Search Results (998)

Understanding the mechanisms that assemble diverse forest communities is a central goal in ecology. Phylogenetic analyses based on DNA barcodes have advanced this field, but their use of sequences evolving at constant rates may not capture adaptations to specific environmental drivers. Light is a critical factor shaping forest structure, particularly in the vertical dimension. This study introduces a novel phylogenetic approach using the blue-light receptor gene, cryptochrome (Cry), which is directly involved in plant light perception and adaptation. We reconstructed a Cry-based phylogeny for 96 tree species in a 20 ha subtropical forest dynamics plot and analyzed community structure using the net relatedness index (NRI) and nearest taxon index (NTI) across horizontal habitats, successional stages, and vertical canopy layers. Compared to traditional DNA barcoding, the Cry phylogeny revealed distinct patterns, showing consistent phylogenetic structure across different habitats—a finding indicative of convergent evolution in light-sensing systems. Furthermore, the Cry-based analysis demonstrated a stronger and more consistent signal in the forest’s vertical structure, with significant phylogenetic clustering in upper canopy layers, directly linking light adaptation to community stratification. Over time, both NRI and NTI values increased, suggesting succession leads to greater phylogenetic overdispersion and highlighting an increased role for environmental filtering among closely related taxa. Our results validate Cry as a powerful functional gene marker for phylogenetics, providing unique insights into how light environment filters species and shapes the vertical assembly of forest communities. Full article

Ecological restoration of mine wastelands is central to biodiversity conservation and ecosystem recovery worldwide. However, the long-term ecological consequences of active restoration versus natural regeneration remain debated, particularly in mountainous karst landscapes. Using a space-for-time substitution, we established a five-stage chronosequence—recently abandoned, 10 years, 20 years, 30 years, and a late-successional forest (>35 years)—in a typical underground coal-mine wasteland in eastern Yunnan, southwest China. Each age class contained paired active restoration and natural regeneration sites; the late-successional forest served as a reference. We surveyed nested vegetation plots (20 × 20 m with shrub and herb subplots) in summer and autumn, recorded vertebrate species with camera traps, and quantified α-diversity (species richness, Shannon–Wiener diversity, Simpson’s diversity, Pielou’s evenness) and β-diversity (Bray–Curtis dissimilarity, non-metric multidimensional scaling). Overall plant α-diversity was highest in natural regeneration and lowest in active restoration, whereas tree-layer diversity was highest in active restoration and shrub and herb layers were richer under natural regeneration. Preliminary data from our camera traps suggested that animal species richness ranked late-successional forest > natural regeneration > active restoration, but evenness peaked in active restoration, suggesting early-stage homogenization. Plant β-diversity indicated stronger compositional divergence among active restoration sites and greater similarity between natural regeneration and the reference forest; both modes converged toward the reference forest over time but followed distinct patterns. These findings suggest that active restoration accelerates structural development yet increases between-site heterogeneity, whereas natural regeneration maintains higher overall diversity and compositional similarity to reference communities. Our results provide preliminary empirical guidance for selecting restoration strategies in similar karst coal-mine landscapes. Full article

DNA methylation is an epigenetic modification that plays a crucial role in the regulation of gene expression, genome defense, and numerous biological processes. DNA methyltransferase (MTase) is the pivotal enzyme catalyzing the DNA methylation reaction. To explore the regulation mechanism of DNA methylation in rubber trees (Hevea brasiliensis), we identified 13 genome-wide MTase genes containing conserved structural domains of DNA methyltransferase based on the rubber tree reference genome. Through phylogenetic analysis, these genes were classified into four subfamilies: MET1, CMT, DRM, and DNMT2. A significant expansion of DNA methyltransferase genes was found in rubber trees, especially in the DRM subfamily. Notably, among the four members of the MET1 subfamily, only HbMET1-1 contains the complete UBA and RFD domains, suggesting its critical role in the function of MET1 in plants, while the other members may have developed different functions during evolution. Gene expression pattern analysis revealed that most DNA methyltransferases were specifically expressed at low levels in latex. However, following tapping from unharvested rubber trees, the expression levels of HbMTase genes are altered, and these alterations exhibit variability. Among them, HbMET1-1 and HbDRM2-1 exhibited a response to tapping stress, with their expression levels rapidly increasing after stress application and subsequently decreasing gradually. The expression levels of HbCMT3-1 and HbCMT3-2 continued to increase as the rubber tapping process progressed, which was consistent with the observed changes in HbMTase enzyme activity. These findings suggest that tapping, as a form of mechanical stress, affects the expression of particular genes. Through subcellular localization analysis, we found that HbDNMT2 is the only DNA methyltransferase located in the cytoplasm its expression level gradually decreases during the rubber tapping process. It is hypothesized that this gene activates a multitude of genes involved in the rubber biosynthesis pathway and participates actively in rubber biosynthesis. In conclusion, the comprehensive analysis of the structural characterization, conserved domains analysis, cis-regulatory elements, subcellular localization, expression profiling, and HbMTase enzyme activity detection provides critical insights into the functional characteristics of DNA methyltransferases in rubber trees and initially reveals the DNA methylation response in rubber tree tapping. Full article

