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Salt stress is the main abiotic stress that limits crop yield and agricultural development. Therefore, it is imperative to study the effects of salt stress on plants and the mechanisms through which plants respond to salt stress. In this study, we used transcriptomics and metabolomics to explore the effects of salt stress on Sophora alopecuroides. We found that salt stress incurred significant gene expression and metabolite changes at 0, 4, 24, 48, and 72 h. The integrated transcriptomic and metabolomic analysis revealed that the differentially expressed genes (DEGs) and differential metabolites (DMs) obtained in the phenylpropanoid biosynthesis pathway were significantly correlated under salt stress. Of these, 28 DEGs and seven DMs were involved in lignin synthesis and 23 DEGs and seven DMs were involved in flavonoid synthesis. Under salt stress, the expression of genes and metabolites related to lignin and flavonoid synthesis changed significantly. Lignin and flavonoids may participate in the removal of reactive oxygen species (ROS) in the root tissue of S. alopecuroides and reduced the damage caused under salt stress. Our research provides new ideas and genetic resources to study the mechanism of plant responses to salt stress and further improve the salt tolerance of plants.

It was recently shown that the gut microbiota of both depression patients and depression model animals is significantly altered, suggesting that gut microbes are closely related to depression. Here, we investigated the effects of Sophora alopecuroides L.-derived alkaloids on the gut microbiota of mice with depression-like behaviors. We first established a mouse model of depression via chronic unpredictable mild stress (CUMS) and detected changes in depression-like behaviors and depression-related indicators. Simultaneously, 16S rRNA sequencing was performed to investigate gut microbiota changes. Sophora alopecuroides L.-derived alkaloids improved depression-like behaviors and depression-related indicators in mice. The alkaloids decreased the gut microbiota diversity of CUMS mice and depleted intestinal differentially abundant “harmful” microbiota genera. Spearman analysis showed that there is a certain correlation between the differential microbiota ( Lactobacillus , Helicobacter , Oscillospira , Odoribacter , Mucispirillum , Ruminococcus ), depression-like behaviors, and depression-related indicators. Combined with the predictive analysis of gut microbiota function, these results indicate that alkaloids improve depression in mice through modulating gut microbiota.

Sophora moorcroftiana, a Leguminosae shrub species that is restricted to the arid and semi-arid regions of the Qinghai-Tibet Plateau, is an ecologically important foundation species and exhibits substantial drought tolerance in the Plateau. There are no functional genomics resources in public databases for understanding the molecular mechanism underlying the drought tolerance of S. moorcroftiana. Therefore, we performed a large-scale transcriptome sequencing of this species under drought stress using the Illumina sequencing technology. A total of 62,348,602 clean reads were obtained. The assembly of the clean reads resulted in 146,943 transcripts, including 66,026 unigenes. In the assembled sequences, 1534 transcription factors were identified and classified into 23 different common families, and 9040 SSR loci, from di- to hexa-nucleotides, whose repeat number is greater than five, were presented. In addition, we performed a gene expression profiling analysis upon dehydration treatment. The results indicated significant differences in the gene expression profiles among the control, mild stress and severe stress. In total, 4687, 5648 and 5735 genes were identified from the comparison of mild versus control, severe versus control and severe versus mild stress, respectively. Based on the differentially expressed genes, a Gene Ontology annotation analysis indicated many dehydration-relevant categories, including 'response to water 'stimulus' and 'response to water deprivation'. Meanwhile, the Kyoto Encyclopedia of Genes and Genomes pathway analysis uncovered some important pathways, such as 'metabolic pathways' and 'plant hormone signal transduction'. In addition, the expression patterns of 25 putative genes that are involved in drought tolerance resulting from quantitative real-time PCR were consistent with their transcript abundance changes as identified by RNA-seq. The globally sequenced genes covered a considerable proportion of the S. moorcroftiana transcriptome, and the expression results may be useful to further extend the knowledge on the drought tolerance of this plant species that survives under Plateau conditions.

