Objectives: Flavonoids are a class of widely distributed secondary metabolites in plants. Ginkgo biloba leaves are rich in flavonoids and thus are utilized for extracting medicinal components to treat and prevent cardiovascular and cerebrovascular diseases. Flavonol synthase (FLS) serves as a key enzyme in the flavonol metabolic pathway. Numerous studies have identified and characterized FLS family genes across various plant species, all of which play crucial roles in regulating the flavonoid biosynthetic pathway. Methods: We measured the flavonoid content in Ginkgo biloba leaves across different months, performed transcriptomic analysis on leaves from months showing an increasing trend, and screened out the GbFLS1045 gene involved in the synthesis of the FLS enzyme. Molecular biology techniques were then employed to explore the function of the GbFLS1045 gene. Results: From June to August, the flavonoid content in Ginkgo biloba leaves exhibited an upward trend, and we found that GbFLS1045 is localized in the cytoplasm, cell membrane, and nucleus through transient transformation in Nicotiana tabacum. Overexpression(OE) of GbFLS1045 in Arabidopsis thaliana resulted in significantly higher levels of total flavonol glycosides, kaempferol, quercetin, and isorhamnetin in OE transgenic plants compared to WT controls. Furthermore, in OE lines of Ginkgo biloba callus, the isorhamnetin content was consistently elevated relative to both WT and Anti lines. Conclusions: GbFLS1045 positively regulates flavonoid synthesis in Ginkgo biloba.

Limonium franchetii is a coastal halophyte endemic to China and is mainly distributed along rocky shores and gravel beaches of the Yellow Sea and Bohai Sea coasts. Its natural populations are increasingly threatened by coastal development, tourism activities, habitat fragmentation, and climate change. In this study, we analyzed 201 individuals from 14 natural populations using three chloroplast DNA fragments (trnL-trnF, matK, and ndhF-rpl32) to evaluate genetic diversity, phylogeographic structure, potential refugial populations, and historical dynamics. L. franchetii exhibited high total genetic diversity (Ht = 0.930) and strong population differentiation (F ST = 0.6958), with 69.59% of the total variation occurring among populations. PERMUT analysis revealed significant phylogeographic structure, and 26 cpDNA haplotypes were identified. Haplotype-network and phylogenetic analyses indicated two major cpDNA haplotype clades with partially structured geographic distributions, broadly corresponding to the northern Shandong-Liaodong region and the eastern/southern Shandong coast, although the two clades were not geographically exclusive. Divergence-time estimates ranged from 3.01 to 0.25 Ma, suggesting that Quaternary sea-level fluctuations, historical land connections, and subsequent coastal isolation contributed to haplotype differentiation. Neutrality tests and mismatch distribution analysis did not support a recent species-wide demographic expansion, although lineage-level spread of several haplotypes may have occurred in association with post-glacial environmental changes. Zhifu Island in Yantai, Zhangjia Village in Dalian, and the Huanglei River population in Weihai were inferred as potential refugial populations. These genetically diverse and refugial populations should be prioritized for in situ conservation, whereas fragmented coastal populations require habitat protection, tourism-pressure control, and restoration of ecological connectivity.

