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Understanding how plants respond to water limitation is increasingly important under accelerating climate change. Lycoris aurea, a widely distributed ornamental and medicinal bulbous plant, frequently inhabits environments with fluctuating soil moisture, yet its molecular drought-response mechanisms remain largely unexplored. In this study, we investigated L. aurea growing under field-based, in situ soil moisture regimes, comparing low (~20% soil water content) and high (~40% soil water content) conditions. We combined soil property assessments with high-resolution transcriptomic and untargeted metabolomic profiling to characterize the adaptive responses of bulb tissues under contrasting soil water conditions. Although total nitrogen, phosphorus, and potassium levels were comparable across treatments, soil moisture, representing the primary contrasting field condition, and soil pH, a correlated environmental factor, were significantly associated with variation in gene expression and metabolite accumulation (p < 0.05, n = 3). Transcriptome analyses identified a total of 1034 differentially expressed genes enriched in pathways related to amino acid metabolism, cuticle formation, cell wall modification, and osmotic adjustment. Metabolomic analysis identified a total of 1867 differentially expressed metabolites belonging to carboxylic acids and prenol lipids, showing alterations involved in amino acids, lipids, phenolic acids, and alkaloids associated with osmoprotection, membrane stabilization, and structural reinforcement under low soil moisture. Pathway-based integration analysis highlighted four core pathways, including “alanine, aspartate and glutamate metabolism” (p = 0.00371) and “cutin, suberine and wax biosynthesis” (p = 0.00873), as central hubs linking transcriptional regulation with metabolic reconfiguration. Gene-metabolite-soil correlation networks further demonstrated that drought adaptation arises from tightly coordinated biochemical and structural adjustments rather than shifts in nutrient acquisition. Together, this species-specific study provides a comprehensive multi-omics framework for understanding drought tolerance in L. aurea, reveals key molecular targets associated with plant resilience, and offers potential targets and insights for the conservation of drought-resilient Lycoris cultivars.

Background The complex physical structure and abundant repeat sequences make it difficult to assemble the mitogenomes of seed plants, especially gymnosperms. Only approximately 33 mitogenomes of gymnosperms have been reported. However, as the most widely distributed and the second largest family among gymnosperms, Cupressaceae has only six assembled mitogenomes, including five draft mitogenomes and one complete mitogenome, which has greatly hindered the understanding of mitogenome evolution within this large family, even gymnosperms. Results In this study, we assembled and validated the complete mitogenome of Thuja sutchuenensis , with a size of 2.4 Mb. Multiple sequence units constituted its complex structure, which can be reduced to three linear contigs and one small circular contig. The analysis of repeat sequences indicated that the numbers of simple sequence repeats increased during the evolutionary history of gymnosperms, and the mitogenome of Thuja sutchuenensis harboured abundant extra-long repeats (more than 5 kb). Additionally, the longest repeat sequence identified in these seven gymnosperms also came from the mitogenome of Thuja sutchuenensis , with a length of up to 47 kb. The analysis of colinear blocks and gene clusters both revealed that the orders of mitochondrial genes within gymnosperms was not conserved. The comparative analysis showed that only four tRNAs were shared by seven gymnosperms, namely, trnD-GUC, trnE-UUC, trnI-CAU and trnY-GUA . Furthermore, four genes have undergone potential positive selection in most gymnosperm species, namely, atp8 , ccmB , mttB and sdh4 . Conclusion We successfully assembled the second complete mitogenome within Cupressaceae and verified that it consisted of multiple sequence units. Our study also indicated that abundant long repeats may contribute to the generation of the complex conformation of the mitogenome of Thuja sutchuenensis . The investigation of Thuja sutchuenensis ’s mitogenome in our study provides new insight into further understanding the complex mitogenome architecture within gymnosperms.

Background The cactus family (Cactaceae) has been reported to have evolved a minimal photosynthetic plastome size, with the loss of inverted-repeat (IR) regions and NDH gene suites. However, there are very limited genomic data on the family, especially Cereoideae, the largest subfamily of cacti. Results In the present study, we assembled and annotated 35 plastomes, 33 of which were representatives of Cereoideae, alongside 2 previously published plastomes. We analyzed the organelle genomes of 35 genera in the subfamily. These plastomes have variations rarely observed in those of other angiosperms, including size differences (with ~ 30 kb between the shortest and longest), dramatic dynamic changes in IR boundaries, frequent plastome inversions, and rearrangements. These results suggested that cacti have the most complex plastome evolution among angiosperms. Conclusion These results provide unique insight into the dynamic evolutionary history of Cereoideae plastomes and refine current knowledge of the relationships within the subfamily.

