Search Results (233)

Cathaya argyrophylla Chun et Kuang is an endangered relict gymnosperm endemic to China. Its habitat has been severely fragmented due to Quaternary glaciations, a condition further exacerbated by modern, fragmented administrative management. We compiled 98 spatially filtered occurrence records across four provinces and developed a combined analysis framework integrating the Biomod2 ensemble model with the Marxan systematic planning algorithm. Our optimal model (TSS = 0.911, AUC = 0.986) identified mean diurnal range and ultraviolet-B seasonality radiation as the dominant ecophysiological drivers of the species’ distribution. Currently, suitable habitats cover 7.10% of the study area, with highly suitable habitats accounting for only 3.08% (21.76 × 10³ km²). Priority conservation areas account for 2.48% (17.55 × 10³ km²) of the total area. A gap analysis revealed that 76.98% (13.51 × 10³ km²) of the optimized priority conservation areas currently lack formal protection under China’s protected area system and the World Database on Protected Areas. Under four future climate scenarios (2030s–2090s), projections indicated overall habitat contraction, with limited spatial expansion observed only under specific scenarios (SSP1-2.6 in the 2030s and 2090s; SSP5-8.5 in the 2030s), and the population centroid was projected to shift southeastward by an average of 42.67 km in Huaihua City. Twenty-one core habitat patches were identified under current climate conditions. As these core habitat patches are concentrated along interprovincial boundaries, specifically the Dalou Mountains and the Yuecheng Ridge, our findings emphasize the need to bridge local administrative barriers. This spatial framework provides actionable guidelines for establishing transboundary protected areas, optimizing in situ conservation networks, and implementing model-based assisted migration. Full article

N⁶-methyladenosine (m⁶A) is an important epigenetic modification of eukaryotic RNA, playing a significant role in various biological processes. Metasequoia glyptostroboides (M. glyptostroboides) is an ancient tree species in China, with a long history and excellent genetic characteristics. In this study, we identified six MgYTH genes in the genome of M. glyptostroboides, elucidating their phylogenetic relationships, conserved domains, gene structures, conserved motifs, chromosome locations, and prediction of LLPS. The analysis of the cis-regulatory elements in the promoter region suggested that MgYTH genes are associated with drought and the ABA-responsive expression patterns signaling pathway, which was further supported by expression pattern analysis. In addition, to directly evaluate the m⁶A binding ability of MgYTH proteins, we selected MgYTH5 as the representative for homology modeling analysis and electrophoretic mobility shift assay (EMSA). The results demonstrated that MgYTH5 has the ability to bind m⁶A in vitro, thereby providing biochemical evidence that MgYTH5 can bind m⁶A-modified RNA in vitro mRNAs. The subcellular localization results showed that MgYTH5 is located in the cytoplasm. These findings provide new insights into the epigenetic regulation mechanisms in gymnosperms and provide a resource for future functional studies in this species. Full article

DNA methylation constitutes a primary layer of epigenetic regulation in plants, operating across three sequence contexts (CG, CHG, and CHH) through distinct enzymatic pathways. Over the past fifteen years, accumulating evidence has shown that DNA methylation varies substantially among individuals and populations of wild plants, sometimes independently of underlying genetic polymorphism. This variation can influence gene expression, transposable element activity, and phenotypic traits relevant to ecological adaptation. Population epigenetics, the study of methylation variation at the population scale, has matured from initial surveys using methylation-sensitive amplified fragment length polymorphism (MS-AFLP) into a discipline increasingly reliant on reduced-representation bisulfite sequencing (epiGBS, bsRADseq), whole-genome bisulfite sequencing (WGBS), enzymatic methyl-seq (EM-seq), and direct long-read detection by nanopore sequencing. These methodological advances are opening population epigenetics to non-model organisms across the full breadth of the plant phylogeny, from angiosperms and gymnosperms to ferns and bryophytes. We cover (i) the molecular machinery underlying plant DNA methylation, including the debated status of N6-methyladenine (6mA); (ii) empirical evidence for natural epigenetic variation in plant populations, spanning clonal, invasive, and outcrossing species; (iii) the methodological toolkit available for population-scale methylation profiling, with emphasis on approaches suitable for non-model taxa; and (iv) the ecological and evolutionary significance of population epigenetic variation, including transgenerational inheritance, stress memory, epigenetic clocks, conservation applications, and the emerging integration of epigenetics into the extended evolutionary synthesis. We identify critical knowledge gaps, particularly the near-complete absence of population-level epigenetic data for bryophytes, ferns, and lycophytes, and outline priorities for future research. Full article

