Search Results (225)

Insect pollination, a critical ecological process, pre-dates the emergence of angiosperms by nearly 200 million years, with fossil evidence indicating pollination interactions between insects and non-angiosperm seed plants during the Late Paleozoic. This review examines the symbiotic relationships between insects and gymnosperms in pre-angiosperm ecosystems, highlighting the complexity of these interactions. Fossil records suggest that the mutualistic relationships between insects and gymnosperms, which facilitated plant reproduction, were as intricate and diverse as the modern interactions between angiosperms and their pollinators, particularly bees. These early pollination systems likely involved specialized behaviors and plant adaptations, reflecting a sophisticated evolutionary dynamic long before the advent of flowering plants. The Anthropocene presents a dichotomy: while climate change and anthropogenic pressures threaten insect biodiversity and risk disrupting angiosperm reproduction, such upheaval may simultaneously generate opportunities for novel plant–insect interactions as ecological niches are vacated. Understanding the deep evolutionary history of pollination offers critical insight into the mechanisms underlying the resilience and adaptability of these mutualisms. The evolutionary trajectory of bees—originating from predatory wasps, diversifying alongside angiosperms, and reorganizing after mass extinctions—exemplifies this dynamic, demonstrating how pollination networks persist and reorganize under environmental stress and underscoring the enduring health, resilience, and adaptability of these essential ecological systems. Full article

A new class of plant phosphotransfer proteins belonging to the multistep phosphorelay (MSP) system implicated in phytohormone cytokinin signaling was discovered based on large-scale bioinformatics methods. Unlike the canonical soluble nucleo-cytosolic forms, these proteins were predicted to have transmembrane (TM) domains and, apparently, should be localized on some kind of cell membrane. To date, 94 predicted TM-containing phosphotransmitter (TM-HPt) homologs were found in 62 plant species belonging to different clades, taxa, and groups of embryophytes: bryophytes, gymnosperms, and mono- and dicotyledons. The conserved HPt motif with phosphorylatable histidine was preserved in most of the TM-HPts under study, which allowed us to consider these proteins potentially active in MSP signaling. For the identified TM-HPts, a Bayesian analysis at the DNA level was performed, and a relevant phylogenetic tree was constructed. According to evolutionary relationships, plant TM-HPts were divided into two main groups corresponding to Arabidopsis AHP1-3,5,6, and AHP4 orthologs. Transcriptomic analysis confirmed the expression of most of the investigated TM-HPt-encoding genes. Their moderate-to-low overall transcription rate may be a consequence of inducible and/or tissue-specific expression. Using molecular modeling methods, a variety of potential spatial organizations of several such proteins are demonstrated. The ability of the uncovered TM domains to tether HPts to membranes was supported by molecular dynamic simulation. Possible roles of TM-HPts as modulators of the MSP signaling pathway and corresponding putative mechanisms of their action are suggested. Full article

Unlike gymnosperms with naked ovules, angiosperms are defined and characterized by their enclosed ovules. According to plant evolution theories, angiosperms should be derived from their gymnospermous ancestors, which have naked ovules. Thus, an assumed transitional plant is expected to have started but not yet completed the enclosing of its ovules; specifically, some of its ovules are enclosed while others are not. This unusual expectation is, although rational, paradoxical: If this is so, is the plant a gymnosperm or an angiosperm? To date, such an expectation has never been met by any fossil evidence. The lack of favorable evidence makes the above expectation speculative and leaves evolutionary theorists vulnerable to attacks from their opponents. Here, I report a fossil plant, Lingyuanfructus hibrida gen. et sp. nov., from the Yixian Formation (Lower Cretaceous) of Liaoning, China, that meets this expectation. With young seeds both naked and enclosed in a single specimen, Lingyuanfructus defies any placement among seed plants and blurs the otherwise distinct boundary between angiosperms and gymnosperms, consolidating the foundation for evolutionary theory. Full article

