Trends and concepts in fern classification

Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls

Ferns are essential for understanding plant evolution; however, their large and intricate genomes have kept their genetic landscape largely unexplored, with only a few genomes sequenced and limited transcriptomic data available. To bridge this gap, we generated extensive RNA-sequencing data across various organs from 22 representative fern species, resulting in high-quality transcriptome assemblies. These data enabled us to construct a time-calibrated phylogeny for ferns, encompassing all major clades, which revealed numerous instances of whole-genome duplication. We highlighted the distinctiveness of fern genetics, discovering that half of the identified gene families are unique to ferns. Our exploration of fern cell walls through biochemical and immunological analyses uncovered the presence of the lignin syringyl unit, along with evidence of its independent evolution in ferns. Additionally, the identification of an unusual sugar in fern cell walls suggests a divergent evolutionary trajectory in cell wall biochemistry, probably influenced by gene duplication and sub-functionalization. To facilitate further research, we have developed an online database that includes preloaded genomic and transcriptomic data for ferns and other land plants. We used this database to demonstrate the independent evolution of lignocellulosic gene modules in ferns. Our findings provide a comprehensive framework illustrating the unique evolutionary journey ferns have undertaken since diverging from the last common ancestor of euphyllophytes more than 360 million years ago.

Global Availability of Plant DNA Barcodes as Genomic Resources to Support Basic and Policy-Relevant Biodiversity Research

Genetic technologies such as DNA barcoding make it easier and less expensive to monitor biodiversity and its associated ecosystem services, particularly in biodiversity hotspots where traditional assessments are challenging. Successful use of these data-driven technologies, however, requires access to appropriate reference data. We reviewed the >373,584 reference plant DNA barcodes in public repositories and found that they cumulatively cover a remarkable quarter of the ~435,000 extant land plant species (Embryophyta). Nevertheless, coverage gaps in tropical biodiversity hotspots reflect well-documented biases in biodiversity science - most reference specimens originated in the Global North. Currently, at least 17% of plant families lack any reference barcode data whatsoever, affecting tropical and temperate regions alike. Investigators often emphasise the importance of marker choice and the need to ensure protocols are technically capable of detecting and identifying a broad range of taxa. Yet persistent geographic and taxonomic gaps in the reference datasets show that these protocols rely upon risk undermining all downstream applications of the strategy, ranging from basic biodiversity monitoring to policy-relevant objectives - such as the forensic authentication of materials in illegal trade. Future networks of investigators could work strategically to improve data coverage, which will be essential in global efforts to conserve biodiversity while advancing more fair and equitable access to benefits arising from genetic resources.

Phylogenomics of Paragymnopteris (Cheilanthoideae, Pteridaceae): Insights from plastome, mitochondrial, and nuclear datasets

Previous studies have shown that at least six genera of the Cheilanthoideae, a subfamily of the fern family Pteridaceae, may not be monophyletic. In these non-monophyletic genera, the Old-World genus Paragymnopteris including approximately five species have long been controversial. In this study, with an extensive taxon sampling of Paragymnopteris, we assembled 19 complete plastomes of all recognized Paragymnopteris species, plastomes of Pellaea (3 species) and Argyrochosma (1 species), as well as transcriptomes from Paragymnopteris (6 species) and Argyrochosma (1 species). We conducted a comprehensive and systematic phylogenomic analysis focusing on the contentious relationships among the genus of Paragymnopteris through 9 plastid makers, the plastomes, mitochondria, nuclear ribosomal cistron genomes, and single-copy nuclear genes. Moreover, we further combined distribution, ploidy, and morphological features to investigate the evolution of Paragymnopteris. The backbone of Paragymnopteris was resolved consistently in the nuclear and plastid phylogenies. Our major results include: (1) Paragymnopteris is not monophyletic including two fully supported clades; (2) confirming that Paragymnopteris delavayi var. intermedia is a close relative of P. delavayi instead of P. marantae var. marantae; (3) the chromosome base number may not be a stable trait which has previously been used as an important character to divide Paragymnopteris into two groups; and (4) gene flow or introgression might be the main reason for the gene trees conflict of Paragymnopteris, but both gene flow and ILS might simultaneously and/or cumulatively act on the conflict of core pellaeids. The robust phylogeny of Paragymnopteris presented here will help us for the future studies of the arid to semi-arid ferns of Cheilanthoideae at the evolutionary, physiological, developmental, and omics-based levels.

Genomic signatures of inbreeding and mutation load in tree ferns

Ferns (Pteridophyta), as the second largest group of vascular plants, play important roles in ecosystem functioning. Homosporous ferns exhibit a remarkable range of mating systems, from extreme inbreeding to obligate outcrossing, which may have significant evolutionary and ecological implications. Despite their significance, the impact of genome-wide inbreeding on genetic diversity and mutation load within the fern lineage remain largely unexplored. In this study, we utilized whole-genome sequencing to investigate the genomic signatures of inbreeding and genetic load in three Alsophila tree fern species. Our analysis revealed extremely high inbreeding in A. spinulosa, in contrast to the predominantly outcrossing observed in A. costularis and A. latebrosa. This difference likely reflects divergent mating systems and demographic histories. Consistent with its extreme inbreeding propensity, A. spinulosa exhibits reduced genetic diversity and a pronounced decline in effective population size. Comparison of genetic load revealed an overall reduction in deleterious mutations in the highly inbred A. spinulosa, highlighting that long-term inbreeding may have contributed to the purging of strongly deleterious mutations, thereby prolonging the survival of A. spinulosa. Despite this, however, A. spinulosa carries a substantive realized genetic load that may potentially instigate future fitness decline. Our findings illuminate the complex evolutionary interplay between inbreeding and mutation load in homosporous ferns, yielding insights with important implications for the conservation and management of these species.

