Search Results (607)

Asteraceae, as the largest angiosperm family, has an architecturally complex capitulum (inflorescences) composed of heteromorphic florets with distinct morphologies and functions. AGAMOUS (AG) MADS-box transcription factors act as key regulators in flower development and are essential for the formation of the characteristic capitulum and florets. To explore the potential functions of the AG genes in Asteraceae, we conducted a genome-wide identification and analysis of 52 AG-like genes across 22 species within this family. Additionally, we studied the functions of the Tagetes erecta class C genes TeAG1 and TeAG2 by introducing these genes into T. erecta and Nicotiana tabacum. Gene structure and phylogenomic analyses indicated that AG-like genes may have conserved and specific biological functions in Asteraceae plants. Phenotypic analyses revealed that the T. erecta class C genes TeAG1 and TeAG2 played a conserved and redundant role in regulating stamen and carpel development. The simultaneous downregulation of TeAG1 and TeAG2 led to the homeotic transformation of both stamens and carpels into corolla-like structures. However, silencing TeAG1 or TeAG2 individually in T. erecta did not affect any floral organ development. Furthermore, the ectopic expression of TeAG1 and TeAG2 in N. tabacum resulted in the transformation of sepals into pistils and corollas into stamens, respectively. Additionally, qRT-PCR analyses revealed that TeAG1 and TeAG2 repressed the expression of class A genes. Our findings expand our understanding of the function of class C genes within Asteraceae and provide strategies for breeding double-flower cultivars. Full article

Grain amaranths are recalcitrant to conventional in vitro plant regeneration by organogenesis de novo or through somatic embryogenesis. Consequently, floral organogenesis by these methods, representing the culminating developmental point in angiosperms, is rarely achieved. In the present study, the manipulation of in vitro flowering was explored as part of a strategy designed to overcome grain amaranth’s regeneration recalcitrance. It led to an efficient and reproducible in vitro protocol in which half-longitudinally dissected zygotic embryos generated fully developed Amaranthus hypochondriacus (Ah) plants. The use of high-irradiance illumination with LED lamps with a 3:1 red–blue irradiance ratio was a critical factor, leading to a 70% rate of early flowering events under flowering-inhibiting long-day photoperiod conditions. Contrariwise, no flowering was induced under LED white lights. All in vitro flowering Ah plants yielded viable seeds. To understand the basic molecular mechanisms of the phenomenon observed, gene expression patterns and principal component analysis of key flowering-related genes were analyzed after cultivation in vitro for 4, 8, and 12 weeks under both lighting regimes. These coded for photoreceptors, photomorphogenetic regulators, embryogenic modulators, and flowering activators/repressors. The results highlighted the upregulation of key flowering-regulatory genes, including CONSTANS, FLOWERING LOCUS T, and LEAFY, together with the downregulation of the floral repressor TERMINAL FLOWER1. Ribosome biogenesis- and seed-development-related genes were also differentially expressed, supporting a key role in this process for protein synthesis and embryogenesis. A model is proposed to explain how this light-regulated molecular framework enables in vitro flowering and seed production in Ah plants kept under long-day photoperiods. Full article

Vitamin B6 is an essential coenzyme involved in various metabolic processes critical for plant growth and development. However, its biosynthesis and regulatory mechanisms remain poorly understood in the ancient gymnosperm Ginkgo biloba. In this study, we identified two members of the PDX2 gene family (Gb_34755 and Gb_34990) through genome-wide analysis and characterized their molecular and functional properties. Bioinformatic analysis revealed distinct physicochemical traits and subcellular localizations, with Gb_34755 predicted in the cytoplasm and Gb_34990 in both chloroplasts and cytoplasm. Both proteins contain the glutaminase-related PLN02832 domain, indicating involvement in VB6 biosynthesis. Chromosomal mapping placed the genes in transcriptionally active regions on chromosomes 6 and 9. Phylogenetic analysis showed close evolutionary relationships between Ginkgo PDX2 genes and those in ferns and gymnosperms, distinct from angiosperms. Promoter analysis revealed differential enrichment of cis-elements: Gb_34990 harbored low-temperature and salicylic acid-responsive elements, while Gb_34755 showed motifs related to development. Gene expression profiling indicated significant upregulation (p < 0.05) of both genes during the late developmental stages of Ginkgo kernels, coinciding with peak VB6 content. Functional validation via transient overexpression in Nicotiana benthamiana confirmed a positive regulatory role, with VB6 levels increasing from 3.38 μg/g to 12.17 μg/g (p < 0.05). This study provides the first comprehensive functional analysis of the PDX2 gene family in Ginkgo and confirms their critical role in VB6 biosynthesis. These findings enhance our understanding of vitamin metabolism in gymnosperms and present promising targets for metabolic engineering in plants. Full article