Ahuehuete (Taxodium mucronatum Ten.) is a riparian tree species of significant ecological, cultural, and economic importance, demonstrating remarkable tolerance to prolonged flooding. However, the underlying mechanism of waterlogging adaptation remains unknown. In this study, we determined the physiological traits of the Ahuehuete leaves at 0, 15, 30, and 60 d under waterlogging conditions. The results showed that no significant difference in MDA content occurred between the Ahuehuete leaves subjected to waterlogging and those under well-watered (CK) conditions. In contrast, the contents of osmoprotectants (soluble sugar, soluble protein, and proline) and the activities of antioxidant enzymes (SOD, POD, and CAT) exhibited similar change trends under both waterlogging and CK conditions, despite minor quantitative differences between the two groups. Subsequent comparative transcriptome analysis was performed to investigate the transcriptional characteristics. A total of 3687 DEGs were expressed in all comparisons throughout the waterlogging process, while 2873, 4617, and 2710 DEGs were comparison group specific. KEGG enrichment analysis revealed that DEGs were enriched in various metabolic pathways, such as Plant hormone signal transduction (ko04075), MAPK signaling pathway-plant (ko04016), ABC transporter (ko02010), and Nitrogen metabolism (ko00910). WGCNA also identified key modules associated with physiological traits, simultaneously emphasizing the importance of plant hormone signal transduction and MAPK signal cascade. Overall, our findings revealed physiological and transcriptomic characteristics of the Ahuehuete under waterlogging conditions, and provided new insights to waterlogging adaptation in woody gymnosperm species. Full article

NAC transcription factors are key regulators involved in diverse cellular processes, stress responses, and developmental pathways in plants. However, their roles in female cone development of Torreya grandis, a representative gymnosperm species, remain largely unexplored. In this study, we performed a comprehensive identification and analysis of NAC transcription factors in T. grandis to investigate their potential functions in female cone development. A total of 82 TgNAC members containing conserved NAM domains were identified, distributed unevenly across 11 chromosomes. Phylogenetic analysis with Arabidopsis NACs classified them into 15 groups, with TgNACs represented in 10 groups and showing a notable enrichment in the TERN clade on chromosome 2. Promoter cis-element analysis revealed correlations between regulatory elements and expression patterns. Tissue-specific expression profiling indicated clear functional specialization, with some TgNACs showing no detectable expression in the examined tissues. During female cone development, several TgNACs were highly expressed in the early stages, whereas TgNAC72, TgNAC76 and TgNAC82 were upregulated during the latter stages. Among these, TgNAC72 exhibited the highest overall expression level. Subcellular localization confirmed TgNAC72 is localized in the nucleus. Dual-luciferase assays further demonstrated that TgNAC72 activates the TgBGLU13 promoter, suggesting its role in starch and sucrose metabolism. Collectively, these findings provide novel insights into the regulatory involvement of TgNACs in reproductive organ development. 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

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

Chloroplast genomes are valuable tools for exploring plant evolution, photosynthesis, and molecular systematics due to their relatively conserved structure and gene content. Here, I present a comprehensive comparative analysis of complete chloroplast genomes from 20 taxonomically diverse plant species, focusing on 16 widely used barcoding genes to investigate patterns of genome structure, gene retention, codon usage bias, and phylogenetic relationships. Genome sizes ranged from ~121 kb in Marchantia polymorpha to over 160 kb in Vitis vinifera, with GC content largely conserved across species. A multi-gene Neighbor-Joining phylogenetic framework recovered major taxonomic groupings and revealed gene-specific topological differences, reflecting locus-specific evolutionary histories. Presence/absence profiling showed that 13 of the 16 barcoding genes were consistently retained across species and classified as core genes, while the remaining three exhibited more variable distributions and were considered accessory. This pattern reflects both broad conservation and lineage-specific gene loss across plastomes. Genome-wide similarity analysis revealed high identity among closely related taxa (e.g., Arabidopsis and Brassica) and greater divergence among bryophytes, gymnosperms, and angiosperms. Codon usage analysis revealed generally conserved patterns, with lineage-specific biases observed in Cucumis sativus and Brassica rapa, suggesting influences from mutational pressure and potential translational selection. This integrative analysis highlights the dynamic yet conserved nature of chloroplast genomes and underscores the value of combining multiple genomic features in plastome evolution studies. The resulting dataset and analytical pipeline offer a useful resource for future phylogenomic, evolutionary, and biodiversity research in plant science. Full article

Background: The genus Ephedra (Ephedraceae) is a dioecious gymnosperm, where female individuals produce the pharmacologically active ephedrine alkaloids. Identifying the sex of specimens without reproductive cones is challenging due to their xeromorphic and morphological similarity. The challenges in sex identification complicate conservation and propagation efforts. Methods: Sequence-Related Amplified Polymorphism (SRAP) markers were applied to distinguish genders in five Ephedra species, particularly the vegetative branches, as well as powdered and fragmented specimens. The fresh material for the five studied Ephedra species and two sexes per species (totaling 10 samples; 5 females & 5 males) was collected from Sinai, Egypt. Results: The SRAP marker results revealed an exclusively male-specific band, and this is not applicable in females in the studied species. The applied SRAP markers grouped males and females in different UPGMA clusters and proved their efficiency in distinguishing between males and females in the five studied species. The Polymorphic Information Content (PIC) values are low (0.16–0.38); this suggests moderate genetic diversity between the females of the studied species, reflecting slow evolutionary rates. Conclusions: The SRAP markers are efficient for identifying Ephedra species at the species and gender levels, even in the absence of sex organs and molecular sequences. Recommendation: This study recommends the use of SRAP markers for conserving and propagating female plants for ephedrine production and suggests sequencing a 95 bp male-specific band to determine if it corresponds to a known sex-linked gene. Full article