Insights into Chemical Diversity and Potential Health-Promoting Effects of Ferns

The scientific community is focusing on how to enhance human health and immunity through functional foods, and dietary supplements are proven to have a positive as well as a protective effect against infectious and chronic diseases. Ferns act as a taxonomical linkage between higher and lower plants and are endowed with a wide chemical diversity not subjected to sufficient scrutinization before. Even though a wealth of traditional medicinal fern uses were recorded in Chinese medicine, robust phytochemical and biological investigations of these plants are lacking. Herein, an extensive search was conducted using the keywords ferns and compounds, ferns and NMR, ferns and toxicity, and the terms ferns and chemistry, lignans, Polypodiaceae, NMR, isolation, bioactive compounds, terpenes, phenolics, phloroglucinols, monoterpenes, alkaloids, phenolics, and fatty acids were utilized with the Boolean operators AND, OR, and NOT. Databases such as PubMed, Web of Science, Science Direct, Scopus, Google Scholar, and Reaxys were utilized to reveal a wealth of information regarding fern chemistry and their health-promoting effects. Terpenes followed by phenolics represented the largest number of isolated active compounds. Regarding the neuroprotective effects, Psilotium, Polypodium, and Dryopteris species possessed as their major phenolics component unique chemical moieties including catechins, procyanidins, and bioflavonoids. In this updated chemical review, the pharmacological and chemical aspects of ferns are compiled manifesting their chemical diversity in the last seven years (2017-2024) together with a special focus on their nutritive and potential health-promoting effects.

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.

Ecological factors affecting minerals and nutritional quality of "Dryopteris filix-mas (L.) Schott": an underutilized wild leafy vegetable in rural communities

Dryopteris filix-mas (hereafter D. filix-mas), a wild leafy vegetable, has gained popularity among high mountain residents in the Hindukush-Himalaya region due to its exceptional nutritional profile, and their commercial cultivation also offers viable income alternatives. Nevertheless, besides phytochemicals with medicinal applications, ecological factors strongly affect their mineral contents and nutritional composition. Despite this, little has been known about how this wild fern, growing in heterogeneous ecological habitats with varying soil physiochemical properties and coexisting species, produces fronds with optimal mineral and nutritional properties. Given its nutritional and commercial significance, we investigated how geospatial, topographic, soil physiochemical characteristics and coexisting plants influence this widely consumed fern's mineral and nutrient content. We collected soil, unripe fern fronds, and associated vegetation from 27 D. filix-mas populations in Swat, NW Pakistan, and were analyzed conjointly with cluster analysis and ordination. We found that the fronds from sandy-loam soils at middle elevation zones exhibited higher nitrogen contents (9.17%), followed by crude fibers (8.62%) and fats (8.09%). In contrast, juvenile fronds from the lower and high elevation zones had lower moisture (1.26%) and ash (1.59%) contents, along with fewer micronutrients such as calcium (0.14-0.16%), magnesium (0.18-0.21%), potassium (0.72-0.81%), and zinc (12% mg/kg). Our findings indicated the fern preference for middle elevation zones with high organic matter and acidic to neutral soil (pH ≥ 6.99) for retaining higher nutritional contents. Key environmental factors emerged from RDA analysis, including elevation (r = -0.42), aspect (r = 0.52), P-3 (r = 0.38), K+ (r = 0.41), EC (r = 0.42), available water (r = -0.42), and field capacity (r = -0.36), significantly impacting fern frond's mineral accumulation and nutrient quality enhancement. Furthermore, coexisting plant species (r = 0.36) alongside D. filix-mas played a pivotal role in improving its mineral and nutritional quality. These findings shed light on the nutritional potential of D. filix-mas, which could help address malnutrition amidst future scarcity induced by changing climates. However, the prevalent environmental factors highlighted must be considered if the goal is to cultivate this fern on marginal lands for commercial exploitation with high mineral and nutrient yields in Hindukush-Himalaya.

Fertile Goeppertella from the Jurassic of Patagonia: mosaic evolution in the Dipteridaceae-Matoniaceae lineage

Goeppertella has been postulated as a monophyletic group, whose precise position within the Gleichenoid families Dipteriaceae and Matoniaceae, remains poorly understood. Previously described Goeppertella specimens are based on frond fragments and its fertile morphology is represented by a few, poorly preserved specimens. We describe a new species based on the largest collection of fertile specimens known to date and discuss the evolutionary history of the genus based on the additional reproductive characters provided by the fossils described. Plant impressions were collected in Early Jurassic sediments of Patagonia, Argentina. The specimens were described, and silicone rubber casts were developed to examine in detail vegetative and reproductive features. The new species was compared with other Goeppertella species. Finally, a backbone analysis was performed in the context of a previously published combined matrix of Dipteridaceae, using the maximum parsimony criterion. The new species is described based on a combination of features that have not been previously reported. The vegetative morphology shows affinities with most fossil and extant Dipteriaceae, contrasting with the reproductive morphology which is more comparable with the scarce number of fossil dipteridaceous forms and it is more spread in the sister family, Matoniaceae. The backbone analysis indicates that the position of the new species vary among different positions among Dipteridaceae and Matoniaceae. Additional analyses, discriminating the signal of reproductive and vegetative character, are provided to discuss the base of this uncertainty. We consider Goeppertella as a member of the family Dipteridaceae since we interpret most shared features with Matoniaceae as plesiomorphic conditions for the family. In contrast, most shared features with Dipteridaceae represent apomorphies for the group. Thus, Goeppertella would represent an early diverging genus in Dipteridaceae, considering the venation characters as the most important in order to define the family.

