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

Enzymatic and quantitative properties of Rubisco in some conifers and lycopods

Information on the kinetic properties of Rubisco, a key enzyme for photosynthesis, is scarce in land plants that emerged early during the evolutionary process. This study examined the carboxylase activity and abundance of Rubisco in five conifers, two lycopods, and three control C3 crops. The turnover rates of Rubisco carboxylation (kcatc) under saturated-CO2 conditions in conifers and lycopods were comparable to those in the control C3 crops. Rubisco carboxylase activity under CO2-unsaturated conditions (vcu) was also measured using reaction mixtures saturated with a N2 gas containing CO2 and O2 at present atmospheric levels to predict the Rubisco CO2 affinity from the percentage of vcu in kcatc. The predicted CO2 affinity in conifers and lycopods tended to be lower than that in the control C3 crops. When the control C3 crops and two previously examined C4 crops were analyzed together, the kcatc of Rubisco with a low CO2 affinity tended to be high. N allocation to Rubisco with a low kcatc tended to be high in these plants. In conifers and lycopods, the kcatc was lower than that expected on the basis of predicted Rubisco CO2 affinity, unlike in the control crops. N allocation to Rubisco also tended to be lower than that expected on the basis of kcatc. These results indicate that Rubisco in the examined conifers and lycopods is not superior in terms of both kcatc and CO2 affinity and that the abundance of Rubisco is not necessarily closely related to its kinetic properties. The reason for these phenomena is discussed in terms of the molecular evolution of Rubisco.

The changing biodiversity of the Arctic flora in the Anthropocene

The plants of the circumpolar Arctic occupy a dynamic system that has been shaped by glacial cycles and climate change on evolutionary timescales. Yet rapid climatic change can compromise the floristic diversity of the tundra, and the ecological and evolutionary changes in the Arctic from anthropogenic forces remain understudied. In this review, we synthesize knowledge of Arctic floral biodiversity across the entirety of the region within the context of its climatic history. We present critical gaps and challenges in modeling and documenting the consequences of anthropogenic changes for Arctic flora, informed by data from the Late Quaternary (~20 ka). We found that previous forecasts of Arctic plant responses to climate change indicate widespread reductions in habitable area with increasing shrub growth and abundance as a function of annual temperature increase. Such shifts in the distribution and composition of extant Arctic flora will likely increase with global climate through changes to the carbon cycle, necessitating a unified global effort in conserving these plants. More data and research on the continuity of tundra communities are needed to firmly assess the risk climate change poses to the Arctic.

From Stem to Spectrum: Phytochemical Characterization of Five Equisetum Species and Evaluation of Their Antioxidant Potential

The Equisetaceae family, commonly known as horsetails, has been of scientific interest for decades due to its status as one of the most ancient extant vascular plant families. Notably, the corresponding species have found their place in traditional medicine, offering a wide array of applications. This study presents a comprehensive phytochemical analysis of polar secondary metabolites within the sterile stems of five distinct Equisetum species using HPLC-DAD-ESI-MSn. For this purpose, fresh plant material was extracted with acetone/water, and the resulting crude extracts were fractionated using dichloromethane, ethyl acetate, and n-butanol, respectively. The results reveal a complex array of compounds, including hydroxycinnamic acids, hydroxybenzoic acids, flavonoids, and other phenolic compounds. In addition, total phenolic contents (Folin-Ciocalteu assay) and antioxidant activities (DPPH assay) of the plant extracts were evaluated using spectrophotometric methods. The present comparative analysis across the five species highlights both shared and species-specific metabolites, providing valuable insights into their chemical diversity and potential pharmacological properties.

Chloroplast genome structure analysis of Equisetum unveils phylogenetic relationships to ferns and mutational hotspot region

Equisetum is one of the oldest extant group vascular plants and is considered to be the key to understanding vascular plant evolution. Equisetum is distributed almost all over the world and has a high degree of adaptability to different environments. Despite the fossil record of horsetails (Equisetum, Equisetaceae) dating back to the Carboniferous, the phylogenetic relationship of this genus is not well, and the chloroplast evolution in Equisetum remains poorly understood. In order to fill this gap, we sequenced, assembled, and annotated the chloroplast genomes of 12 species of Equisetum, and compared them to 13 previously published vascular plants chloroplast genomes to deeply examine the plastome evolutionary dynamics of Equisetum. The chloroplast genomes have a highly conserved quadripartite structure across the genus, but these chloroplast genomes have a lower GC content than other ferns. The size of Equisetum plastomes ranges from 130,773 bp to 133,684 bp and they encode 130 genes. Contraction/expansion of IR regions and the number of simple sequences repeat regions underlie large genomic variations in size among them. Comparative analysis revealed we also identified 13 divergence hotspot regions. Additionally, the genes accD and ycf1 can be used as potential DNA barcodes for the identification and phylogeny of the genus Equisetum. Twelve photosynthesis-related genes were specifically selected in Equisetum. Comparative genomic analyses implied divergent evolutionary patterns between Equisetum and other ferns. Phylogenomic analyses and molecular dating revealed a relatively distant phylogenetic relationship between Equisetum and other ferns, supporting the division of pteridophyte into Lycophytes, Equisetaceae and ferns. The results show that the chloroplast genome can be used to solve phylogenetic problems within or between Equisetum species, and also provide genomic resources for the study of Equisetum systematics and evolution.