Efficient protoplast isolation and gene transfection remain significant challenges in gymnosperms, particularly in Pinus species, where stable transformation is highly limited. Conventional pine protoplast preparation methods have resulted in extremely low transfection efficiencies, hindering functional genomic studies. This study presents an optimized method for isolating high-yield, viable protoplasts from Pinus densiflora (Korean red pine), providing a robust system for transient gene expression assays. Splitting one-month-old cotyledons produced the highest mesophyll protoplast yield (5.0 × 10⁶ cells/g FW), which further increased to 1.2 × 10⁷ cells/g FW after optimizing the enzyme mixture (4.5% cellulase, 0.7% pectinase, 3% hemicellulase), maintaining viability above 86%. Developing xylem and whole-stem protoplasts were also successfully isolated by mitigating resin leakage and debris contamination, with a 17% sucrose gradient yielding 7.4 × 10⁴ cells/g FW at 81.9% viability. Overcoming prior inefficiencies, this protocol significantly enhances gene transfection efficiency, achieving 94.1% GFP transformation with 82.9% viability. Furthermore, transient activation assays confirmed strong activation of pine-derived reporters by native effectors, underscoring the assay’s suitability for studying gymnosperm-specific gene regulation. Given the limited stable transformation strategies available for Pinus species, this optimized protoplast transient gene expression system provides a practical and reliable platform for transient gene expression analysis, offering valuable opportunities for studying gene function and regulation in gymnosperms. Full article

The miR156 family, crucial for phase transition and stress responses in plants, remains functionally uncharacterized in the ecologically and commercially important gymnosperm Larix kaempferi. This study systematically investigated L. kaempferi miR156 through phylogenetic analysis, structural prediction, expression profiling during somatic embryogenesis, and heterologous functional validation in Arabidopsis. Four MIR156 family members (LkMIR156s) were identified in Larix kaempferi, each with a characteristic stem-loop structure and highly conserved mature sequences. Computational predictions indicated that these LkMIR156s target four LkSPL family genes (LkSPL1, LkSPL2, LkSPL3, and LkSPL9). qRT-PCR analysis showed that mature LkmiR156s expression remained relatively low during early embryonic development but was significantly upregulated at the cotyledonary stage (21–42 days). Precursor transcript levels peaked earlier (around 28 days) than those of the mature LkmiR156, which remained highly expressed throughout cotyledonary embryo development. This sustained high expression coincided with cotyledon morphogenesis and embryonic dormancy. Functional validation via heterologous overexpression of LkMIR156b1 in Arabidopsis resulted in increased rosette leaf numbers (42.86% ± 6.19%) and individual leaf area (54.90% ± 6.86%), phenotypically consistent with the established role of miR156 in growth regulation. This study reveals the temporal expression dynamics of LkmiR156s during L. kaempferi somatic embryogenesis and its coordinated expression patterns with cotyledon development and embryonic dormancy. The functional conservation of the miR156-SPL module was confirmed in a model plant, providing key molecular insights into the developmental regulatory network of conifers. These findings offer potential strategies for optimizing somatic embryogenesis techniques in conifer species. Full article