The sulfo-Embden–Meyerhof–Parnas (sulfo-EMP) pathway enables Escherichia coli to utilize sulfoquinovose, (SQ) a sulfonated sugar derived from plant sulfolipids, as a carbon source. This pathway is encoded by the yih gene cassette. However, structural and functional diversity of this cassette across E. coli strains has not been fully characterized. We identified two structural variants of the yih cassette across E. coli and Shigella strains: a long form (ompL-yihOPQRSTUVW) and a truncated short form (yihTUVW). Both forms occupy the same genomic location but differ in orientation and are scattered across the phylogenetic tree, suggesting frequent recombination events. Transcriptome analyses revealed that only the long cassette, as found in E. coli K-12 MG1655, is transcriptionally induced during growth on sulfoquinovose. The short cassette, found in E. coli Nissle 1917 and other host-adapted strains, showed no differential expression. Despite this, both strains grew comparably on sulfoquinovose, indicating different metabolic adaptation strategies. Gene expression profiling revealed shared stress responses but distinct central metabolic patterns. Electrophoretic mobility shift assays further demonstrated that the transcription factor YihW from Nissle 1917 binds its DNA targets with lower affinity than the homolog from K-12 and shows weaker sulfoquinovose-dependent dissociation. Full article

Background: PAL genes are crucial for plant growth and stress response, yet studies on the PAL gene family in Camellia nitidissima are sparse. Methods: The PAL gene family was screened from the entire genome of C. nitidissima, and their physicochemical properties, chromosomal locations, intraspecific and interspecific collinearity, conserved motifs, phylogenetic trees, cis-acting elements, and gene structures were analyzed. The expression patterns of the CnPAL genes were compared across different tissues, and the highly expressed CnPAL1 gene was expressed in prokaryotes, and its enzyme activity was validated using UPLC-MS technology. Results: The results revealed that six CnPALs were identified in the C. nitidissima genome, distributed unevenly across six chromosomes. The CnPAL proteins shared similar physicochemical properties, with highly conserved motifs and gene structures. Promoter analysis showed multiple cis-acting elements in the CnPALs genes. Intra-species collinearity analysis revealed that all CnPALs were collinear with multiple PAL genes in C. nitidissima, while inter-species collinearity analysis indicated that CnPALs were collinear with the PAL genes in Camellia oleifera and Camellia sinensis. Furthermore, the transcriptomic data of C. nitidissima demonstrated tissue-specific expression of the CnPALs, although qRT-PCR validation showed some discrepancies with the sequencing result. The qRT-PCR revealed varied expression patterns among the six CnPALs, with the CnPAL1 gene showing relatively higher expression levels. Subsequently, cloning, prokaryotic expression, and enzyme activity analysis confirmed the effective catalytic activity of the CnPAL1 protein. Conclusions: This study lays the foundation for understanding the functions of CnPAL genes and offers insights for genetic improvement of C. nitidissima. Full article

Advances in Earth observation technology using multispectral imagery from satellite Earth observation systems and sensors mounted on unmanned aerial vehicles (UAVs) are enabling more accurate crop monitoring. These images, once processed, facilitate the analysis of crop health by enabling the study of crop vigour, the calculation of biomass indices, and the continuous temporal monitoring using vegetation indices (VIs). These indicators allow for the identification of diseases, pests, or water stress, among others. This study compares images acquired with the Altum PT sensor (UAV) and Super Dove (satellite) to evaluate their ability to detect specific problems in super-intensive olive groves at two critical times: January, during pruning, and April, at the beginning of fruit development. Four different VIs were used, and multispectral maps were generated for each: the Normalized Difference Vegetation Index (NDVI), the Green Normalized Difference Vegetation Index (GNDVI), the Normalized Difference Red Edge Index (NDRE) and the Leaf Chlorophyll Index (LCI). Data for each plant (n = 11,104) were obtained for analysis across all dates and sensors. A combined methodology (Spearman’s correlation coefficient, Student’s t-test and decision trees) was used to validate the behaviour of the variables and propose predictive models. The results showed significant differences between the sensors, with a common trend in spatial patterns and a correlation range between 0.45 and 0.68. Integrating both technologies enables multiscale assessment, optimizing agronomic management and supporting more sustainable precision agriculture. Full article