Background/Objectives: Miscanthus Andersson, a genus of perennial grasses that includes wild relatives of key crop species, remains poorly characterized in terms of genetic diversity and evolutionary relationships. The aim of this study was to elucidate the phylogenetic structure of Miscanthus through comparative genomic analysis of the chloroplast genomes of six Korean species. Methods: Complete chloroplast genomes were assembled and analyzed for six Miscanthus species. Informative nucleotide motifs and their associated gene locations were identified as potential markers, and their phylogenetic relationships with related crops were examined. Results: The chloroplast genomes exhibited a conserved quadripartite structure, with genome sizes and GC contents within typical ranges. Analysis of codon usage showed a preference for A/U-ending codons, consistent with patterns in other angiosperms. Simple sequence repeats and long repeats demonstrated non-random distributions, indicating their value as molecular markers for phylogenetic and population studies. Comparative analyses confirmed structural conservation across Miscanthus species, whereas variation in non-coding regions provided important phylogenetic signals. Phylogenetic reconstruction based on 21 chloroplast genomes revealed four major clades, corroborating previous findings and highlighting complex evolutionary relationships within Miscanthus, including close affinities between African and Himalayan species and the genus Saccharum L. Conclusions: This study provides complete chloroplast genomes of six Miscanthus species, contributing to enhanced understanding of the relationships within the subtribe Saccharinae. The findings support the inclusion of Miscanthus species in the Korea Crop Wild Relatives inventory and highlight their potential as a genetic resource for breeding programs aimed at enhancing crop resilience to environmental stress. Full article

Calcium-dependent protein kinases (CDPKs) are key Ca²⁺ sensors in plants, mediating responses to abiotic stresses via phosphorylation signaling. In the halophyte Nitraria sibirica, which thrives in saline soils, we identified 19 CDPK genes (NsCDPKs) and classified them into four canonical angiosperm clades, highlighting conserved functional modules. Promoter analysis revealed diverse cis-acting elements responsive to light, hormones (ABA, MeJA, auxin, GA, SA), and abiotic stresses (drought, cold, wounding), along with numerous MYB binding sites, suggesting complex transcriptional regulation. Transcriptome profiling under salt stress (100 and 400 mM NaCl) showed induction of most NsCDPKs, with several genes significantly upregulated in roots and stems, indicating coordinated whole-plant activation. These salt-responsive NsCDPKs were also upregulated by cold but repressed under PEG-simulated drought, indicating stress-specific regulatory patterns. Fifteen MYB transcription factors, differentially expressed under salt stress, were predicted to interact with NsCDPK promoters, implicating them as upstream regulators. This study identified a potential salt- and cold-responsive CDPK regulatory module and a MYB-mediated transcriptional hierarchy in N. sibirica, providing insights into the molecular mechanisms of salinity adaptation and highlighting candidate genes that could be explored for improving salt tolerance in crop species. Full article

The Bełchatów Lignite Mine (BLM) in central Poland, one of Europe’s largest Neogene lignite deposits, provides key insights into palaeofloral evolution. Located in the Kleszczów Graben, the BLM consists of four distinct lithological units: subcoal, coal, clayey-coal, and clayey-sandy units. The study presents a palynological investigation of 31 samples from all units, identifying 78 sporomorph taxa, including 10 plant spores, 15 gymnosperm pollen, and 53 angiosperm pollen taxa. Pollen grains from angiosperms and gymnosperms were consistently observed in all samples, while plant spores were scarce. The analysis reveals three distinct palynological zones, reflecting shifts in vegetation. The first zone is characterized by swamp, riparian, and mixed mesophilous forests, dominated by Taxodium/Glyptostrobus, Ulmus, Carya, Engelhardia, Pterocarya, and Quercus. In the second zone, slightly cooler climatic conditions led to the decline of Taxodium/Glyptostrobus and Alnus, indicating a deterioration of swamp forests. The third zone marks a subsequent recovery of these forests. Palaeoclimatic interpretations indicate three phases: a subtropical-humid climate during the Early Miocene, fluctuating humidity in the late Early Miocene, and a transition to a warm-temperate and humid climate in the Late Miocene. Full article