Urban trees are increasingly deployed as nature-based infrastructure to mitigate heat and manage stormwater, yet quantitative guidance on how species traits and site context shape transpiration remains fragmented. We conducted a systematic metadata analysis of seven field studies that measured daily transpiration rate in urban settings using heat-pulse methods. The units and spatial scales reported were harmonized with the sap flow density across active sapwood (J_s, g H₂O/${\mathrm{cm}}^2$/day) by converting reported stand transpiration and the outer 2 cm of sapwood sap flux using established Gaussian radial distribution functions for angiosperms and gymnosperms, which account for the non-linear decline in sap flux from the vascular cambium to the heartwood boundary. We then summarized distributions and tested group differences with Kruskal–Wallis and Dunn post hoc comparisons across wood anatomy, climate, soil texture, and planting configuration. Conifers exhibited significantly lower median $J_s$ (39.76 g/${\mathrm{cm}}^2$/day) than angiosperms, while the ring-porous group (median $J_s$ = 92.25 g/${\mathrm{cm}}^2$/day) and diffuse-porous groups (median $J_s$ = 96.70 g/${\mathrm{cm}}^2$/day) had similar distributions overall. Climate-modulated responses within wood anatomy groups differed, with diffuse-porous species exhibiting the highest median $J_s$ (152.59 g/${\mathrm{cm}}^2$/day) in semi-arid regions, ring-porous species maintaining comparatively stable median $J_s$ across climates (varying slightly between 80.72 and 99.32 g/${\mathrm{cm}}^2$/day), and conifers reaching their highest median $J_s$ (69.90 g/${\mathrm{cm}}^2$/day) in humid continental sites. Soil texture effects were consistent with moisture availability: sandy loam generally reduced $J_s$ relative to loam or silt loam for conifers and diffuse-porous species. Across anatomies, single trees transpired more than clustered trees or closed canopies. For example, planting as single trees increased median $J_s$ by 86% in conifers (from 33.01 to 61.37 g/${\mathrm{cm}}^2$/day) and by 45% in diffuse-porous species (from 81.31 to 118.25 g/${\mathrm{cm}}^2$/day). These results provide actionable ranges and contrasts to inform species selection and planting design for urban greening and runoff reduction, while highlighting data gaps for future research. Ultimately, by matching specific wood anatomies and planting configurations to local soil and climatic conditions, urban planners and ecohydrologists can strategically optimize urban forests to maximize targeted ecosystem services. Full article

Sulfated peptides, such as PSK, PSY, CIF, and RGF, are crucial regulators of plant growth, development, and stress responses, with their activity dependent on post-translational tyrosine sulfation by tyrosylprotein sulfotransferase (TPST). This study explores the evolutionary history and the interaction mechanisms between TPST and sulfated peptides in plants. Systematic analyses of multi-species genomes show that TPST can be traced back to the chlorophyte lineage, whereas PSK, a sulfated peptide, appears to have emerged in gymnosperms. TPST is evolutionarily conserved, typically present in low copy numbers across plant lineages, while its peptide substrates have expanded in angiosperms. In Liriodendron chinense, TPST-sulfated peptide gene promoters are enriched with cis-regulatory elements linked to abscisic acid, gibberellin responsiveness, and anaerobic induction. Synteny analyses revealed collinearity between sulfated peptide genes in L. chinense, Magnolia biondii, Arabidopsis thaliana, and Populus trichocarpa, but not with Oryza sativa. Molecular docking identified key TPST-PSK interaction sites in the sulfotransferase domain, with several critical residues facilitating binding. Transcriptomic and co-expression network analyses revealed that LcTPST was expressed at lower levels than its peptide precursor genes, while LcPSK2 remained highly expressed after the torpedo stage of somatic embryogenesis. Stress conditions significantly increased PSK-associated module connectivity, enriched in transcription factors such as WRKY, bHLH, bZIP, and MADS. This study provides insights into the evolutionary, structural, and regulatory aspects of the TPST-sulfated peptide system in plants. Full article