Flora diversity survey and establishment of a plant DNA barcode database of Lomas ecosystems in Peru

Lomas formations or "fog oases" are islands of vegetation in the desert belt of the west coast of South America, with a unique vegetation composition among the world's deserts. However, plant diversity and conservation studies have long been neglected, and there exists a severe gap in plant DNA sequence information. To address the lack of DNA information, we conducted field collections and laboratory DNA sequencing to establish a DNA barcode reference library of Lomas plants from Peru. This database provides 1,207 plant specimens and 3,129 DNA barcodes data corresponding with collections from 16 Lomas locations in Peru, during 2017 and 2018. This database will facilitate both rapid species identification and basic studies on plant diversity, thereby enhancing our understanding of Lomas flora's composition and temporal variation, and providing valuable resources for conserving plant diversity and maintaining the stability of the fragile Lomas ecosystems.

CromoCat: Chromosome Database of the Vascular Flora of the Catalan Countries-25 years

CromoCat is a plant chromosome database that evolved from previous versions, as a repository of karyological information on the vascular flora of the Catalan Countries. CromoCat is designed as an independent database, managed by a team based at the University of Barcelona directed by J. Simon, available from its own webpage ( http://www.cromo.cat/ ) and from the Flora section of the Catalan Biodiversity Database - BDBC ( http://biodiver.bio.ub.es ). CromoCat contains at present (mid 2022) more than 68,000 records of karyological data belonging to more than 5000 taxa. A synthesis of the development of CromoCat, its functional system, achievements, limitations, and adopted solutions, during 25 years (1996-2021) and updated 2022, as well as the application to biodiversity conservation and management are outlined.

Study on the morpho-anatomy of Lepisorus species through light microscopy and scanning electron microscopy and its systematic implications

The genus Lepisorus is often associated with complex lineages in Polypodiaceae, which leads to difficulty in understanding taxonomic relationships among the species. The taxa is mostly epiphytic with some distinct features like rhizomes covered with clathrate scales, simple fronds, sori in a single row, intermixed with peltate paraphyses. In this study, we precisely focus on the Lepisorus species and seek a broader understanding of the taxonomic relationships that prevail in this genus. The morpho-anatomical traits of rhizomes, stipe, lamina, and sporangia were explored in nine species with the aid of light microscopy and scanning electron microscopy techniques for gathering the qualitative and quantitative data sets. These character traits were resolved into groups based on degree of similarity and principal component analysis to comprehend the covariance among the variables. The data were then employed to prepare an artificial dichotomous key and hierarchical cluster analysis was established that revealed five related clades with eight members whereas one member emerged as outgroup. The results correspond with other recent phylogenetic studies of the concerned genus hence confirming immense reliability and thrust of light microscopy, scanning electron microscopy, and morphology-based studies that are being less utilized in fern taxonomy.

Characterization of a novel arsenite long-distance transporter from arsenic hyperaccumulator fern Pteris vittata

Pteris vittata is an arsenic (As) hyperaccumulator that can accumulate several thousand mg As kg^-1 DW in aboveground biomass. A key factor for its hyperaccumulation ability is its highly efficient As long-distance translocation system. However, the underlying molecular mechanisms remain unknown. We isolated PvAsE1 through the full-length cDNA over-expression library of P. vittata and characterized it through a yeast system, RNAi gametophytes and sporophytes, subcellular-location and in situ hybridization. Phylogenomic analysis was conducted to estimate the appearance time of PvAsE1. PvAsE1 was a plasma membrane-oriented arsenite (AsIII) effluxer. The silencing of PvAsE1 reduced AsIII long-distance translocation in P. vittata sporophytes. PvAsE1 was structurally similar to solute carrier (SLC)13 proteins. Its transcripts could be observed in parenchyma cells surrounding the xylem of roots. The appearance time was estimated at c. 52.7 Ma. PvAsE1 was a previously uncharacterized SLC13-like AsIII effluxer, which may contribute to AsIII long-distance translocation via xylem loading. PvAsE1 appeared late in fern evolution and might be an adaptive subject to the selection pressure at the Cretaceaou-Paleogene boundary. The identification of PvAsE1 provides clues for revealing the special As hyperaccumulation characteristics of P. vittata.

Metal Detoxification in Land Plants: From Bryophytes to Vascular Plants. STATE of the Art and Opportunities

Potentially toxic elements are a widespread concern due to their increasing diffusion into the environment. To counteract this problem, the relationship between plants and metal(loid)s has been investigated in the last 30 years. In this field, research has mainly dealt with angiosperms, whereas plant clades that are lower in the evolutive scale have been somewhat overlooked. However, recent studies have revealed the potential of bryophytes, pteridophytes and gymnosperms in environmental sciences, either as suitable indicators of habitat health and elemental pollution or as efficient tools for the reclamation of degraded soils and waters. In this review, we summarize recent research on the interaction between plants and potentially toxic elements, considering all land plant clades. The focus is on plant applicability in the identification and restoration of polluted environments, as well as on the characterization of molecular mechanisms with a potential outlet in the engineering of element tolerance and accumulation.