Limonium sinense is a recretohalophyte with both ecological and economic value inhabiting China’s coastal saline-alkali zones, and it can play an important role in saline-alkali soil amelioration and coastal vegetation restoration. Impacted by coastal development and habitat fragmentation, the size of its wild populations has declined sharply in recent years; thus, elucidating its population genetic and evolutionary characteristics is urgently needed to inform conservation strategy development. This study employed whole-genome resequencing technology to analyze 170 individuals from 17 wild populations covering the complete natural distribution range of this species, yielding a total of 2, 558.79 Gb of high-quality clean sequencing reads and detecting 126, 690, 413 SNP loci. Analysis revealed north–south divergence in genetic diversity: southern populations exhibited higher genetic diversity (mean Ho = 0.330, He = 0.296) with heterozygote excess, whereas northern populations displayed lower genetic diversity (mean Ho = 0.221, He = 0.258) and potential inbreeding depression risk. Population genetic structure analysis confirmed that the 17 populations could be delineated into two major genetic lineages, northern and southern, with a clear demarcation between them; southern populations exhibited a relatively complex ancestral composition, whereas northern populations remained comparatively homogeneous. Inter-population genetic differentiation analysis combined with the isolation-by-distance model revealed that contemporary gene flow among northern populations is restricted, whereas southern populations experience relatively weak differentiation and more frequent gene exchange. Treemix historical gene flow model detected no large-scale cross-regional gene flow events; only intra-lineage gene flow events were identified: a high-intensity historical gene flow event occurred within the northern lineage, reflecting past connectivity, while only weak genetic introgression was detected within the southern lineage. Demographic history reconstruction, together with genome-wide neutrality tests (Tajima’s D and Fu’s Fs) and folded site frequency spectrum (SFS), consistently supported that all populations experienced a phased trajectory of prolonged stability, Holocene climatic oscillation-driven bottleneck contraction, and synchronous rapid recovery, with southern populations exhibiting a greater recovery magnitude than northern populations. Genome-wide runs of homozygosity (ROH) further confirmed divergent inbreeding patterns between northern and southern lineages. Our results indicate that populations of this species can be classified into two major genetic lineages: northern and southern. Geographic isolation is the core factor driving genetic divergence; the current patterns of genetic diversity, genetic structure, and lineage distribution are shaped primarily by the combined effects of geographic isolation, climatic oscillations, and anthropogenic disturbance together with habitat fragmentation. Based on these findings, this study proposes region-specific targeted conservation strategies, providing a theoretical basis for the germplasm conservation and sustainable utilization of this species, as well as a representative case study for research on adaptive evolution in coastal halophytes.

The molecular mechanisms underlying the complex floral color patterns in Catalpa bungei, which are characterized by purplish-red spots and yellow nectar guides, are not fully understood. To elucidate these mechanisms, we integrated metabolomic and transcriptomic analyses of three accessions (P, B, and W) with distinct floral phenotypes. Phenotypic and colorimetric analyses revealed that accession P exhibits dense purplish-red spots and deep orange-yellow nectar guides, which correlated with the highest a* values in petals and highest b* values in nectar guides, whereas accession W shows sparse spots and pale yellow guides, and accession B displays an intermediate phenotype. Metabolomic profiling identified 2217 metabolites, highlighting the accumulation of specific anthocyanin derivatives, such as pelargonidin-3-p-coumarylglucoside in P and various acylated anthocyanins in B. The yellow nectar guides were primarily proposed to be attributed to flavonol glycosides. Transcriptomic analysis indicated that key anthocyanin pathway genes (e.g., CHS, CHI, F3H, DFR, ANS, UFGT) were significantly upregulated in P, whereas most FLS genes were downregulated. Weighted Gene Co-expression Network Analysis (WGCNA) identified eight modules (e.g., MEyellow, MEblue) strongly associated with color patterning, which are regulated by transcription factors (e.g., MYB, bHLH, WD40, bZIP) that show co-expression with modification genes such as UGT and AOMT. The expression patterns of 12 key genes were validated using qRT-PCR. This study provides the first comprehensive analysis of the metabolic and transcriptional networks controlling floral color patterning in C. bungei, proposing a synergistic regulatory mechanism and offering critical targets for molecular breeding.

Prunus mume, an important ornamental and fruit tree in East Asia, has plant height and branching regulation mechanisms valuable for breeding new varieties that require less artificial shaping and are suitable for potting and high-yield cultivation. This study focused on the TCP family transcription factor PmTCP18, cloned from the leaf buds of the P. mume 'Feilve', and systematically investigated its expression patterns, biological functions, and regulatory mechanisms to elucidate its role in regulating plant height and branching. The results showed that PmTCP18 expression peaked during the bud break stage and was significantly induced by gibberellin and cytokinin. Overexpression of PmTCP18 in poplar notably increased plant height, stem diameter, and lateral branch formation. Furthermore, it promoted elongation of stem epidermal cells, widening of xylem and phloem tissues, and an increase in cambium cell layers, indicating that PmTCP18 regulates processes of cell division, differentiation, and elongation. Transcriptome analysis revealed that PmTCP18 overexpression affected multiple plant hormone signaling pathways and significantly upregulated the expression of ABC transporters and cell cycle-related genes. The transcription factor PmHB1 directly binds to the PmTCP18 promoter. And in the stem tips where the PmHB1 gene was silenced by VIGS, the expression level of the PmTCP18 was also significantly reduced, suggesting the PmHB1 positively regulates its expression. Collectively, this study provides novel insights into the role of PmTCP18 in regulating shoot length and branching and serves as a critical reference for deciphering the functional mechanisms of class I TCP genes in plant architectural development.