Equisetum praealtum and E. hyemale have abundant Rubisco with a high catalytic turnover rate and low CO2 affinity

The kinetic properties of Rubisco, a key enzyme for photosynthesis, have been examined in numerous plant species. However, this information on some plant groups, such as ferns, is scarce. This study examined Rubisco carboxylase activity and leaf Rubisco levels in seven ferns, including four Equisetum plants (E. arvense, E. hyemale, E. praealtum, and E. variegatum), considered living fossils. The turnover rates of Rubisco carboxylation (kcatc) in E. praealtum and E. hyemale were comparable to those in the C4 plants maize (Zea mays) and sorghum (Sorghum bicolor), whose kcatc values are high. Rubisco CO2 affinity, estimated from the percentage of Rubisco carboxylase activity under CO2 unsaturated conditions in kcatc in these Equisetum plants, was low and also comparable to that in maize and sorghum. In contrast, kcatc and CO2 affinities of Rubisco in other ferns, including E. arvense and E. variegatum were comparable with those in C3 plants. The N allocation to Rubisco in the ferns examined was comparable to that in the C3 plants. These results indicate that E. praealtum and E. hyemale have abundant Rubisco with high kcatc and low CO2 affinity, whereas the carboxylase activity and abundance of Rubisco in other ferns were similar to those in C3 plants. Herein, the Rubisco properties of E. praealtum and E. hyemale were discussed regarding their evolution and physiological implications.

Genus Equisetum L: Taxonomy, toxicology, phytochemistry and pharmacology

INTRODUCTION

The genus Equisetum (Equisetaceae) is cosmopolitan in distribution, with 41 recognized species. Several species of Equisetum are widely used in treating genitourinary and related diseases, inflammatory and rheumatic problems, hypertension, and wound healing in traditional medicine practices worldwide. This review intends to present information on the traditional uses, phytochemical components, pharmacological activities, and toxicity of Equisetum spp. and to analyze the new insights for further study.

METHODS

Relevant literature has been scanned and collected via various electronic repositories, including PubMed, Science Direct, Google Scholar, Springer Connect, and Science Online, from 1960 to 2022.

RESULTS

Sixteen Equisetum spp. were documented as widely used in traditional medicine practices by different ethnic groups throughout the world. A total of 229 chemical compounds were identified from Equisetum spp. with the major group of constituents being flavonol glycosides and flavonoids. The crude extracts and phytochemicals of Equisetum spp. exhibited significant antioxidant, antimicrobial, anti-inflammatory, antiulcerogenic, antidiabetic, hepatoprotective, and diuretic properties. A wide range of studies have also demonstrated the safety of Equisetum spp.

CONCLUSION

The reported pharmacological properties of Equisetum spp. support its use in traditional medicine, though there are gaps in understanding the traditional usage of these plants for clinical experiments. The documented information revealed that the genus is not only a great herbal remedy but also has several bioactives with the potential to be discovered as novel drugs. Detailed scientific investigation is still needed to fully understand the efficacy of this genus; hence, very few Equisetum spp. were studied in detail for phytochemical and pharmacological investigation. Moreover, its bioactives, structure-activity connection, in vivo activity, and associated mechanism of action ought to be explored further.

Nitrogen fixation and other biogeochemically important features of Atacama Desert giant horsetail plant microbiomes inferred from metagenomic contig analysis

BACKGROUND AND AIMS

Canyon stream beds in the hyperarid Atacama Desert surprisingly harbour magnificent groves of endemic giant horsetail wetland plants, Equisetum xylochaetum. Our previous metagenomic study of eukaryotes closely associated with this plant indicated that the microbiome included prokaryotes that might likewise influence host success and environment. We explored this possibility by using the metagenomic sequence to characterize prokaryote taxa and functional genes present in the microbiome of E. xylochaetum sampled from remote sites differing in the degree of anthropogenic disturbance. We focused on biogeochemical functions known to be important in wetland ecosystems.