Fatty acid transporters (FAXs) play an important role in fatty acid synthesis by facilitating transport fatty acids from the plastid to the endoplasmic reticulum. This process is essential for providing precursor substances necessary for triglycerides (TAGs). Although FAX genes have been identified in variety of plant species, the identification and molecular functions of the GmFAX gene members in soybean are still unclear. In this study, soybean FAX genes were identified through the utilization of the Phytozome (v13) and NCBI online websites. Subsequently, phylogenetic trees, expression patterns, gene structures, and qRT-PCR were analyzed. A total of eight GmFAX members were identified at the whole genome level, and further phylogenetic analysis revealed that these members can be categorized into four subfamilies. In addition, all members of GmFAX contain a highly conserved domain Tmemb_14. Through qRT-PCR analysis, it was found that the expression level of the GmFAX8 gene is relatively high in leaves and stems. Further investigation revealed that the total fatty acid content in hairy roots overexpressing the GmFAX8 gene was significantly greater than that observed in the control strain. The results presented above suggest that the GmFAX8 gene may play an important role in the accumulation of oil within soybeans. Full article

Sulfur metabolism plays an important role in plant growth and environmental adaptation. Sulfate transporters (SULTRs) are essential players that mediate sulfur acquisition and distribution in many plants, thereby influencing the cellular redox homeostasis under abiotic stress. In this study, we identified 16 putative HvSULTRs genes in barley at the genome-wide level. The conservation and divergence of the SULTR gene family were assessed through a phylogenetic tree and gene structure analysis, revealing that these genes are closely distributed along the chromosomes. Furthermore, the expression pattern of SULTRs in multiple tissues, including flower, root, leaf, stem, seeds, female, male, root meristem, and apical meristem, were analyzed among ten land plants using a public database. Interestingly, the expression of HvSULTR2, HvSULTR4, and HvSULTR5 was upregulated after four days of heat treatment, suggesting their importance in barley’s adaptive response to heat stress. In addition, HvSULTR11 was confirmed to be localized at the plasma membrane and display functional interactions with Hv14-3-3A/Hv14-3-3D. In addition, haplotypes of the HvSULTR11 based on SNP (Single Nucleotide Polymorphism) were divided into ten types across 123 barley varieties. Together, these results provide a new clue to clarify the molecular mechanism of SULTRs in stress response and a new candidate gene resource to enhance the stress (e.g., heat and drought) tolerance in barley. Full article

Phoebe bournei is an important economic tree species in China, its large-scale propagation is limited by the difficulty of adventitious root (AR) formation in cuttings. In this study, morphological, physiological, and transcriptomic analyses were conducted to investigate the process of AR formation in P. bournei. The results showed that ARs mainly originated from callus tissue. During AR formation, soluble sugar and soluble protein contents changed significantly. Malondialdehyde (MDA) and oxygen free radicals (OFRs) peaked at first sampling stage (PB0), while the activities of polyphenol oxidase (PPO) and indoleacetic acid oxidase (IAAO) exhibited similar patterns. Lignin content increased during callus induction stage, whereas phenolic content continuously declined throughout rooting. Endogenous hormone levels also changed markedly, and Orthogonal partial least squares discriminant analysis (OPLS-DA) analysis indicated that indole-3-acetic acid (IAA) and abscisic acid (ABA) played dominant roles in this process. KEGG enrichment analysis revealed significant enrichment of the phenylpropanoid biosynthesis pathway in all three comparison groups. A total of 48 differentially expressed genes (DEGs) were enriched in plant hormone signal transduction pathways, with 22 and 14 genes associated with IAA and ABA signaling, respectively. Weighted gene co-expression network analysis (WGCNA) further identified two hub modules related to IAA and ABA contents, including eight hub genes such as D6PKL1 and ISTL1. Correlation analysis revealed that the hub genes D6PKL1 and HSP were significantly positively correlated with IAA4 in the IAA signaling pathway. Overall, this study provides new insights into the mechanisms underlying AR formation in P. bournei cuttings and offers a theoretical basis for optimizing its clonal propagation system. Full article