Rosa rugosa is an important edible and spice plant with great economic value. However, Rose black spot disease caused by Marssonina rosae is a devastating disease that severely hampers its development. Although WRKY transcription factors were widely involved in plant stress responses, their role in the molecular mechanisms underlying resistance to M. rosae in roses remains unclear. In this study, we got two RrWRKY genes, and employed Nicotiana benthamiana as experimental material to investigate and analyze their functions. The overexpression of these RrWRKY22 and RrWRKY51 in transgenic tobacco significantly enhanced resistance to rose black spot disease, thereby validating their potential role in disease resistance. The disease index of RrWRKY22 and RrWRKY51 transgenic N. benthamiana decreased under the stress of M. rosae. The number of dead cells in transgenic leaves decreased after Trypan blue staining. Compared with wild type (WT) N. benthamiana, RrWRKY22 and RrWRKY51 transgenic lines had significantly higher contents of osmoregulatory substances and antioxidant enzyme activities in leaves. ROS and MDA accumulation decreased significantly. Moreover, our findings revealed an interaction between RrWRKY22 and RrWRKY51. This study provides valuable candidate genes for disease resistance breeding and offers a theoretical framework for elucidating the disease resistance mechanisms mediated by the WRKY transcription factor family.

Rosa rugosa hips are a valuable resource rich in flavonoids with significant health benefits, though the regulatory mechanisms underlying flavonoid biosynthesis remain unclear. In R. rugosa hip, the chlorophyll content decreased significantly during hip ripening from the green (F0) to the yellow (F1) and red (F2) stages. In contrast, total flavonoid content peaked at the F1 stage, while anthocyanin and carotenoid levels showed a concomitant increase. To investigate the regulatory mechanisms, we performed integrated transcriptomic and metabolomic analyses of wild R. rugosa hips at the F1 and F2 stages. Transcriptomic data revealed 4,329 DEGs, which were predominantly enriched in 'Metabolic pathways' and 'Biosynthesis of secondary metabolites' by KEGG pathway enrichment analysis. Notably, 62 upregulated DEGs were assigned to specific flavonoid-related biosynthesis pathways. Meanwhile, metabolomic profiling identified 729 flavonoids, 308 of which were differentially accumulated metabolites (DAMs). Importantly, anthocyanin content increased upon ripening, while most other flavonoids decreased. Association analysis highlighted critical genes in anthocyanin biosynthesis, including upregulated BZ1, AOMT, 3MaT1, and 3MaT2, which correlated with the accumulation of specific derivatives like cyanidin 3-0-(6-027 malonyl)-beta-D-glucoside and peonidin 3-glucoside, contributing to the hip's red color. Similarly, CYP81E genes were linked to isoflavonoid accumulation, while downregulated CYP75B1 genes corresponded to decreased quercetin levels. These findings systematically elucidate the transcriptional and metabolic landscape of flavonoid biosynthesis during R. rugosa hip ripening, providing crucial insights for future genetic engineering aimed at enhancing flavonoid content and hip quality.