Biodiverse composts obtained through composting are widely used in regenerative agriculture due to their ability to improve soil quality, crop growth, and productivity, primarily by promoting beneficial microorganisms. These composts result from the decomposition of mixtures containing nitrogenous and plant biomass. During plant biomass preparation, litter serves as a source of beneficial microorganisms, which transition from endophytes to decomposers. This study tested the hypothesis that the type of litter influences the composition of bacterial and fungal communities in biodiverse composts, thereby affecting species abundance and diversity. To this end, litter from the tree species Handroanthus impetiginosus (Angiosperm—AC) and Pinus elliottii (Gymnosperm—GC) was evaluated in compost preparation, also investigating the impact of litter type on the concentration of macronutrients, chemical parameters (such as organic carbon, cation exchange capacity—CEC; carbon/nitrogen ratio—C/N; organic matter—OM; pH, and humic substances fractions, including humic and fulvic acids), and microbiological quality (assessed by Microbial Biomass Carbon—MBC). The microbial composition of composts prepared with both AC and GC litter was more influenced by the composting method than by plant origin, with bacterial genera such as Thermobacillus (representing 1.27% and 1.23% of the genera present in AC and GC, respectively) and thermotolerant species, adapted to the high temperatures of the thermophilic phase, being notably present. GC litter favored a higher abundance of bacterial (pi = 0.027) and fungal species (pi = 0.042), despite the antimicrobial properties of P. elliottii. In contrast, AC compost accumulated higher levels of macronutrients and OM (39.5%), reflecting the efficacy of specific fungi in decomposition, particularly species from the phyla Chytridiomycota and Zoopagomycota, identified exclusively in this compost. MBC analysis indicated that composts reach optimal efficiency and nutritional quality between 60 and 90 days of maturation, suggesting that this period is the most suitable for leveraging the resident microbiota and producing high-quality composts for agricultural use. Full article

Seed wings are widely recognized for facilitating dispersal and influencing germination in angiosperms, but their functional role in gymnosperm germination is poorly understood. To assess the effect of seed wings on the germination ecology of Smith fir (Abies georgei var. smithii), we evaluated the germination of three seed treatments—intact seeds, mixed seeds (de-winged seeds mixed with detached wings), and de-winged seeds—under varying light and temperature conditions. Results showed that de-winged seeds achieved a final germination percentage of 48.5 ± 5.0%, which was significantly higher than that of intact seeds (26.0 ± 2.4%) and mixed seeds (32.5 ± 3.5%) (p < 0.001), confirming that seed wings significantly inhibit germination. There was no significant difference between intact and mixed seeds, and both were significantly lower than de-winged seeds (p < 0.001), suggesting that germination inhibition is likely mediated by chemical inhibitors in the wings rather than mechanical restriction. Optimal germination occurred at 15/2 °C–25/5 °C, while light significantly enhanced germination under cold conditions (5/1 °C), indicating conditional dormancy. These findings suggest that seed wings optimize the regulation of germination timing by imposing chemical inhibition that, combined with conditional dormancy, delays germination until favorable spring conditions, reflecting an adaptive strategy to seasonal environmental cues in subalpine ecosystems. Full article

The middle–late Cenomanian paleontological area of Algora represents the main concentration of vertebrate remains from the basal Late Cretaceous for southwestern Europe. An unpublished macro-plant assemblage is studied here, being recognized as composed of ferns, conifers, and various other types of gymnosperms and angiosperms, constituting the first well-defined reference of a Cenomanian macro-flora in Spain. Comparison of this assemblage with other coeval ones from the western Tethys region suggests a possible influence of both Central European Laurasian plant elements and those from northern Gondwana (originating in North Africa and the Middle East) in this area of the Iberian Plate, a key region for understanding the dispersal of fauna and flora during the early Late Cretaceous. Full article

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