To effectively address the issues of poor ventilation, light deficiency, increased pest and disease pressure, and declining fruit quality in closed-canopy walnut orchards, this study was conducted in a standard, densely planted ‘Xinwen 185’ walnut orchard. Three treatments were established: an unthinned control (CK), a 1-year thinning treatment (T1), and a 2-year thinning treatment (T2). All parameters were uniformly investigated during the 2023 growing season to analyze the effects of thinning on orchard population structure, microenvironment, leaf physiological characteristics, fruit quality, and yield. The results demonstrated that tree thinning significantly optimized the population structure: crown width expanded by 6.22–6.76 m, light transmittance increased to 27.74–33.64%, and orchard coverage decreased from 100% to 75.94–80.51%. The microenvironment was improved: inter-row temperature increased by 2.34–4.08 °C, light intensity increased by 5.38–25.29%, and relative humidity decreased by 2.15–3.30%. Furthermore, leaf physiological functions were activated: in the T2 treatment, the chlorophyll content in outer-canopy leaves increased by 15.23% and 12.45% at the kernel-hardening and maturity stages, respectively; the leaf carbon-to-nitrogen ratio increased by 18.67%; the net photosynthetic rate (Pn) during fruit expansion increased by 34.21–46.10%; and the intercellular CO₂ concentration (Ci) decreased by 10.18–10.31%. Fruit quality and yield were synergistically enhanced: single fruit weight increased by 23.39~37.94%, and kernel weight increased by 26.79–41.13%. The total sugar content in inner-canopy fruits increased by 16.50–16.67%, while the protein and fat content in outer-canopy fruits increased by 0.69–12.50% and 0.60–2.18%, respectively. Yield exhibited a “short-term adjustment and long-term gain” pattern: the T2 treatment (after 2 years of thinning) achieved a yield of 5.26 t·ha⁻¹, which was 20.38% higher than the CK. The rates of diseased fruit and empty shells decreased by 65.71% and 93.22%, respectively, and the premium fruit rate reached 90.60%. This study confirms that tree thinning is an effective measure for improving the growing environment and enhancing overall productivity in closed-canopy walnut orchards, providing a scientific basis for sustainable orchard management and increased orchard profitability. Full article

Climate change continues to threaten global biodiversity, making it essential to assess how keystone species may shift their distributions and to use these findings to inform conservation planning. This study evaluated the current and future habitat suitability of D. macropodum, an important tree species within subtropical evergreen broad-leaved forests in China, using 354 occurrence records and a suite of environmental variables. A parameter-optimized MaxEnt model (calibrated with ENMeval; RM = 4, FC = QHPT) was applied to simulate the species’ present distribution and projected changes under three climate scenarios (SSP126, SSP245, SSP585). The main factors influencing distribution were determined to be moisture and temperature seasonality, with the precipitation of the coldest quarter (Bio19, 36.3%), the mean diurnal range (Bio2, 37.5%), and the precipitation of the warmest quarter (Bio18, 14.2%) jointly contributing 88.0% of the total influence. The model projections indicated a 40.1% reduction in the total number of suitable habitats under high-emission scenarios (SSP585) by the 2090s, including a loss of over 80% of highly suitable areas. Centroid movements also diverged across the scenarios: a southwestern shift under SSP126 and SSP245 contrasted with a southeastern shift under SSP585, with each accompanied by significant habitat fragmentation. Key climate refugia were identified primarily in central Taiwan Province and the mountainous zones of Zhejiang and Fujian Provinces, which should be prioritized for conservation activities. These insights offer a foundational understanding for the conservation of D. macropodum and other ecologically similar subtropical evergreen species. However, direct extrapolation to other taxa should be made cautiously, as specific responses may vary based on differing ecological tolerances and dispersal capacities. Further research is needed to test the generalizability of these patterns across diverse plant functional types. Full article

Tree peony is an important horticultural plant with both ornamental and oil value. The tree peony genome and databases were used to search for calmodulin family genes to explore their function in the pollination of tree peony. The CaM gene family was identified, and then the basic protein characteristics of the family members, such as gene structure, isoelectric point, molecular weight, subcellular localization, and conserved protein domain, were analyzed. The expression levels of these genes in the pistil tissue of Paeonia ostii ‘Fengdan’ at different developmental stages after pollination were also analyzed. Further, qRT-PCR was used to detect the expression levels of six PsCaMs during the development process of the pistil under bee pollination conditions. The results showed that there were six CaM family members located on three chromosomes and one non-chromosome. There were a large number of hormone response and stress response elements on the gene promoter of this family. During the development of pistil tissue after pollination, CaM family gene expression showed a trend of first increasing and then decreasing, which may be related to its function during pollination. The purpose of this study is to identify the gene characteristics and expression patterns of the CaM family during pollination, and to lay a foundation for the functional study of the CaM family in tree peony pollination. Full article