IntroductionAs a native tree species in China, Machilus thunbergii is highly responsive to nitrogen fertilization. However, related studies are scarce. This research seeks to elucidate how different nitrogen fertilizers affect its growth and nitrogen metabolism across different growth stages, thereby determining the most suitable type and establishing a scientific foundation for its fertilization.MethodsThis study aimed to investigate the effects of topdressing with different nitrogen fertilizers on the growth and nitrogen metabolism of M. thunbergii seedlings, with the goal of providing a scientific basis for optimized nitrogen fertilization management in M. thunbergii cultivation. The study used 3-year-old M. thunbergii seedlings as the material, and the fertilization rate was 3 g per seedling. The experiment was conducted in a one-way randomized block design with four treatments, including the control treatment and three nitrogen fertilizer treatments: urea (amide nitrogen fertilizer), ammonium sulfate (ammonium nitrogen fertilizer), and sodium nitrate (nitrate nitrogen fertilizer). From the start of the experiment, the branch and leaf morphology, the height growth, and the basal diameter growth of the seedlings in each treatment were monitored periodically. The activities of the nitrogen-metabolizing enzymes, such as nitrate reductase, glutamine synthetase, glutamate synthetase, and glutamate dehydrogenase, in the leaves were also measured. At growth cessation, all treatments were evaluated for biomass production, root morphological characteristics, and total nitrogen content in different plant parts (i.e., roots, stems, and leaves).ResultsDue to the high nitrogen content in the cultivation substrate, the application of the different nitrogen fertilizers induced varying levels of fertilizer injury. Temporal analysis revealed that the growth inhibition was not uniform across stages. While all nitrogen treatments ultimately suppressed the overall height and diameter growth compared with the control, the timing and the intensity of these effects varied. For instance, the urea treatment initially showed less inhibition, whereas the sodium nitrate treatment consistently exhibited the strongest inhibitory effect throughout the experiment. Similarly, the promotion of nitrogen metabolism enzyme activity by the different fertilizers also displayed distinct temporal patterns, with peaks occurring at different measurement points. All nitrogen treatments increased the nitrogen content in the root, stem, and leaf parts, but decreased the nitrogen translocation efficiency of M. thunbergii seedlings. All nitrogen treatments increased the nitrogen accumulation in the roots and stems of seedlings. Urea treatment enhanced foliar nitrogen accumulation, whereas both the ammonium sulfate and sodium nitrate treatments reduced foliar nitrogen accumulation.ConclusionAll three nitrogen treatments significantly influenced both the growth and physiological indices of M. thunbergii seedlings. While generally enhancing the nitrogen metabolism and accumulation, improper selection of fertilizer types or excessive application rates elevated the tissue nitrogen concentration, inducing phytotoxic effects that ultimately inhibited seedling growth. In this research, sodium nitrate had the greatest toxic effect on M. thunbergii seedlings, followed by ammonium sulfate and urea. Among the nitrogen fertilizers tested, urea proved superior at an application rate of 3 g per plant for 3-year-old M. thunbergii seedlings.

Abstract Objectives Toona sinensis, commonly known as Chinese toon, is a perennial woody plant with significant economic and ecological importance. This study employed whole-genome resequencing of 180 T. sinensis samples collected from Shandong to analyze genetic variation and diversity, ultimately identifying 18,231 high-quality SNPs after rigorous quality control and linkage disequilibrium pruning. This comprehensive genomic resource provides novel insights into the genetic architecture of T. sinensis, facilitating the elucidation of population structure and supporting future breeding programs. Data description We performed whole-genome resequencing on 180 Toona sinensis samples, generating 1170.26 Gbp of clean data with a Q30 percentage of 93.69%. The average alignment rate to the reference genome was 96.72%, with an average coverage depth of 8 × and a genome coverage of 88.71%. Following data quality control and alignment, we performed SNP calling and filtering to identify high-quality SNPs across all samples. Population structure analyses were then conducted using the identified SNPs, including principal component analysis (PCA), structure analysis, and phylogenetic tree construction. These comprehensive analyses provide a foundation for understanding the genetic diversity and evolutionary dynamics of T. sinensis.

Flower color serves as a vital ornamental feature of landscape plants; Sophora japonica L. mutant ‘AM’ exhibits the different colors from the common S. japonica. ‘AM’, presenting with a light purple-red wing and keel and yellowish-white flag petals, while common S. japonica is yellow and white. The metabolites contributing to this color specificity in red-flowered S. japonica ‘AM’ are not yet fully understood. In this study, the flag, wing, and keel petals were collected from ‘AM’ at various phases, including the flower bud phase, initial flowering phase, full bloom phase, and final flowering phase, for conducting the metabolic assays targeting anthocyanins. Subsequently, we identified 45 anthocyanin-related metabolites, including nine flavonoids and 36 anthocyanins. Ten major floral chromoside metabolites were found to affect the coloration differences among the petals, where the most abundant anthocyanin was cyanidin-3-O-glucoside (Cy3G), which was much higher in the keel petal (LGB) and wing petal (YB) than in the flag petal (QB), and similarly, during the four periods of different petal types, the Cy3G content was higher in the initial flowering stage (S2), the full bloom stage (S3), and the final flowering stage (S4) than the flower bud stage (S1), which was in accordance with the trend of the observed petal floral color phenotypic difference measurement correlation. This suggested that the Cy3G accumulation was the primary factor driving the distinct coloration of varying types of petals. These findings could contribute to the understanding of the biochemical mechanisms underlying S. japonica petal coloration and may support future efforts in flower color improvement.