Background Sophora tonkinensis Gagnep. has long been utilized in the treatment of anti-inflammatory and pain-relieving, with its principal active compounds being alkaloids and flavonoids. NAC transcription factors, a large family of plant-specific regulators, play pivotal roles in growth, development, stress responses, and secondary metabolism. However, comprehensive genome-wide characterization of S. tonkinensis NAC gene family ( StNAC ) remains unexplored. Results This study identified 85 NAC proteins from the S. tonkinensis genome database. Phylogenetic analysis revealed that StNAC proteins were categorized into 15 subgroups based on their homology with Arabidopsis thaliana NAC proteins. Gene structure analysis demonstrated a variation in intron numbers ranging from 1 to 7, with a majority of StNAC genes containing 2–3 introns. Chromosomal distribution analysis indicated an uneven spread of StNAC genes across 9 chromosomes, with the highest number of StNAC genes on Chr3. Detection of 4 tandem duplicates and 32 segmental duplicates revealed that segmental duplication primarily drive StNAC genes amplification. Prediction of cis-regulatory elements suggested the involvement of StNAC genes in growth, stress responses, and hormone regulation. Gene expression analysis showed substantial variability expression of StNAC genes across different tissues. Notably, eight StNAC genes were identified as significantly associated alkaloid and flavonoid levels. qRT-PCR validation indicated that five genes were highly expressed in tissues, corroborating transcriptome data. Conclusion These findings offer valuable insights for further functional characterization of NAC genes and their potential roles in alkaloid and flavonoid biosynthesis in S. tonkinensis .

We used fresh leaves of Sophora japonica L. variety ‘Qingyun 1’ (A0) and 10 superior clones of the same species (A1–A10) to explore leaf morphological characteristics and total particle retention per unit leaf area under natural and artificial simulated dust deposition treatments. Our objectives were to explore the relationship between the two methods and to assess particle size distribution, X-ray fluorescence (XRF) heavy metal content, and scanning electron and atomic force microscopy (SEM and AFM) characteristics of leaf surface microstructure. Using the membership function method, we evaluated the dust retention capacity of each clone based on the mean degree of membership of its dust retention index. Using correlation analysis, we selected leaf morphological and SEM and AFM indices related significantly to dust retention capacity. Sophora japonica showed excellent overall dust retention capacity, although this capacity differed among clones. A5 had the strongest overall retention capacity, A2 had the strongest retention capacity for PM 2.5 , A9 had the strongest retention capacity for PM 2.5–10 , A0 had the strongest retention capacity for PM >10 , and A2 had the strongest specific surface area (SSA) and heavy metal adsorption capacity. Overall, A1 had the strongest comprehensive dust retention ability, A5 was intermediate, and A7 had the weakest capacity. Certain leaf morphological and SEM and AFM characteristic indices correlated significantly with the dust retention capacity.

Background Sophora moorcroftiana , a key stone shrub in Xizang (Tibet), has significant ecological and economic value. However, its populations face severe degradation. Understanding key evolutionary drivers of genetic variation within and among populations is critical for conserving and managing this species. Previous studies indicate a strong genetic structure correlated with altitude, but limited knowledge exists about the drivers of its geographic structure and evolutionary history. To address this, we conducted genomic research on 225 samples from 15 populations of S. moorcroftiana . Results Populations of S. moorcroftiana exhibited distinct population structure, divided into four subpopulations. Subpopulation P1 (Gongbu Jiangda County, Nyingchi) showed the greatest genetic differentiation from other populations (average F st = 0.2477), with the lowest genetic diversity ( Pi  = 1.1 × 10 −4 ) and the smallest effective population size. P2, in the lower altitude area (Nyingchi), had larger genetic differentiation from the mid–altitude P3 ( F st = 0.168) and the high–altitude P4 ( F st = 0.227), with lower genetic diversity and effective population size. P3 and P4 had smaller genetic differentiation, with P3 having the largest genetic diversity and effective population size, followed by P4. D –statistics and Treemix revealed predominant gene flow from lower to higher altitude populations, with geographic proximity enhancing genetic sharing. SMC + + analyses suggested that the subpopulations experienced severe bottlenecks, genetic drift, and population expansion due to glacial–interglacial cycles and geological events. Partial Mantel tests revealed that the genetic variation distribution of S. moorcroftiana populations was more influenced by geographic isolation. Through genotype–environment association analysis, 90 single nucleotide polymorphisms (SNPs) were found to be significantly associated with environmental factors, of which 55 SNPs were annotated to genes, involving 20 genes. Conclusions The uplift of the plateau and intense climatic fluctuations during the Quaternary have profoundly impacted the genetic structure and geographic distribution of species in the region. The current genetic distribution characteristics were shaped by the subsequent influences of geography, environment, and gene flow. These findings provide a theoretical basis for the utilization of genetic resources, the formulation and implementation of conservation strategies for S. moorcroftiana , and the exploration of its adaptation mechanisms to the plateau environment.