A taxonomic, genetic and ecological data resource for the vascular plants of Britain and Ireland

The vascular flora of Britain and Ireland is among the most extensively studied in the world, but the current knowledge base is fragmentary, with taxonomic, ecological and genetic information scattered across different resources. Here we present the first comprehensive data repository of native and alien species optimized for fast and easy online access for ecological, evolutionary and conservation analyses. The inventory is based on the most recent reference flora of Britain and Ireland, with taxon names linked to unique Kew taxon identifiers and DNA barcode data. Our data resource for 3,227 species and 26 traits includes existing and unpublished genome sizes, chromosome numbers and life strategy and life-form assessments, along with existing data on functional traits, species distribution metrics, hybrid propensity, associated biomes, realized niche description, native status and geographic origin of alien species. This resource will facilitate both fundamental and applied research and enhance our understanding of the flora's composition and temporal changes to inform conservation efforts in the face of ongoing climate change and biodiversity loss.

Reproductive innovations and pulsed rise in plant complexity

[Figure: see text].

The patterns of vascular plant discoveries in China

AIM

(1) To understand geographic patterns of species discovery by examining the effect of growth form, range size, and geographic distribution on discovery probability of vascular plant species in China; (2) to find out which taxa harbor the largest number of undiscovered species and where those species locate; and (3) to find out the determinants of province-level mean discovery time and inventory completeness.

LOCATION

China.

METHODS

We compiled the discovery time and province-level geographic distributions of ~31,000 vascular plant species described between 1753 and 2013 from Flora of China. We used a Cox proportional hazard model to determine the biological and geographic correlates of discovery probability. Accumulation curves of species discoveries were fitted by a logistic discovery model to estimate inventory completeness of different growth forms and of different provinces. We then used linear regression to identify the determinants of mean discovery time and beta regression to identify the determinants of inventory completeness.

RESULTS

We found that species with larger range size and distributed in northeastern part of China have a higher discovery probability. Coastal species were discovered earlier than inland species. Trees and shrubs of seed plants have the highest discovery probability while ferns have the lowest discovery probability. Herbs have the largest number of undiscovered species in China. Most undiscovered species will be found in southwest China, where three global biodiversity hot spots locate. Spatial patterns of mean discovery time and inventory completeness are mainly driven by the total number of species, human population density in an area, and latitude and longitude of a province.

MAIN CONCLUSIONS

Socioeconomic factors primarily determine the discovery patterns of vascular plants in China. Undiscovered species are most likely to be narrow-ranged, inconspicuous endemic species such as herbs and ferns, which are prone to extinctions and locate in biodiversity hot spots in southwestern China.

The complete chloroplast genome of Alsophila latebrosa, a common and widespread tree fern (Cyatheaceae)

Alsophila latebrosa is a common and widespread tree fern of Cyatheaceae. Its complete chloroplast genome is first assembled and reported with 155,724 bp in length, including a large single copy (LSC) region of 85,800 bp, a small single copy (SSC) region of 21,620 bp, and a pair of inverted repeats (IRs) of 24,152 bp. The genome has 133 genes, including 89 protein-coding genes, 33 tRNA genes, eight rRNA genes and three pseudogenes. Maximum likelihood approach was employed to construct the phylogenetic relationship among ten ferns including A. latebrosa. The result showed that A. latebrosa was most related to A. costularis as a sister group with 100% bootstrap support. The complete chloroplast genome sequences of A. latebrosa will provide valuable genomic information to further illuminate phylogenetic classification of Cyatheacea.

Application of Polypodiopsida Class in Nanotechnology-Potential towards Development of More Effective Bioactive Solutions

The area of phytosynthesized nanomaterials is rapidly developing, with numerous studies being published yearly. The use of plant extracts is an alternative method to reduce the toxic potential of the nanomaterials and the interest in obtaining phytosynthesized nanoparticles is usually directed towards accessible and common plant species, ferns not being explored to their real potential in this field. The developed nanoparticles could benefit from their superior antimicrobial and antioxidant properties (compared with the nanoparticles obtained by other routes), thus proposing an important alternative against health care-associated and drug-resistant infections, as well as in other types of applications. The present review aims to summarize the explored application of ferns in nanotechnology and related areas, as well as the current bottlenecks and future perspectives, as emerging from the literature data.

Using near-infrared spectroscopy to discriminate closely related species: a case study of neotropical ferns

Identifying plant species requires considerable knowledge and can be difficult without complete specimens. Fourier-transform near-infrared spectroscopy (FT-NIR) is an effective technique for discriminating plant species, especially angiosperms. However, its efficacy has never been tested on ferns. Here we tested the accuracy of FT-NIR at discriminating species of the genus Microgramma. We obtained 16 spectral readings per individual from the adaxial and abaxial surfaces of 100 specimens belonging to 13 species. The analyses included all 1557 spectral variables. We tested different datasets (adaxial + abaxial, adaxial, and abaxial) to compare the correct identification of species through the construction of discriminant models (Linear discriminant analysis and partial least squares discriminant analysis) and cross-validation techniques (leave-one-out, K-fold). All analyses recovered an overall high percentage (> 90%) of correct predictions of specimen identifications for all datasets, regardless of the model or cross-validation used. On average, there was > 95% accuracy when using partial least squares discriminant analysis and both cross-validations. Our results show the high predictive power of FT-NIR at correctly discriminating fern species when using leaves of dried herbarium specimens. The technique is sensitive enough to reflect species delimitation problems and possible hybridization, and it has the potential of helping better delimit and identify fern species.

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.