Background: Catalpa bungei ‘Jinsi’ has excellent wood properties and golden texture, which is widely used in producing furniture and crafts. The lignin content and structural composition often determine the use and value of wood. Hence, investigating the characteristics of the annual dynamics of lignin anabolic metabolites in C. bungei ‘Jinsi’ and analyzing their synthesis pathways are particularly important. Methods: We carried out targeted metabolomics analysis of lignin synthesis metabolites using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) on the xylem samples of C. bungei ‘Jinsi’ in February, April, July, October 2022, and January 2023. Results: A total of 10 lignin synthesis–related metabolites were detected: L-phenylalanine, cinnamic acid, p-coumaraldehyde, sinapic acid, p-coumaric acid, coniferaldehyde, ferulic acid, sinapaldehyde, caffeic acid, and sinapyl alcohol (annual total content from high to low). These metabolites were mainly annotated to the synthesis of secondary metabolites and phenylpropane biosynthesis. The annual total content of the 10 metabolites showed the tendency of “decreasing, then increasing, and then decreasing”. Conclusions: C. bungei ‘Jinsi’ is a typical G/S-lignin tree species, and the synthesis of G-lignin occurs earlier than that of S-lignin. The total metabolite content decreased rapidly, and the lignin anabolism process was active from April to July; the metabolites were accumulated, and the lignin anabolism process slowed down from July to October; the total metabolite content remained basically unchanged, and lignin synthesis slowed down or stagnated from October to January of the following year. This reveals the annual dynamic pattern of lignin biosynthesis, which contributes to improving the wood quality and yield of C. bungei ‘Jinsi’ and provides a theoretical basis for its targeted breeding.

Catalpa bungei is one of important economic tree species for widespread cultivation in China, but little is known about the endophytic and rhizospheric bacteria especially how tree age affects their community diversity. The research assessed tree ages of 2, 4, 8, and 12 years, respectively, affect the community diversity of endophytic and rhizospheric bacteria in C. bungei using high-throughput 16S rRNA gene sequencing. Findings revealed that the diversity and abundance of rhizospheric bacteria were significantly higher than that of endophytic bacteria, and both endophytic and rhizospheric bacterial flora, especially the dominant bacteria, showed a certain degree of regular variations with the tree age increasing. The dominant endophytic and rhizospheric bacteria were Cyanobacteria and Proteobacteria, respectively, at a phylum level, which were Streptophyta, Acidobacterium or Flavobacterium at a genus level. Correspondingly, photophosphorylation was a dominant ecological function for the endophytic bacteria, while chemoheterotrophy and aerobic chemoheterotrophy were important ecological functions for the rhizospheric bacteria. This study highlights dynamic changes in the endophytic and rhizospheric bacterial communities of C. bungei and provides references for the follow-up development of agricultural inputs.

Machilus thunbergii Siebold & Zucc. is recognized as an excellent tree species for landscaping and shelter forest. Excessive drought can affect the changes of physiological and biochemical substances in plants. However, little is known at present regarding the drought stress of M. thunbergii seedlings. In this paper, matrix water content, the anatomical structure of leaves, relative water content of leaves, and physiological characteristics index of leaves under droughting stress were dynamically observed. Droughting stress led to the wilting of M. thunbergii leaves, gradual closure of stomata on leaf epidermis, increases in stomatal density, gradual loosening of leaf cell structure arrangement, a thickening in leaf palisade tissue, and reductions in spongy tissue. Droughting stress caused the relative water content of the cultivation substrate to decline, the cultivation substrate reached the moderate drought level, and the seedlings began to die. Droughting stress led to the destruction of activity and balance of the leaf protective enzyme system, excessive accumulation of free radicals, the destruction of enzyme structure and function, and the production of lipid peroxidation product MDA. Droughting stress reduced the relative water content of leaves as a whole, the content of osmotic adjustment substances proline and soluble protein continued to decline, and a large number of electrolyte leakage in cells, causing serious damage to seedlings.