Magnoliids represent one of the most basal lineages within angiosperms, and their ancestral floral morphology provides crucial insights into the evolution of flowers in angiosperms. MCM1-AGAMOUS-DEFICIENS-SRF (MADS)-box transcription factors play crucial roles in specifying floral organs. To understand their evolutionary history and functional divergence in magnoliids, we identified MADS-box genes, and conducted phylogenetic and expression analysis in 33 magnoliids and 8 other angiosperm plants. A total of 1310 MADS-box genes were identified and classified into Type I and Type II. The expansion of MADS-box genes in magnoliids mainly arose from whole-genome duplication events. In Liriodendron chinensis and Chimonanthus praecox, we identified floral homeotic MADS-box genes that are orthologous to the ABCDE model genes of floral organ identity determination. The broad expression pattern of A and B genes in floral organs and overlapping activity of ABCDE-model genes are consistent with the “shifting−fading borders” scheme proposed in basally diverging angiosperm lineages. Our results not only elucidate the driving forces underlying the diversification of MADS-box genes in magnoliids, but also shed light on the evolutionary models of floral development in angiosperms. Full article

Humans have been using lipids for many centuries; these are oils found in plants, particularly in seeds. However, relatively recently, it has become clear that lipids are the primary metabolites of any living organism. Fatty acids (FAs) are a structural component of lipids, and their role in building the framework of the lipid bilayer cannot be overstated. They participate in maintaining homeostasis by controlling membrane permeability. Changes in the FA composition of lipid bilayers can modulate the transition of the membrane from a liquid crystalline to a gel-like state. Thus, knowledge of a plant’s FA profile can aid in understanding the physiological mechanisms underlying their interaction with the environment and the ways in which they adapt to various stress factors. Throughout the colonization of terrestrial habitats, plants evolved, and new phylogenetic groups appeared; at present, some features of the FA composition of their individual representatives are known. However, the overall change in the composition of lipid FAs during the evolution of higher plants is still not understood. Our analysis of the literature showed that the FA diversity tends to decrease from mosses to angiosperms, mainly due to a reduction in polyunsaturated very-long-chain FAs, while the average acyl chain length remains unchanged. It is important to recognize the trends in this process in order to understand the adaptive capabilities of higher plants. This knowledge can be useful not only from a fundamental point of view, but also in practical human activities. Full article

Background: Plastid RNA editing is widespread in angiosperms yet remains underexplored in the medicinal non-model species Glycyrrhiza uralensis. This study aimed to (i) comprehensively identify plastid RNA editing sites in G. uralensis, and (ii) compare the detection performance of three library construction strategies: total RNA-seq, rRNA-depleted RNA-seq, and mRNA-seq. Methods: Leaf tissue was used from three wild-sampled individual plants. Plastomes were assembled with GetOrganelle v1.7.0 and annotated using PGA. Strand-specific RNA-seq libraries were mapped to sample-matched plastomes using HISAT2 v2.2.1. Variants were identified using REDItools v2.0 under uniform thresholds. Candidate sites were visually verified in IGV v2.12.3, and read origins were confirmed by BLAST v2.13.0+; artifacts were removed via strand-specific filtering. Results: After stringent filtering, 38 high-confidence RNA editing sites were identified across 19 genes. Total RNA seq performed the best, detecting 37/38 sites consistently, whereas rRNA-depleted libraries detected fewer genuine sites and produced numerous rRNA-linked, noncanonical, noncoding-strand-dominant artifacts. Despite very low rates of plastid mapping, mRNA seq recovered a large fraction of bona fide sites under stringent, strand-aware filtering. Conclusions: We establish a set of 38 high-confidence plastid RNA editing sites in G. uralensis and suggest potential adaptive implications of editing in ndh-related genes. Methodologically, total RNA-seq is recommended for identification using de novo RNA editing due to its high sensitivity and low false-positive rate; publicly available poly(A)-selected mRNA-seq datasets can be repurposed to reliably retrieve plastid RNA editing sites when stringent strand-specific filtering is applied. Full article