Ionomic variation in leaves of 819 plant species growing in the botanical garden of Hokkaido University, Japan

Ionomics is the measurement of total metal, metalloid, and nonmetal accumulation in living organisms. Plant ionomics has been applied to various types of research in the last decade. It has been reported that the ionome of a plant is strongly affected by its evolution and by environmental factors. In this study, we analyzed the concentration of 23 elements in leaves of 819 plant species (175 families) growing in the Botanic Garden of Hokkaido University, Japan. Relative variation estimated by the coefficient of variation in foliar concentrations of essential elements among various plant species tended to be low, whereas nickel concentration showed exceptionally large relative variation. By contrast, the relative variation in nonessential elements was high, particularly in sodium, aluminum, and arsenic. The higher relative variations in these element concentrations can be explained by the occurrence of plants that are hyperaccumulators for these elements. Differences in life forms such as herbaceous/woody species, deciduous/evergreen woody species and annual/perennial herbaceous species affected the concentration of several elements in the leaves. These differences were considered to be due to the combined factors including differences in lifespan, growth rate, and cell wall thickness of the leaves. Results of principal component analyses (based on concentration data of essential and nonessential elements in leaf samples) indicated phylogenetic influences on plant ionomes at the family level in Polypodiales, Pinales, Poales, and Ericales. Furthermore, when analyzing correlations among concentrations of all elements in each order and comparing among different orders, the results also suggested that Polypodiales, Pinales, and Poales each had a specific ion homeostasis network.

De Novo Transcriptome Assembly of Two Microsorum Fern Species Identifies Enzymes Required for Two Upstream Pathways of Phytoecdysteroids

Microsorum species produce a high amount of phytoecdysteroids (PEs), which are widely used in traditional medicine in the Pacific islands. The PEs in two different Microsorum species, M. punctatum (MP) and M. scolopendria (MS), were examined using high-performance liquid chromatography (HPLC). In particular, MS produces a high amount of 20-hydroxyecdysone, which is the main active compound in PEs. To identify genes for PE biosynthesis, we generated reference transcriptomes from sterile frond tissues using the NovaSeq 6000 system. De novo transcriptome assembly after deleting contaminants resulted in 57,252 and 54,618 clean transcripts for MP and MS, respectively. The clean Microsorum transcripts for each species were annotated according to gene ontology terms, UniProt pathways, and the clusters of the orthologous group protein database using the MEGAN6 and Sma3s programs. In total, 1852 and 1980 transcription factors were identified for MP and MS, respectively. We obtained transcripts encoding for 38 and 32 enzymes for MP and MS, respectively, potentially involved in mevalonate and sterol biosynthetic pathways, which produce precursors for PE biosynthesis. Phylogenetic analyses revealed many redundant and unique enzymes between the two species. Overall, this study provides two Microsorum reference transcriptomes that might be useful for further studies regarding PE biosynthesis in Microsorum species.

Leaf dorsoventrality candidate gene CpARF4 has conserved expression pattern but divergent tasiR-ARF regulation in the water fern Ceratopteris pteridoides

PREMISE

Leaves are traditionally classified into microphylls and megaphylls, and recently have been regarded as independently originating in lycophytes, ferns, and seed plants. The developmental genetics of leaf dorsoventrality, a synapomorphy in vascular plants, has been extensively studied in flowering plants. AUXIN RESPONSE FACTOR4 (ARF4) genes are key to leaf abaxial identity in flowering plants, but whether they exist in ferns is still an open question.

METHODS

ARF4 genes from Ceratopteris pteridoides, Cyrtomium guizhouense, and Parathelypteris nipponica were mined from transcriptomes and investigated in terms of evolutionary phylogeny and sequence motifs, with a focus on the tasiR-ARF binding site. In situ hybridization was used to localize expression of CpARF4 in Ceratopteris pteridoides. 5'RNA ligase-mediated-RACE was employed to verify whether CpARF4 transcripts were sliced by tasiR-ARF.

RESULTS

ARF4 genes exist in ferns, and this lineage originates from a gene duplication in the common ancestor of ferns and seed plants. ARF4 genes are of a single copy in the ferns studied here, and they contain divergent and, at most, one tasiR-ARF binding site. CpARF4 is expressed in the abaxial but not the adaxial domain of leaf primordia at various developmental stages. Transcript slicing guided by tasiR-ARF is active in C. pteridoides, but CpARF4 probably has not been affected by it.

CONCLUSIONS

Fern ARF4 genes differ in copy number and tasiR-ARF regulation relative to flowering plants, though they can be similarly expressed in the abaxial domain of leaves, revealing a key role for ARF4 genes in the evolution of leaf dorsoventrality of vascular plants.

Structural Determination of a New Cycloartane Glycoside from Asplenium ruprechtii

We characterized a new cycloartane glycoside, herein known as aspleniumside F (1), along with five known compounds as kaempferol-3-O-[(6-O-(E)-feruloyl)-β-D-glucopyranosyl]-(1→2)-β-D-galacopyranoside (2), quercetin-3-O-[(6-O-(E)-feruloyl)-β-D-glucopyranosyl]-(1→2)-β-D-glucopyranoside (3), kaempferol-3-O-[(6-O-(E)-caffeoyl)-β-D-glucopyranosyl]-(1→2)-β-D-glucopyranoside (4), kaempferol-3-O-[(6-O-(E)-caffeoyl)-β-D-glucopyranosyl]-(1→2)-β-D-glucopyranosyl-7-O-β-D-glucopyranoside (5), and kaempferol-3-O-[(6-O-p-coumaroyl)-β-D-glucopyranosyl]-(1→2)-β-D-glucopyranosyl-7-O-β-D-glucopyranoside (6), from Asplenium ruprechtii Sa. Kurata, a folk medicine widely used to treat Thromboangiitis obliterans in China, Japan, and Korea. Based on spectroscopic, mainly 1D-, 2D-NMR and (+)-HR-ESI-MS, analyses as well as through comparisons with previous reports, its chemical structure was determined as 3β,24,30-tri-β-D-glucopyranosyl-23,25-dihydroxycycloartane (= (23R,24R)-3β,24-bis-(β-D-glucopyranosyloxy)-23,25-dihydroxy-9β-9,19-cyclolanostan-29-yl β-D-glucopyranoside). According to the ¹ H coupling constant of anomeric protons and co-TLC of the acid hydrolysate with D-glucose, all three glycoside groups in 1 were revealed as β-D-glucopyranosyl. Furthermore, SOD-like antioxidant activity evaluation via IC₅₀ of 12.43, 6.78, 9.12, 6.94 and 4.85 μM revealed that compounds 2-6 had bioactivity.