Background As one of the largest families of transcription factors (TFs), the WRKY gene family plays a significant role in plant growth, development, and response to hormone and environmental stress. Currently, there is no systematic analysis of the WRKY gene family in Artocarpus nanchuanensis . Results To explore its evolutionary mechanism and potential function, we performed a comprehensive analysis. A total of 113 AnWRKYs were identified, and 109 were mapped onto 28 chromosomes. These genes could be classified into 3 groups (Group I, Group IIa-IIe, Group III) based on phylogenetic analysis and the sequence characteristics of the AnWRKY domain. Syntenic analyses revealed 4 pairs of tandem repeats and 123 pairs of large fragment repeats. Furthermore, the expression profiles of AnWRKYs in roots, stems, and leaves showed that AnWRKYs had different spatial expression patterns. AnWRKY2 , AnWRKY14 , AnWRKY46 , AnWRKY55 , and AnWRKY105 may play important roles in the response to abiotic stress. In addition, subcellular localization analysis indicated that AnWRKY55 was localized in the nucleus. Conclusions This study is the first to report the identification and characterization of AnWRKYs in A. nanchuanensis and provides an important basis for future comprehensive evolutionary and functional analyses of AnWRKYs in A. nanchuanensis .

Salix variegata , a typical dioecious plant with high reproductive and adaptive ability, has important ecological and ornamental value. To understand the potential mechanisms and metabolite dynamics of male and female flowers development, the first comparative analysis of the transcriptome and metabolome of S. variegata was applied. As a result, 12,245 differentially expressed genes (DEGs) and 4,145 differently expressed metabolites (DEMs) were identified. Transcriptomic analysis showed that the male and female flowers development processes were related to phenylpropanoid and flavonoid biosynthesis. According to the metabolic profile, the main amino acids, flavonoids, phenylpropanoids, and their derivatives were accumulated during the development of male and female flowers of the S. variegata . Combined transcriptomic and metabolomic analyses indicated that the AUX/IAA , bHLH , MIKC , MYB , NAC , ERF and RLK transcription factors (TFs) and their associated key DEGs may mediate the metabolism of phenylpropanoids and flavonoids, which in turn regulate the development of male and female flowers in S. variegata . These results provide important insights to elucidate the development of male and female flowers of S. variegata at the molecular level. Our results will contribute to understanding the molecular and genetic mechanisms of male and female flower development in typical dioecious plants.

Atopic dermatitis (AD) is a chronic inflammatory skin disorder characterized by dysregulated immunity, skin barrier dysfunction, and cutaneous microbiome dysbiosis. While current therapies face limitations, Thuja sutchuenensis essential oil (TEO) shows promise due to its multi-target potential. We sought to explore the beneficial effects of TEO and delve into its mechanistic actions in a mouse model of AD. We combined network pharmacology with in vivo validation to evaluate the therapeutic efficacy and mechanisms of TEO in an AD model, and confirmed network-predicted targets in an in vitro inflammatory cell model. In AD mice, TEO alleviated pruritus and epidermal hyperplasia, suppressed systemic IL-4/TNF-α and IgE, and partially normalized serum ALB, LDL-C, and HDL-C. Microbial diversity increased after treatment, although potentially pathogenic taxa (Arthrobacter sp. and Corynebacterium mastitidis) remained enriched. Machine-learning analysis indicated the highest predicted metabolic activity in CK controls, whereas the AD and TEO groups showed elevated pathogenic phenotype scores. Network pharmacology prioritized active compounds [(E)-ligustilide, senkyunolide A, 3-butylisobenzofuran-1(3H)-one, butylated hydroxytoluene, Z-buthlidenephthalide, and β-Myrcene] and core targets (TNF, PTPRC, CCR5, JAK1), implicating T-cell receptor signaling, Staphylococcus aureus infection, and STAT3 pathways. Docking and molecular dynamics supported strong, stable binding of major constituents to JAK1, and Western blotting confirmed TEO-mediated inhibition of the JAK1/STAT3 axis. TEO effectively alleviates atopic dermatitis symptoms by modulating immune responses and enhancing microbial diversity. It targets key signaling pathways, such as JAK1/STAT3, highlighting its potential as a therapeutic option for AD.