Rosa rugosa Thunb., mainly distributed on the coast in China, has strong salt tolerance, making it a good material to study the salt tolerance mechanism of plants. This study showed that under 200 mM NaCl stress, the activities of superoxide dismutase (SOD) and peroxidase (POD), and soluble sugar content, as well as malondialdehyde (MDA) content in R. rugosa roots and leaves first increased and then decreased. The differentially expressed genes (DEGs) and differentially abundant metabolites (DAMs) enriched in the leaves were significantly more than those in the roots, and they played a dominant role in the response to salt stress. Combined metabolome and transcriptome analyses showed that starch and sucrose metabolism, tryptophan metabolism and purine metabolism played essential roles dealing with salt stress in root. The flavonoid biosynthesis pathway and glycerophospholipid metabolism pathway were significantly enriched in the leaves, which improved antioxidant ability. In addition, abscisic acid (ABA) accumulated in the leaves and roots and was the most important anti-salt hormone in R. rugosa. The study elucidated the molecular mechanism underlying the response of R. rugosa to salt stress and supplied breeding of salt-tolerant R. rugosa with theoretical support.

Quercus acutissima seeds exhibit high desiccation sensitivity, posing significant challenges for long-term preservation. This study investigates the physiological and metabolic responses of soluble osmoprotectants—particularly soluble proteins and proline—during the desiccation process. Seeds were sampled at three critical moisture content levels: 38.8%, 26.8%, and 14.8%, corresponding to approximately 99%, 52%, and 0% germination, respectively. We measured germination ability, soluble protein content, and proline accumulation, and we performed untargeted metabolomic profiling using LC-MS. Soluble protein levels increased early but declined later during desiccation, while proline levels continuously increased for sustained osmotic adjustment. Metabolomics analysis identified a total of 2802 metabolites, with phenylpropanoids and polyketides (31.12%) and lipids and lipid-like molecules (29.05%) being the most abundant. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that differentially expressed metabolites were mainly enriched in key pathways such as amino acid metabolism, energy metabolism, and nitrogen metabolism. Notably, most amino acids decreased in content, except for proline, which showed an increasing trend. Tricarboxylic acid cycle intermediates, especially citric acid and isocitric acid, showed significantly decreased levels, indicating energy metabolism imbalance due to uncoordinated consumption without effective replenishment. The reductions in key amino acids such as glutamic acid and aspartic acid further reflected metabolic network disruption. In summary, Q. acutissima seeds fail to establish an effective desiccation tolerance mechanism. The loss of soluble protein-based protection, limited capacity for proline-mediated osmotic regulation, and widespread metabolic disruption collectively lead to irreversible cellular damage. These findings highlight the inherent metabolic vulnerabilities of recalcitrant seeds and suggest potential preservation strategies, such as supplementing critical metabolites (e.g., TCA intermediates) during storage to delay metabolic collapse and mitigate desiccation-induced damage.

Paeonia suffruticosa Andr. (tree peony) and Paeonia lactiflora Pall. (herbaceous peony) are traditional Chinese flowers with great ornamental value. To maintain the aesthetic value and show the characteristics of these species, preserved flowers named ‘germplasm display balls’ were developed. Firstly, dried flowers were obtained by vacuum freeze-drying. Secondly, to embed dried flowers and develop germplasm display balls, highly transparent crystal glue (in wrapped display balls type 1 and drop-type display balls type 2) and highly transparent silicone gel (in wrapped display balls, type 3) were used. Finally, the first pass yield (FPY), labor productivity (LP), average cost (AC), and popularity of three kinds of germplasm display balls were compared. The results showed that with the support of a paper cup, the deformation rate of flowers significantly decreased by 91.11%. The FPY of dried flowers was as high as 98.89% at 18 °C. The optimal process for type 1 and type 2 was a glue dosage of 20 g, stirring time of 3 min, and room temperature of 25 °C. Although there was a higher AC in type 3 display ball process, moderate LP and higher FPY and popularity than in other two types, accompanied by high durability, render it the best choice.