Identification and Evaluations of Novel Insecticidal Proteins from Plants of the Class Polypodiopsida for Crop Protection against Key Lepidopteran Pests

Various lepidopteran insects are responsible for major crop losses worldwide. Although crop plant varieties developed to express Bacillus thuringiensis (Bt) proteins are effective at controlling damage from key lepidopteran pests, some insect populations have evolved to be insensitive to certain Bt proteins. Here, we report the discovery of a family of homologous proteins, two of which we have designated IPD083Aa and IPD083Cb, which are from Adiantum spp. Both proteins share no known peptide domains, sequence motifs, or signatures with other proteins. Transgenic soybean or corn plants expressing either IPD083Aa or IPD083Cb, respectively, show protection from feeding damage by several key pests under field conditions. The results from comparative studies with major Bt proteins currently deployed in transgenic crops indicate that the IPD083 proteins function by binding to different target sites. These results indicate that IPD083Aa and IPD083Cb can serve as alternatives to traditional Bt-based insect control traits with potential to counter insect resistance to Bt proteins.

Serratene triterpenoids and their biological activities from Lycopodiaceae plants

The plants of Lycopodiaceae family, distributed across China, India and also Southeast Asia, have been used as folk medicines. The phytochemical constitutent studies of this family was widely reported. Serratene trierpenoids is one of phytochemical constitutent type, which have been mainly isolated from this plant family. To date, more than 100 serratene-type triterpenoids have been reported and several of them have been shown promising biological activities, especially cytotoxicity and chemopreventive activity. This review covers the structural classification, biological activities and hypotheses about biosynthetic pathways of serratene-type triterpenes.

Evaluation of Anti-Tyrosinase and Antioxidant Properties of Four Fern Species for Potential Cosmetic Applications

Ferns are poorly explored species from a pharmaceutical perspective compared to other terrestrial plants. In this work, the antioxidant and tyrosinase inhibitory activities of hydrophilic and lipophilic extracts, together with total polyphenol content, were evaluated in order to explore the potential cosmetic applications of four Spanish ferns collected in the Prades Mountains (Polypodium vulgare L., Asplenium adiantum-nigrum L., Asplenium trichomanes L., and Ceterach officinarum Willd). The antioxidant activity was evaluated using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical, oxygen radical absorbance capacity (ORAC) and xanthine/xanthine oxidase (X/XO) assays. The potential to avoid skin hyperpigmentation was tested by inhibiting the tyrosinase enzyme, as this causes melanin synthesis in the epidermis. All ferns were confirmed as antioxidant and anti-tyrosinase agents, but interestingly hydrophilic extracts (obtained with methanol) were more potent and effective compared to lipophilic extracts (obtained with hexane). Polypodium vulgare, Asplenium adiantum-nigrum, and Ceterach officinarum methanolic extracts performed the best as antioxidants. Polypodium vulgare methanolic extract also showed the highest activity as a tyrosinase inhibitor.

Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns

Background

Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial.

Results

With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata.

Conclusions

Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants.

Studies on the complementary relationship of surface ornamentations between megaspores and microspores of Selaginella P. Beauv. (Selaginellaceae)

In the present study, the surface ornamentations of both megaspores and microspores of 20 species of Selaginella were studied using scanning electron microscopy. The results of the present study showed that the megaspore surface ornamentations are complementary to the corresponding microspore surface ornamentations. In detail, reticulate surface ornamentation of megaspores is complementary to granulate and baculate ornamentations of microspores; verrucate ornamentation of megaspores is complementary to scabrate ornamentation of microspores; granulate ornamentation of megaspores is complementary to verrucate-rugulate or verrucate ornamentations of microspores; verrucate-rugulate ornamentation of megaspores is complementary to spinulate, verrucate, or verrucate-rugulate ornamentations of microspores; tuberculate ornamentation of megaspores is complementary to lamellate, tuberculate or verrucate ornamentations of microspores. Complementary ornamentation between megaspores and microspores allows microspores to adhere to megaspores. Our observations support the "synaptospory" hypothesis, that is, spore surface ornamentation plays a part in keeping or bringing spores together during their dispersal in the pteridophytes.

The first complete chloroplast genome of Pteris vittata (Pteridaceae), an arsenic hyperaccumulating fern

It is the first report on complete chloroplast genome of Pteris vittata, an arsenic hyperaccumulating fern. Its genome size is 154,130 bp, with a typical circular structure including a large single-copy (LSC) (82,623 bp) and a small single-copy (SSC) (20,957 bp) regions separated by a pair of inverted repeats (25,275 bp each). The plastome encodes 132 genes, including 87 protein-coding genes, 35 tRNA genes, eight rRNA genes, and two pseudogenes. The overall Guanine+Cytosine (GC) content is 41.7% and GC content in the IR regions is higher than in the LSC and SSC regions. Maximum likelihood (ML) tree indicated that P. vittata was clustered with Ceratopteris richardii.