METHODS

To ensure that analyses were conducted on microbes most closely associated with plants, we extracted DNA from well-washed plant organs whose microbial biofilms were revealed with scanning electron microscopy. To assess the benefits of longer sequences for taxonomic and gene classifications, results of analyses performed using contigs were compared with those obtained with unassembled reads. We employed methods widely used to estimate genomic coverage of single taxa for genomic analysis to infer relative abundances of taxa and functional genes.

KEY RESULTS

Key functional bacterial genera (e.g. Hydrogenophaga, Sulfuritalea and Rhodoferax) inferred from taxonomic and functional gene analysis of contigs - but not unassembled reads - to occur on surfaces of (or within) plants at relatively high abundance (>50× genomic coverage) indicated roles in nitrogen, sulfur and other mineral cycling processes. Comparison between sites revealed impacts on biogeochemical functions, e.g. reduced levels of the nifH gene marker under disturbance. Vanadium nitrogenases were more important than molybdenum nitrogenases, indicated by both functional genes and taxa such as Rhodomicrobium and Phaeospirillum inferred from contigs but not unassembled reads.

CONCLUSIONS

Our contig-based metagenomic analyses revealed that microbes performing key wetland biogeochemical functions occur as tightly adherent biofilms on the plant body, not just in water or sediments, and that disturbance reduces such functions, providing arguments for conservation efforts.

Plastid Genome of Equisetum xylochaetum from the Atacama Desert, Chile and the Relationships of Equisetum Based on Frequently Used Plastid Genes and Network Analysis

The modern pteridophyte genus Equisetum is the only survivor of Sphenopsida, an ancient clade known from the Devonian. This genus, of nearly worldwide distribution, comprises approximately 15 extant species. However, genomic information is limited. In this study, we assembled the complete chloroplast genome of the giant species Equisetum xylochaetum from a metagenomic sequence and compared the plastid genome structure and protein-coding regions with information available for two other Equisetum species using network analysis. Equisetum chloroplast genomes showed conserved traits of quadripartite structure, gene content, and gene order. Phylogenetic analysis based on plastome protein-coding regions corroborated previous reports that Equisetum is monophyletic, and that E. xylochaetum is more closely related to E. hyemale than to E. arvense. Single-gene phylogenetic estimation and haplotype analysis showed that E. xylochaetum belonged to the subgenus Hippochaete. Single-gene haplotype analysis revealed that E. arvense, E. hyemale, E. myriochaetum, and E. variegatum resolved more than one haplotype per species, suggesting the presence of a high diversity or a high mutation rate of the corresponding nucleotide sequence. Sequences from E. bogotense appeared as a distinct group of haplotypes representing the subgenus Paramochaete that diverged from Hippochaete and Equisetum. In addition, the taxa that were frequently located at the joint region of the map were E. scirpoides and E. pratense, suggesting the presence of some plastome characters among the Equiseum subgenera.

Genome size evolution of the extant lycophytes and ferns

Ferns and lycophytes have remarkably large genomes. However, little is known about how their genome size evolved in fern lineages. To explore the origins and evolution of chromosome numbers and genome size in ferns, we used flow cytometry to measure the genomes of 240 species (255 samples) of extant ferns and lycophytes comprising 27 families and 72 genera, of which 228 species (242 samples) represent new reports. We analyzed correlations among genome size, spore size, chromosomal features, phylogeny, and habitat type preference within a phylogenetic framework. We also applied ANOVA and multinomial logistic regression analysis to preference of habitat type and genome size. Using the phylogeny, we conducted ancestral character reconstruction for habitat types and tested whether genome size changes simultaneously with shifts in habitat preference. We found that 2C values had weak phylogenetic signal, whereas the base number of chromosomes (x) had a strong phylogenetic signal. Furthermore, our analyses revealed a positive correlation between genome size and chromosome traits, indicating that the base number of chromosomes (x), chromosome size, and polyploidization may be primary contributors to genome expansion in ferns and lycophytes. Genome sizes in different habitat types varied significantly and were significantly correlated with habitat types; specifically, multinomial logistic regression indicated that species with larger 2C values were more likely to be epiphytes. Terrestrial habitat is inferred to be ancestral for both extant ferns and lycophytes, whereas transitions to other habitat types occurred as the major clades emerged. Shifts in habitat types appear be followed by periods of genomic stability. Based on these results, we inferred that habitat type changes and multiple whole-genome duplications have contributed to the formation of large genomes of ferns and their allies during their evolutionary history.

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.