Background Salinity, alkalinity, and drought stress are the main abiotic stress factors affecting plant growth and development. Sophora alopecuroides L., a perennial leguminous herb in the genus Sophora , is a highly salt-tolerant sand-fixing pioneer species distributed mostly in Western Asia and northwestern China. Few studies have assessed responses to abiotic stress in S. alopecuroides . The transcriptome of the genes that confer stress-tolerance in this species has not previously been sequenced. Our objective was to sequence and analyze this transcriptome. Results Twelve cDNA libraries were constructed in triplicate from mRNA obtained from Sophora alopecuroides for the control and salt, alkali, and drought treatments. Using de novo assembly, 902,812 assembled unigenes were generated, with an average length of 294 bp. Based on similarity searches, 545,615 (60.43%) had at least one significant match in the Nr, Nt, Pfam, KOG/COG, Swiss-Prot, and GO databases. In addition, 1673 differentially expressed genes (DEGs) were obtained from the salt treatment, 8142 from the alkali treatment, and 17,479 from the drought treatment. A total of 11,936 transcription factor genes from 82 transcription factor families were functionally annotated under salt, alkali, and drought stress, these include MYB , bZIP , NAC and WRKY family members. DEGs were involved in the hormone signal transduction pathway, biosynthesis of secondary metabolites and antioxidant enzymes; this suggests that these pathways or processes may be involved in tolerance towards salt, alkali, and drought stress in S. alopecuroides . Conclusion Our study first reported transcriptome reference sequence data in Sophora alopecuroides, a non-model plant without a reference genome. We determined digital expression profile and discovered a broad survey of unigenes associated with salt, alkali, and drought stress which provide genomic resources available for Sophora alopecuroides .

Sophora japonica is an important native tree species in northern China, with high ornamental, medicinal, and ecological value. In order to elucidate the genetic resources of ancient S. japonica, 16 simple sequence repeat (SSR) markers were used to evaluate its genetic diversity and population structure and build a core collection of 416 germplasms from the Shandong, Shanxi, and Hebei provinces. A total of 160 alleles were detected, the mean major allele frequency (MAF)was 0.39, and the mean effective number of alleles (Ne) was 4.08. Shannon’s information index (I), the observed heterozygosity (Ho), the expected heterozygosity (He), and the polymorphism information content (PIC) were 1.58, 0.64, 0.74, and 0.70, respectively, indicating relatively high genetic diversity in ancient S. japonica germplasms. Low genetic differentiation coefficient (Fst = 0.04) and frequent gene flow (Nm = 9.74) were found in the tested S. japonica populations, and an analysis of molecular variance (AMOVA) indicated that the genetic variation mainly came from within individuals (84%). A genetic structure and cluster analysis indicated that 416 ancient S. japonica germplasms could be divided into five subgroups, and there were obvious genetic exchanges among different subgroups. A core collection consisting of 104 (25% of the original collection) germplasms was constructed using the R language package Genetic Subsetter version 0.8 based on the stepwise regression method. The retention rates of the number of alleles (Na), Ne, I, He, and PIC were 87.50%, 106.24%, 103.02%, 102.50%, and 102.74%, respectively. The t-test analysis suggested that there were no significant differences between the core collection and the original collection. The principal coordinate analysis (PCoA) showed that the core collection was uniformly distributed within the initial collection and was able to fully represent the genetic diversity of the original collection. These results provide a scientific basis for the conservation and utilization of ancient S. japonica germplasms.

Background Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood. Results To identify genes and miRNAs involved in drought stress responses in S. tonkinensis , both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. A total of 10 and 30 transcription factors (TFs) were identified among the DEGs under mild and severe drought stress, respectively. Moreover, small RNA sequencing revealed a total of 368 miRNAs, including 255 known miRNAs and 113 novel miRNAs. The differentially expressed miRNAs and their target genes were involved in the regulation of plant hormone signal transduction, the spliceosome, and ribosomes. Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs. Conclusion This is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis . Our results suggest that S. tonkinensis implements diverse mechanisms to modulate its responses to drought stress.

A dereplication strategy was developed for the screening of secondary metabolites from Sophora flavescens . The strategy consisted of 4 procedures. First, the extract of the Sophora flavescens root was subjected to LC–MS/MS analysis with both data-independent acquisition (DIA) mode and data-dependent acquisition (DDA) mode. Then the DIA results were used to construct a molecular networking (MN) according to the GNPS workflow and consequently obtain annotations. In parallel, the DDA results were projected to both MN analysis and direct databases matching to obtain annotations. Finally, the isomers were discriminated and annotated by their extracted ion chromatogram. Through the combination of these approaches, a total of 51 compounds were annotated and dereplicated in the Sophora flavescens samples. The annotation results showed DIA and DDA approach are complementary to each other. MN on GNPS can overcome the challenges of trace compound identification compared to direct DB matching. This strategy provides a powerful tool for the dereplication study in plant chemistry.