Taxonomy in the Kunming Institute of Botany (KIB): Progress during the past decade (2008-2018) and perspectives on future development

The development of new taxonomical theories and approaches, particularly molecular phylogenetics, has led to the expansion of traditional morphology-based taxonomy into the concept of "integrative taxonomy." Taxonomic knowledge has assumed greater significance in recent years, particularly because of growing concerns over the looming biodiversity crisis. Since its establishment in 1938, the Kunming Institute of Botany (KIB), which is located in Yunnan province in Southwest China, has focused attention on the taxonomy and conservation of the flora of China. For the forthcoming 80th anniversary of KIB, we review the achievements of researchers at KIB and their associates with respect to the taxonomy of land plants, fungi, and lichen. Major taxonomic advances are summarized for families of Calymperaceae, Cryphaeaceae, Lembophyllaceae, Neckeraceae, Polytrichaceae and Pottiaceae of mosses, Pteridaceae and Polypodiaceae of ferns, Taxaceae and Cycadaceae of gymnosperms, Asteraceae, Begoniaceae, Ericaceae, Euphorbiaceae, Gesneriaceae, Lamiaceae, Orchidaceae, Orobanchaceae, Poaceae, Theaceae and Urticaceae of angiosperms, Agaricaceae, Amanitaceae, Boletaceae, Cantharellaceae, Physalacriaceae Russulaceae, Suillaceae and Tuberaceae of fungi, and Ophioparmaceae and Parmeliaceae of lichens. Regarding the future development of taxonomy at KIB, we recommend that taxonomists continue to explore the biodiversity of China, integrate new theories and technologies with traditional taxonomic approaches, and engage in creative monographic work, with support from institutions, funding agencies, and the public.

Are dominant plant species more susceptible to leaf-mining insects? A case study at Saihanwula Nature Reserve, China

Dominant species significantly affect interspecific relationships, community structure, and ecosystem function. In the field, dominant species are often identified by their high importance values. Selective foraging on dominant species is a common phenomenon in ecology. Our hypothesis is that dominant plant groups with high importance values are more susceptible to leaf-mining insects at the regional level. Here, we used the Saihanwula National Nature Reserve as a case study to examine the presence-absence patterns of leaf-mining insects on different plants in a forest-grassland ecotone in Northeast China. We identified the following patterns: (1) After phylogenetic correction, plants with high importance values are more likely to host leafminers at the species, genus, or family level. (2) Other factors including phylogenetic isolation, life form, water ecotype, and phytogeographical type of plants have different influences on the relationship between plant dominance and leafminer presence. In summary, the importance value is a valid predictor of the presence of consumers, even when we consider the effects of plant phylogeny and other plant attributes. Dominant plant groups are large and susceptible targets of leaf-mining insects. The consistent leaf-mining distribution pattern across different countries, vegetation types, and plant taxa can be explained by the "species-area relationship" or the "plant apparency hypothesis."

The complete chloroplast genome of Leptochilus hemionitideus, a traditional Chinese medical fern

The complete chloroplast genome of Leptochilus hemionitideus was sequenced. Its length is 156,083 bp with 44.2% GC content. The genome exhibits typical quadripartite with two inverted repeat regions (24,594 bp, each) separated by a large single-copy (LSC, 81,403 bp) region and a small single-copy (SSC, 25,492 bp) region. It has 131 genes, including 87 protein-coding genes, 34 tRNA genes, eight rRNA genes and two pseudogenes. Maximum-likelihood phylogenetic tree indicated that L. hemionitideus was closely related to Lepisorus clathratus. The complete chloroplast genome of L. hemionitideus would provide very valuable molecular information for further inferring the relationships of the microsoroid ferns.

Flora do Espírito Santo: Hymenophyllum (Hymenophyllaceae)

Resumo É apresentado o inventário das espécies do gênero Hymenophyllum (Hymenophyllaceae) ocorrentes no estado do Espírito Santo. O tratamento taxonômico inclui descrições das espécies, comentários e imagens dos táxons, bem como, chaves de identificação dos gêneros de Hymenophyllaceae ocorrentes na área de estudo e no Brasil e das espécies de Hymenophyllum ocorrentes no Espírito Santo. O padrão de distribuição das espécies, juntamente com observações ecológicas também estão inclusos. No total foram encontradas 15 espécies pertencentes a cinco subgêneros. As espécies ocorrem amplamente no bioma Mata Atlântica, em florestas ombrófilas e nebulares, com exceção de Hymenphyllum caparaoense que é endêmica no Parque Nacional do Caparaó.

Quantifying progress toward a conservation assessment for all plants

The Global Strategy for Plant Conservation (GSPC) set an ambitious target to achieve a conservation assessment for all known plant species by 2020. We consolidated digitally available plant conservation assessments and reconciled their scientific names and assessment status to predefined standards to provide a quantitative measure of progress toward this target. The 241,919 plant conservation assessments generated represent 111,824 accepted land plant species (vascular plants and bryophytes, not algae). At least 73,081 and up to 90,321 species have been assessed at the global scale, representing 21-26% of known plant species. Of these plant species, at least 27,148 and up to 32,542 are threatened. Eighty plant families, including some of the largest, such as Asteraceae, Orchidaceae, and Rubiaceae, are underassessed and should be the focus of assessment effort if the GSPC target is to be met by 2020. Our data set is accessible online (ThreatSearch) and is a baseline that can be used to directly support other GSPC targets and plant conservation action. Although around one-quarter of a million plant assessments have been compiled, the majority of plants are still unassessed. The challenge now is to build on this progress and redouble efforts to document conservation status of unassessed plants to better inform conservation decisions and conserve the most threatened species.

