interactions involving 208 species (c. 2% of all ferns). About 65% of studied species respond to antheridiogen. Multiple antheridiogen types were delimited and their evolution is discussed. Antheridiogen responsiveness was not significantly affected by apomixis or polyploidy. Antheridiogens are widely used by ferns to direct sex expression. The antheridiogen system likely evolved multiple times and provides homosporous ferns with the benefits often associated with heterospory, such as increased rates of outcrossing. Despite expectations, antheridiogens may be beneficial to polyploids and apomicts.

Vascular Plant Herbarium at the Kandalaksha Strict Nature Reserve (KAND), Russia

BACKGROUND

The present-day demand for digital availability of distributional data in biodiversity studies requires a special effort in assembling and editing the data otherwise scattered in paper literature and herbarium collections, which can be poorly accessible or little understood to present-day users and especially automatic data processors. Our project on developing the information resource for the vascular plant flora of Murmansk Region, Russia, includes processing and making digitally available all the data on the taxonomy and distribution of this flora. So far, published distribution maps are limited to the old set in the Flora of Murmansk Region (published in 1953-1966) and the Red Data Book of Murmansk Region (ed. 2, published in 2014). These publications did not take into account the main part of the herbarium collections kept at the Kandalaksha Strict Nature Reserve, which are the basis for numerous local publications that appear scattered and, therefore, little accessible nowadays.

NEW INFORMATION

We present a complete dataset of all holdings of vascular plants in the Herbarium of the Kandalaksha Strict Nature Reserve, totalling 10,218 specimens collected during 1947-2019, which are referable to 764 species and 19 subspecies. All specimens were georeferenced with the utmost precision available. This dataset offers a complete and dense coverage of the Nature Reserve's territory (islands and adjacent mainland coastal areas of the Barents and White Seas, Murmansk Region and Republic of Karelia, Russia); these data are little represented in herbarium collections elsewhere.