Tilia amurensis, a deciduous broad-leaved tree, is distributed in regions neighboring those of Tilia japonica populations in China; these plants belong to the Malvaceae family. To date, the genetic status and demographic history of T. japonica remain unknown, and the demographic history of T. amurensis is not well defined. This study uses standard population genetic and approximate Bayesian computation (ABC) analyses of SSR data to determine the genetic status and divergence times of these two lime taxa. The results revealed that the genetic diversity of T. japonica (I = 1.181, HO = 0.484, HE = 0.602) was high at the population level. The results of the genetic structure revealed that the genetic variation was dominated primarily by within-population variation. Additionally, there was significant genetic differentiation and bidirectional introgression between T. amurensis and T. japonica. The ABC analysis suggests a (Middle) Pleistocene divergence. These findings have important implications for the formulation of appropriate conservation strategies. Specifically, the clarified divergence time and evidence of genetic exchange indicate that the two species should be protected based on their respective population conditions.

Saline-alkali stress significantly hinders plant growth and distribution. Paeonia rockii demonstrates remarkable tolerance to such conditions. This research aimed to uncover the molecular bases of saline-alkali stress tolerance in P. rockii through transcriptomic and metabolomic analyses. We observed several stress responses in P. rockii, including leaf curling, discoloration, enhanced osmoregulatory substance content, and increased antioxidant enzyme activity, particularly at a 300 mM stress concentration. The study identified 7,118 differentially expressed genes (DEGs) and 75 differentially accumulated metabolites (DAMs) post-stress exposure. Notably, KEGG pathway enrichment revealed glutathione metabolism as a pivotal mechanism in stress adaptation. Activation of genes such as gpx, GR, G6PD, E1.11.1.11, and GST enhances glutathione signaling, improving the plant's antioxidant capacity and overall stress tolerance. Additionally, the activation of the ODC1 gene family and the suppression of the speE gene family contribute to the accumulation of polyamine antistress factors, facilitating better adaptation. This research highlights the dual roles of glutathione and polyamine pathways in saline-alkali stress tolerance, presenting novel insights into P. rockii's adaptive strategies. These findings insight into the molecular mechanisms of P. rockii and offers a theoretical foundation for screening genes related to saline tolerance, thus expanding planting areas and breeding resistant varieties.

Flavonoids are key secondary metabolites involved in plant stress responses. As ultraviolet (UV) radiation intensity increases, plants experience heightened UV stress. To elucidate Ginkgo biloba's molecular adaptation to ultraviolet-B (UV-B) stress, we subjected G. biloba seedlings to daily UV-B irradiation at 10 kJ/m². The total flavonoid glycoside content in leaves increased significantly by Day 13 (2.64-fold compared to the CK), with quercetin accounting for over 90% of the accumulated flavonoids. Transcriptome analysis identified 3652 differentially expressed genes (DEGs), 209 lncRNAs (DElncRNAs), and 52 miRNAs (DEmiRNAs). Notably, UV-B radiation upregulated key genes involved in flavonoid biosynthesis, including the F3'H family gene evm. MODEL:chr2.812 and the MYB transcription factor (TF) evm. MODEL:chr11.568. Trans-regulation analysis suggested lncRNAs modulate target genes: MSTRG.5750.1 and MSTRG.13336.1 potentially enhance evm. MODEL:chr2.812 and evm. MODEL:chr11.568 expression, while UV-B-repressed MSTRG.845.1 and MSTRG.3390.1 indirectly upregulated them. A ceRNA network revealed nine regulatory pairs, though associated miRNAs (gbi-miR-nov634-3, gbi-miR-nov789-3p) exhibited low abundance, indicating minor roles in UV-B response. These findings provide insights into the transcriptional regulation of flavonoid biosynthesis in G. biloba under UV-B stress, advancing understanding of plant secondary metabolic adaptation.