Understanding the mechanisms and speed of paleo-aridification in the Qaidam Block—driven by tectonic uplift and shifts in atmospheric circulation—provides critical long-term context for assessing modern climate variability and anthropogenic impacts on water resources and desertification. This knowledge is essential for informing sustainable development strategies. We reconstruct the post-Triassic–Jurassic extinction tectonic-climatic evolution of the Qaidam Block on the northern Qinghai-Tibet Plateau margin through an integrated analysis of sedimentary facies, palynological assemblages, and Chemical Index of Alteration values from Late Triassic to Jurassic strata. The Indo-Eurasian convergence drove the uplift of the East Kunlun Orogen and strike-slip movement along the Altyn Tagh Fault, establishing a basin-range system. During the initial Late Triassic to Early Jurassic period, warm-humid conditions supported gymnosperm/fern-dominated ecosystems and facilitated coal formation. A Middle Jurassic shift from extensional to compressional tectonics coincided with a climatic transition from warm-humid, through cold-arid, to hot-arid states. This aridification, evidenced by a Bathonian-stage surge in drought-tolerant Classopollis pollen and a sharp decline in Chemical Index of Alteration values, intensified in the Late Jurassic due to the Yanshanian orogeny and distal subduction effects. Resultant thrust-strike-slip faulting and southeastward depocenter migration, under persistent aridity and intensified atmospheric circulation, drove widespread development of aeolian dune systems (e.g., Hongshuigou Formation) and arid fluvial-lacustrine environments. The tectonic-climate-ecosystem framework reveals how Jurassic tectonic processes amplified feedback to accelerate aridification. This mechanism provides a critical geological analog for addressing the current sustainability challenges facing the Qaidam Basin. Full article

GATA transcription factors are crucial for plant development and environmental responses, yet their roles in plant evolution and root nodule symbiosis are still not well understood. This study identified GATA genes across the genomes of 77 representative plant species, revealing that this gene family originated in Charophyta and significantly expanded in both gymnosperms and angiosperms. Phylogenetic analyses, along with examinations of conserved motifs and cis-regulatory elements in Glycine max and Arabidopsis, clearly demonstrated structural and functional divergence within the GATA family. Chromosomal mapping and synteny analysis indicated that GATA gene expansion in soybean primarily resulted from whole-genome duplication events. These genes also exhibit high conservation and signs of purifying selection in Glycine max, Lotus japonicus, and Medicago truncatula. Furthermore, by integrating phylogenetic and transcriptomic data from eight nitrogen-fixing legume species, several GATA genes were identified as strongly co-expressed with NIN1, suggesting their potential co-regulatory roles in nodule development and symbiosis. Collectively, this study offers a comprehensive overview of the evolutionary dynamics of the GATA gene family and highlights their potential involvement in root nodule symbiosis in legumes, thus providing a theoretical foundation for future mechanistic studies. Full article

SnRK kinases, central regulators of plant stress response, remain uncharacterized in Taxus—an ancient gymnosperm valued for paclitaxel production. This study aimed to identify the Taxus SnRK family and elucidate its functional roles. Specifically, we identified SnRK genes through genomic analysis and assessed tissue-specific expression via transcriptomics, while regulatory networks were deciphered using WGCNA. To overcome experimental constraints, a PEG-mediated protoplast transient expression system was developed using calli, followed by dual-luciferase assays. Consequently, 19 SnRK genes (2 SnRK1, 4 SnRK2, 13 SnRK3) were identified, with tissue-specific expression revealing TaSnRK1.2 upregulation under methyl jasmonate (MeJA) and in stress-resilient tissues (bark/root). Subsequently, WGCNA uncovered a bark/root-specific module containing TaSnRK1.2 with predicted TF interactions (TaGRAS/TaERF). Critically, homologous dual-luciferase assays demonstrated TaSnRK1.2 activates TaGRAS and TaERF promoters (4.34-fold and 3.11-fold induction, respectively). This study establishes the Taxus SnRK family and identifies TaSnRK1.2 as a hub integrating stress signals (e.g., MeJA) to modulate downstream TF networks, while the novel protoplast system enables future functional studies in this medicinal plant. Full article

Chromosome rearrangements during plant evolution can lead to alterations in genome structure and gene function, thereby influencing species adaptation and evolutionary processes. Gymnosperms, as an ancient group of plants, offer valuable insights into the morphological, physiological, and ecological characteristics of early terrestrial flora. The reconstruction of ancestral karyotypes in gymnosperms may provide critical clues for understanding their evolutionary history. In this study, we inferred the ancestral gymnosperm karyotype (AGK), which comprises 12 chromosomes, and conducted a collinearity analysis with existing gymnosperm genomes. Our findings indicate that chromosome numbers have remained remarkably stable throughout the evolution of gymnosperms. For species with multiplied chromosome numbers, such as gnetophytes, weak collinearities with the AGK were observed. Comparisons between the AGK and gnetophyte genomes revealed a biased pattern regarding retained duplication blocks. Furthermore, our analysis of transposable elements in Welwitschia mirabilis identified enriched regions containing LINE-1 retrotransposons within the syntenic blocks. Syntenic analysis between the AGK and angiosperms also demonstrated a biased distribution across chromosomes. These results provide a fundamental resource for further characterization of chromosomal evolution in gymnosperms. Full article