A synopsis of the bryocorine tribes (Heteroptera : Miridae : Bryocorinae): key, diagnoses, hosts and distributional patterns

The higher classification of the mirid subfamily Bryocorinae has received comparatively little attention. It is not highly species-rich in comparison with other mirid subfamilies but does exhibit extraordinary morphological heterogeneity. In this work we provide a synthesis of the subfamily on a global basis, providing a new key and updated diagnoses of supraspecific taxa. Five tribes are recognised: Bryocorini, Dicyphini, Eccritotarsini, Felisacini and Monaloniini. The genus Campyloneura Fieber is transferred from the tribe Dicyphini to the Eccritotarsini. Analysis of distributional patterns and a survey of host plant associations are provided. Available data on distribution of the main bryocorine lineages are summarised in tabular form and evaluated using UPGMA methods, and geographically structured patterns were detected. The synthesis will enable users to identify bryocorines to tribal level with confidence and provides a classificatory framework for future revisionary and phylogenetic studies.

Phylogeny, historical biogeography and characters evolution of the drought resistant fern Pyrrosia Mirbel (Polypodiaceae) inferred from plastid and nuclear markers

Pyrrosia s.l. comprises ca. 60 species with a disjunct Africa/Asia and Australia distribution. The infrageneric classification of Pyrrosia s.l. is controversial based on the phylogenetic analyses of chloroplast markers and morphology. Based on the expanded taxon sampling of Pyrrosia s.l. (51 species), we investigated its phylogeny, biogeography, character evolution and environmental adaptation by employing five chloroplastid markers (rbcL, matK, psbA-trnH, and rps4 + rps4-trnS) and one single (low)-copy nuclear gene, LEAFY. Pyrrosia s.l. was divided into six major clades and eight subclades. Reticulate evolution was revealed both among clades and among species in Pyrrosia s.l. Ancestral character state optimization revealed high levels of homoplastic evolution of the diagnostic characters in Pyrrosia s.l., while the crassulacean acid metabolism pathway seems to have an independent origin. Molecular dating and biogeographic diversification analyses suggested that Pyrrosia s.l. originated no later than the Oligocene and the main clades diversified during the Oligocene and Miocene, with southern Asia, the Indo-China Peninsula and southwestern and southern China as the most likely ancestral areas. Transoceanic long-distance dispersal, rather than vicariance, contributed to the intercontinental disjunction. Diversification scenarios of Pyrrosia s.l. under geological movements and climate fluctuation are also discussed.

Phytochemicals from fern species: potential for medicine applications

Ferns are an important phytogenetic bridge between lower and higher plants. Historically they have been used in many ways by humans, including as ornamental plants, domestic utensils, foods, and in handicrafts. In addition, they have found uses as medicinal herbs. Ferns produce a wide array of secondary metabolites endowed with different bioactivities that could potentially be useful in the treatment of many diseases. However, there is currently relatively little information in the literature on the phytochemicals present in ferns and their pharmacological applications, and the most recent review of the literature on the occurrence, chemotaxonomy and physiological activity of fern secondary metabolites was published over 20 years ago, by Soeder (Bot Rev 51:442-536, 1985). Here, we provide an updated review of this field, covering recent findings concerning the bioactive phytochemicals and pharmacology of fern species.

Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns

Currently, complete mitochondrial genomes (mitogenomes) are available from all major land plant lineages except ferns. Sequencing of fern mitogenomes could shed light on the major evolutionary transitions that established mitogenomic diversity among extant lineages. In this study, we generated complete mitogenomes from the adder's tongue fern (Ophioglossum californicum) and the whisk fern (Psilotum nudum). The Psilotum mitogenome (628 kb) contains a rich complement of genes and introns, some of which are the largest of any green plant organellar genome. In the Ophioglossum mitogenome (372 kb), gene and intron content is slightly reduced, including the loss of all four mitochondrial ccm genes. Transcripts of nuclear Ccm genes also were not detected, suggesting loss of the entire mitochondrial cytochrome c maturation pathway from Ophioglossum. Both fern mitogenomes are highly repetitive, yet they show extremely low levels of active recombination. Transcriptomic sequencing uncovered ˜1000 sites of C-to-U RNA editing in both species, plus a small number (< 60) of U-to-C edit sites. Overall, the first mitochondrial genomes of ferns show a mix of features shared with lycophytes and/or seed plants and several novel genomic features, enabling a robust reconstruction of the mitogenome in the common ancestor of vascular plants.

Palhicerines A-F, Lycopodium alkaloids from the club moss Palhinhaea cernua

Four fawcettimine-type (palhicerines A-D, resp.) and two lycopodine-type (palhicerines E and F) Lycopodium alkaloids together with twenty known ones were isolated from the whole plant of Palhinhaea cernua. The structures and absolute configurations of the palhicerines A-F were determined by extensive spectroscopic methods, single-crystal X-ray diffraction analyses, chemical transformation, and electronic circular dichroism (ECD) calculations or induced electronic circular dichroism (IECD) spectra. Among the isolates, the new C/D-ring of the palhicerines A-C (trans-fused fawcettimine-type alkaloids) are rare, and each possesses a β-oriented C-16 methyl group and a distinctive tertiary methoxy group at C-13. Chemotaxonomy for differentiating species in the genus Palhinhaea is briefly discussed.