CRABS CLAW (CRC) is a member of the plant-specific YABBY transcription factor family, defined by the presence of a C2C2 zinc-finger domain and a C-terminal YABBY domain. CRC is essential for proper floral development, functioning in the termination of the floral meristem, maintenance of adaxial–abaxial polarity within the gynoecium, and regulation of nectary and leaf morphogenesis. CRC orchestrates its diverse regulatory functions through interaction networks comprising other transcription factors and plant developmental regulators, including chromatin-modifying enzymes and proteins involved in auxin biosynthesis, transport, and signaling. The roles of genes and proteins interacting with CRC or CRC have been characterized in several model plant species, and the number of identified CRC/CRC-associated interactions continues to expand, revealing both species-specific and conserved functional roles across angiosperms. Many functions of CRC and its interacting partners have been elucidated through the analysis of anatomical and physiological phenotypes associated with specific gene mutations. The functional roles of CRC in plant development appear to have been acquired progressively through evolutionary diversification. These evolutionary changes have been associated with the relative conservation of CRC gene copy number and a predominant role of mutations occurring in non-coding regulatory regions. These properties are attributed to the relatively limited number of genes comprising the CRC regulatory network and the capacity to induce dosage-dependent effects via the emergence of novel proteins with overlapping or analogous functions. The identification and functional characterization of CRC transcription factors across diverse plant species has advanced rapidly in recent years, yet a comprehensive synthesis of these findings has not been presented in a dedicated article. Therefore, this study reviews the current knowledge on CRC transcription factors, with a focus on their identification, expression patterns, and functional roles in plant development. Full article

Background: Grewia is a genus of flowering plants belonging to the Malvaceae family. Grewia tembensis is used in traditional medicine for the treatment of several microbial diseases as well as a livestock feed. Methods: In the current study, the complete chloroplast (cp) genome of G. tembensis was constructed using data derived from high-throughput sequencing, followed by comprehensive analyses and comparison with phylogenetically related species. Results: The chloroplast genome of G. tembensis is 158,040 bp long and has the typical quadripartite structure found in angiosperms. The large single-copy (LSC) segment measures 86,956 bp, whereas the small single-copy (SSC) regions encompass 20,142 bp. The two inverted repeat (IRa and IRb) regions have an identical length of 25,471 bp and display a higher degree of conservation relative to the single-copy (SC) regions based on nucleotide diversity analysis. The genome of G. tembensis possesses 130 genes. The simple sequence repeat (SSR) numbers ranged between 202 and 234 repeats in Grewioideae subfamily species under this study. Furthermore, nucleotide diversity analysis demonstrated a marked elevation in polymorphism information (Pi) values across 30 genes in Grewioideae. Conclusions: cpSSRs can be used for the examination of population genetic variability within and between Grewia species, as well as the categorization of populations and their biogeographical distribution. In addition, loci with high Pi values can contribute substantial genetic variability, which is crucial for addressing taxonomic dilemmas in phylogenetic investigations. Full article

Pelletizing enhances competitiveness of lignocellulosic biomass (LCB) as a fuel by increasing its bulk and energy density. However, LCB pellets are prone to degradation from moisture, have high ash, and pose safety risks due to carbon monoxide (CO) emissions during storage. Hot water extraction (HWE), a mild hydrothermal treatment particularly effective for angiosperms, removes most hemicelluloses (xylans), reduces ash, and increases lignin content in remaining HWE-LCB. Based on the current understanding of CO formation, these changes suggested that HWE could reduce CO emissions. In this study, we evaluated the effects of HWE on pellets made from shrub willow, miscanthus, and wheat straw. A statistical analysis was conducted on ash, energy content, bulk density, durability, pellet length and density, moisture absorption, and CO emissions. All HWE-LCB pellets demonstrated significant increases in energy content (up to 3.54%) and reductions in moisture absorption (up to 23.84%). Although not all effects reached statistical significance, HWE generally had positive effects on ash content, bulk density, durability, and average pellet length and density. Contrary to expectations, HWE-LCB pellets emitted significantly more CO under both ambient and isothermal temperature conditions (up to 4.25 times overall increase), although still less than commercial hardwood/softwood blend pellets (<200 ppm in HWE-LCB vs. >300 ppm). Full article