Species of section are predominantly distributed in alpine environments above 2,000 meters and represent an important group for studying environmental adaptation and phylogenetic evolution. , holds important ecological, ornamental, and conservation value. However, genomic resources for this species remain unavailable, hindering further research on its genetic evolution and conservation strategies. In this study, we sequenced and assembled the complete mitochondrial and chloroplast genomes of for the first time. Comprehensive analyses were conducted on their structural characteristics, repetitive sequences, RNA editing site prediction, codon usage bias, intracellular gene transfer, phylogenetic inference, and selective pressure. The results show that both the mitochondrial and chloroplast genomes exhibit typical master circular structures, with sizes of 340,219 bp and 150,733 bp, respectively. The mitochondrial genome has more abundant repetitive sequences and has undergone genomic rearrangements. There are only 9 MTPTs between mitochondria and chloroplasts, totaling 2,028 bp. In the regulation of mitochondrial genome expression, we predicted 475 RNA editing sites, with and showing the highest potential editing frequencies. We found that exhibits similar codon usage bias to most plants, and based on ENC-GC3s analysis, some genes appear to be under natural selection. Chloroplast genes , , , and exhibit branch-specific positive selection in Primula, reflecting adaptive evolution of photosynthesis and protein synthesis functions in high-altitude environments. Based on phylogenetic trees constructed from PCGs, Primulaceae are most closely related to Ebenaceae. Furthermore, phylogenetic analysis based on chloroplast genomes and PCGs of species showed that sect. is not monophyletic, with being a sister species to . These findings provide crucial genomic resources and insights into the adaptive evolution of , while also clarifying phylogenetic relationships within sect. and Primulaceae, thereby offering valuable guidance for conservation strategies and further evolutionary studies.

The purpose of this study was to evaluate the antibacterial activity and mechanism of linalool against Methicillin-resistant (MRSA). The determination of the antibacterial activity of linalool against clinically isolated MRSA strains was based on the minimum inhibitory concentration (MIC) and growth curve analysis. Finally, the inhibition mechanism of linalool was elucidated through metabolomic analysis and molecular docking. Among the isolated strains, penicillin resistance was found to be the highest, while resistance to daptomycin/quinupristin-dalfopristin, linezolid, vancomycin, tetracycline, telithromycin, and levofloxacin was not observed. The MIC range of linalool was 211.24-1.65 μg/mL, with MIC and MIC values of 13.2 μg/mL and 105.62 μg/mL, respectively. Metabolomic analysis revealed that linalool interferes with various substance metabolisms and energy metabolism in MRSA, with the glutathione pathway potentially being a key pathway affected by linalool. Molecular docking revealed that linalool exhibited good binding potential to the target glutathione. This study suggests that linalool could be developed as a drug or preservative to inhibit MRSA growth.

Whole-genome resequencing technology covers almost all nucleotide variations in the genome, which makes it possible to carry out conservation genomics research on endangered species at the whole-genome level. In this study, based on the whole-genome resequencing data of 101 critically endangered individuals, we evaluated the genetic diversity and population structure, inferred the demographic history and genetic load, predicted the potential distributions in the past, present and future, and classified conservation units to propose targeted suggestions for the conservation of this critically endangered species. Whole-genome resequencing for generated approximately 2 Tb of data. Based on abundant mutation sites (25,312,571 single nucleotide polymorphisms sites), we revealed that the average genetic diversity (nucleotide diversity, π) of different populations of was relatively low compared with other trees that have been studied. And we also revealed that the NHZ and QJT populations harboured unique genetic backgrounds and were significantly separated from the other five populations. In addition, positive genetic selective signals, significantly enriched in biological processes related to terpene synthesis, were identified in the NHZ population. The analysis of demographic history of revealed the existence of three genetic bottleneck events. Moreover, abundant genetic loads (48.56% protein-coding genes) were identified in , especially in genes related to early development and immune function of plants. The predication analysis of suitable habitat areas indicated that the past suitable habitat areas shifted from the north to the south due to global temperature decline. However, in the future, the actual distribution area of will still maintain high suitability. Based on total analyses, we divided the populations of into four conservation units and proposed a number of practical management suggestions for each conservation unit. Overall, our study provides meaningful guidance for the protection of and important insight into conservation genomics research.

As a hot issue, the precipitation characteristics of the Three Gorges Reservoir (TGR) area drew widespread interest from domestic and overseas academic circles. Based on China's surface-based meteorological monthly precipitation data from 1961 to 2016 in the TGR area, the spatial, inter-annual and inter-decadal, and multi-time-scale changes of precipitation in the TGR area are analyzed by using Collaborative Kriging (Co-Kriging, CK) Interpolation, linear regression analysis, Morlet wavelet analysis and 5-year sliding average processing, which provide the reference basis for further discussion on the impact of climate change, flood control and drought relief work in the reservoir area. Research shows that in the past 56 years, the average annual precipitation in most areas of the TGR ranges from 1,000 to 1,200 mm; the variation of precipitation in the TGR area shows a weak decreasing trend, with great fluctuation between year and generation, and the precipitation in each decade has a ‘less-more-less’ changing trend; the annual precipitation in the TGR area has periodic changes on multi-time scales, mainly including 25, 16 and 8 years. The smaller the scale the shorter the average period of precipitation change.