Karyotype analysis and the investigation of chromosomal variations in Populus are challenging due to its small and morphologically similar chromosomes. Despite its utility in chromosome identification and karyotype evolutionary research, satellite DNA (satDNA) remains underutilized in Populus. In the present study, 12 satDNAs were identified from P. trichocarpa, and the copy numbers and chromosomal distributions of each satDNA were analyzed bioinformatically in the reference genomes of P. trichocarpa, P. simonii, and P. nigra. Ten satDNA probes for fluorescence in situ hybridization (FISH) were successfully developed and validated on chromosomes of P. xiaohei (poplar hybrid P. simonii × P. nigra). By integrating bioinformatic genomic satDNA distribution patterns with experimental FISH signals, we constructed a molecular karyotype of P. xiaohei. Comparative analysis revealed errors in current poplar genome assemblies. Comparative karyotype analysis of P. xiaohei and its doubled haploid (DH) lines revealed chromosomal variations in the DH lines relative to the donor tree. The results demonstrate that the newly developed satDNA probes constitute robust cytogenetic tools for detecting structural variations in Populus, while molecular karyotyping provides new insights into the genetic mechanisms underlying chromosome variations in P. xiaohei and the DH plants derived. Full article

In recent years, the rise in food allergies and intolerances, combined with the increasing consumer preference for healthier, plant-based alternatives to traditional dairy products, has driven the development of a diverse range of plant-based beverages. Among these, tree nut-based beverages, “ready-to-drink” products made from nuts such as almonds, hazelnuts, pistachios, walnuts, brazil nut, macadamia, cashew nut, coconut, pine nut, have gained significant popularity. This review offers a comprehensive analysis of the microbiological, nutritional, and sensory properties of tree nut-based beverages, highlighting their ability to deliver essential nutrients such as healthy fats, proteins, fiber, vitamins, and minerals. Additionally, these beverages provide a rich source of bioactive compounds (e.g., antioxidants, polyphenols) that can contribute to health benefits such as reducing oxidative stress, supporting cardiovascular health, and promoting overall well-being. The review also highlights the ability of different species of lactic acid bacteria to enhance flavour profiles and increase the bioavailability of certain bioactive compounds. Nevertheless, further research is essential to optimize the production methods, improve sensory characteristics, and address challenges related to cost, scalability, and consumer acceptance. Continued innovation in this area may position tree nut beverages as a key component of plant-based food models, contributing to the promotion of healthier eating patterns. Full article

Tree rings, tree needles, and moss can be used as biomonitors to evaluate atmospheric pollutant concentrations and deposition patterns spanning different timescales. This study compares output from air quality modeling and measurements to patterns observed using a combination of sulfur concentration and isotope composition in moss (using moss bags and controls) as biomonitors in a region of southern Alberta, Canada influenced by industrial emissions. Tree rings allow comparisons of historical to current sulfur deposition patterns. Moss, which integrates atmospheric nutrients during growth, allows for concurrent comparisons. The contrast of inorganic and organic sulfur within conifer tree needles provides a measure of pollutant uptake over their short lifespans. Sulfur uptake within biomonitors in a southern Alberta ecosystem allow assessment of the presence (in moss, needles) and effects (on conifer growth) of atmospheric sulfur deposition from industrial emissions. These data were examined relative to California Puff (CALPuff) model projections and traditional active and passive air quality sampling. Patterns in sulfur isotope abundance (δ³⁴S) from moss bags placed throughout the eastern slopes of the southern Alberta foothills of the Rocky Mountains implicate local industry as the dominant atmospheric sulfur source over winter, with the tissues of conifers (needles and cores) and moss decreasing with distance from industrial emissions. This was consistent with apportionment calculations based on active and passive sampling, which also showed a surprising trend of sulfur deposition upwind of the industrial stack in the mountains to the west. δ³⁴S values for pine needles and tree rings were consistent with greater sulfur stress and reductions in tree growth associated with increased industrial sulfur concentrations and deposition. We conclude that plant biomonitors are effective short-term (tree needles and moss) and long-term (tree cores) indicators of sulfur pollution in a complex, mountainous landscape. Full article