The transition from outcrossing to self-pollination is an evolutionary process in angiosperms. However, the changes in floral volatile composition during this process and their impacts on the behavior of pollinators are poorly understood. Therefore, this study investigated the potential differences in the floral volatile profiles and pollinator attraction capabilities of three invasive Bidens species. The results indicated that Bidens pilosa var. radiata (BH), which serves as a transitional species between facultative outcrossing and obligate outcrossing attracts a greater diversity and abundance of pollinators such as Apis cerana compared to the more self-compatible Bidens frondosa (DL) and Bidens pilosa var. pilosa (SY). Furthermore, a total of 37, 33, and 34 Volatile Organic Compounds (VOCs) were identified in the floral volatiles of BH, DL, and SY, respectively, with no discernible trend of decreased number of floral VOCs owing to increased self-pollination ability. Moreover, eleven significantly different compounds in the floral volatiles of the three Bidens species were obtained. Among these (E)-β-Ocimene (18.31 ± 1.10%) and (Z)-β-Ocimene (33.93 ± 3.49%) in the floral volatiles of BH (52.24 ± 4.59%) was significantly higher than that of DL (1.72 ± 0.50%) and SY (0.32 ± 0.19%). Additionally, Y-tube olfactometer behavioral assays indicated that (E)- and (Z)-β-Ocimene significantly attracted A. cerana. These findings suggested that (E)- and (Z)-β-Ocimene contribute to the attractiveness of BH to local pollinators. Furthermore, it can be inferred that within Bidens, stronger self-pollination ability reduces the relative content of VOCs—such as (E)- and (Z)-β-Ocimene—used to attract generalist pollinators. Full article

Tree ferns are ubiquitous in New Zealand forests, but there is limited knowledge of their role in urban plant communities and potential use in restoration. We assessed sixteen sites by measuring 200 m² plots to investigate how tree ferns influence vascular plant composition in Hamilton, North Island, New Zealand. The sixteen plots were assigned to four site type combinations based on restoration status (restored or unrestored) and tree fern presence, each with four plots. Average native plant species richness was higher at sites with tree ferns (36 ± 16; S = 68) than at sites without (19 ± 14; S = 41), with more diverse ground fern and epiphyte assemblages. Higher native plant richness at restored sites (34 ± 18; S = 62) compared to unrestored sites (20 ± 14, S = 44) was partially attributed to increased plant abundances. Multivariate analyses revealed differences in plant community composition among our site types. Angiosperms and conifers were less prevalent in plots with tree ferns, suggesting competitive relationships among these groups. However, tree ferns were associated with some shade-tolerant trees, such as Schefflera digitata J.R.Forst. & G.Forst. Indicator species of sites with tree ferns were mainly ground ferns and epiphytes (e.g., Blechnum parrisiae Christenh. and Trichomanes venosum R.Br.), whereas species with high fidelity to sites without tree ferns were pioneer trees and shrubs (e.g., Pittosporum eugenioides A.Cunn.). Community structure analyses revealed that total basal areas were highest at unrestored sites with tree ferns, but restored sites exhibited more diverse tree communities. Environmental predictors that correlated significantly with the compositional differences among our site types were tree fern basal area and restoration age. Our results highlight the need to reconsider the potential of tree ferns in current restoration practice. Tree ferns were found to augment native plant diversity in our study, indicating their potential to enhance urban ecological restoration projects in New Zealand. Full article

The nymphaeum originated as a monument dedicated to the nymphs and defined as a natural cave with a water source. Over time, it has been transformed into an artificial cave with the presence of fountains, statues and wall paintings. The nymphaeum is exposed to specific environmental conditions, leading to biodeterioration caused by vegetal organisms that find an ideal environment for their growth. This study aimed to document the vegetation present inside and outside the Carolei’s Nymphaeum, as well as the biofilm on the interior walls, particularly the painted walls. The biological work is part of a large-scale project involving building materials, thermo-hygrometric parameters, and partial pilot restoration work. Multiple approaches were used for biological analysis by combining microscopic, culture, and molecular techniques. We identified Pteridophytes, Angiosperms, and mosses, as well as fungal taxa, cyanobacteria, and chlorophytes in the biofilms. The results indicate that there is a very heterogeneous organism composition with significant biodeterioration potential. Biodeterioration is one of the major problems in the prevention, conservation, and restoration of cultural heritage, and the data gathered in this research may help to enhance the understanding of issues and develop suitable strategies for restoration, upkeep, and accessibility and usability. Full article