Transcriptome and metabolome analysis of the developmental changes in Cynanchum thesioides anther.

Cynanchum thesioides, a xerophytic species utilized both as a medicinal herb and a food source, plays a significant role in arid and desert ecosystem management. Its inflorescence is an umbellate cyme, each carrying nearly a thousand flowers; however, its fruiting rate remains remarkably low. The normal development of the anther is a necessary prerequisite for plants to produce seeds. However, our understanding of the anther development process in Cynanchum thesioides remains limited. To better understand the pollen development process in Cynanchum thesioides, the stages of pollen development were determined through paraffin sectioning, and observations were made on the distribution characteristics of polysaccharides and lipid droplets in the pollen development of Cynanchum thesioides using Periodic Acid-Schiff stain (PAS) and 0.5% Sudan Black B tissue staining. Concurrently, the gene expression patterns and metabolite profiles were delineated across various developmental stages of Cynanchum thesioides anthers (T1: microspore stage, T2: tetrad stage, T3: mononuclear stage, and T4: maturation stage). The findings revealed that Cynanchum thesioides pollen is in an aggregate form. Polysaccharides gradually accumulate during maturation and lipid droplets form a surrounding membrane, thereby preventing pollen dispersion. Furthermore, transcriptomic and metabolomic analyses across distinct developmental phases uncovered a plethora of differentially expressed genes and metabolites associated with the flavonoid biosynthesis pathway. Flavonoid levels exhibited dynamic changes concurrent with anther development, aligning with the gene regulatory patterns of the corresponding biosynthetic pathways. The study identified 63 differentially accumulated flavonoid compounds and 21 differentially expressed genes associated with flavonoid biosynthesis. Weighted gene co-expression network analysis revealed six MYB and ten bHLH transcription factors as key candidates involved in flavonoid biosynthesis, with CtbHLH (Cluster-6587.1050) and CtMYB (Cluster-6587.31743) specifically regulating structural genes within the pathway. These findings underscore the pivotal role of flavonoid biosynthesis in anther development of Cynanchum thesioides. In conclusion, this research offers a comprehensive insight into the anther development process in Cynanchum thesioides.

Fosfenopril Attenuates Inflammatory Response in Diabetic Dry Eye Models by Inhibiting the TLR4/NF-κB/NLRP3 Signaling Pathway.

Purpose: The purpose of this study was to investigate the involvement of the TLR4/NF-κB/NLRP3 signaling pathway and its underlying mechanism in diabetic dry eye. Methods: Two models of diabetic dry eye were established in high glucose-induced human corneal epithelial (HCE-T) cells and streptozotocin (STZ)-induced C57BL/6 mice, and the TLR4 inhibitor fosfenopril (FOS) was utilized to suppress the TLR4/NF-κB/NLRP3 signaling pathway. The expression changes in TLR4, NF-κB, NLRP3, and IL-1ß, and other factors were detected by Western blot and RT‒qPCR, the wound healing rate was evaluated by cell scratch assay, and the symptoms of diabetic mice were evaluated by corneal sodium fluorescein staining and tear secretion assay. Results: In the diabetic dry eye model, the transcript levels of TLR4, NF-κB, NLRP3, and IL-1ß were raised, and further application of FOS, a TLR4 inhibitor, downregulated the levels of these pathway factors. In addition, FOS was found to be effective in increasing the wound healing rate of high glucose-induced HCE-T cells, increasing tear production, and decreasing corneal fluorescence staining scores in diabetic mice, as measured by cell scratch assay, corneal sodium fluorescein staining assay, and tear production. Conclusions: The current study found that the TLR4/NF-κB/NLRP3 signaling pathway regulates diabetic dry eye in an in vitro and in vivo model, and that FOS reduces the signs of dry eye in diabetic mice, providing a new treatment option for diabetic dry eye.

Temperature-dependent jumonji demethylase modulates flowering time by targeting H3K36me2/3 in Brassica rapa.

Global warming has a severe impact on the flowering time and yield of crops. Histone modifications have been well-documented for their roles in enabling plant plasticity in ambient temperature. However, the factor modulating histone modifications and their involvement in habitat adaptation have remained elusive. In this study, through genome-wide pattern analysis and quantitative-trait-locus (QTL) mapping, we reveal that BrJMJ18 is a candidate gene for a QTL regulating thermotolerance in thermotolerant B. rapa subsp. chinensis var. parachinensis (or Caixin, abbreviated to Par). BrJMJ18 encodes an H3K36me2/3 Jumonji demethylase that remodels H3K36 methylation across the genome. We demonstrate that the BrJMJ18 allele from Par (BrJMJ18Par) influences flowering time and plant growth in a temperature-dependent manner via characterizing overexpression and CRISPR/Cas9 mutant plants. We further show that overexpression of BrJMJ18Par can modulate the expression of BrFLC3, one of the five BrFLC orthologs. Furthermore, ChIP-seq and transcriptome data reveal that BrJMJ18Par can regulate chlorophyll biosynthesis under high temperatures. We also demonstrate that three amino acid mutations may account for function differences in BrJMJ18 between subspecies. Based on these findings, we propose a working model in which an H3K36me2/3 demethylase, while not affecting agronomic traits under normal conditions, can enhance resilience under heat stress in Brassica rapa.

Oridonin ameliorates ocular surface inflammatory responses by inhibiting the NLRP3/caspase-1/GSDMD pyroptosis pathway in dry eye.

Chronic inflammation is one of the central drivers in the development of dry eye disease (DED), in which pyroptosis induced by the NLRP3/caspase-1/gasdermin D (GSDMD) pathway plays a key role. This pathway has become a major target for the treatment of a variety of inflammatory disorders. Oridonin (Ori) is a naturally occurring substance with anti-inflammatory properties obtained from Rabdosia rubescens. Whether Ori can exert an anti-inflammatory effect on DED, and its anti-inflammatory mechanism of action, are still unknown. This experiment is intended to investigate the impact of Ori on the hyperosmolarity-induced NLRP3/caspase-1/GSDMD pyroptosis pathway in immortalized human corneal epithelial (HCE-T) cells, as well as its efficacy and mechanism of action on ocular surface injury in DED mice. Our study showed that Ori could inhibit hyperosmotic-induced pyroptosis through the NLRP3/caspase-1/GSDMD pathway in HCE-T cells, and similarly, Ori inhibited the expression of this pathway in DED mice. Moreover, Ori was protective against hyperosmolarity-induced HCE-T cell damage. In addition, we found that the morphology and number of HCE-T cells were altered under culture conditions of various osmolarities. With increasing osmolarity, the proliferation, migration, and healing ability of HCE-T cells decreased significantly, and the expression of N-GSDMD was elevated. In a mouse model of DED, Ori application inhibited the expression of the NLRP3/caspase-1/GSDMD pyroptosis pathway, improved DED signs and injury, decreased corneal sodium fluorescein staining scores, and increased tear volume. Thus, our study suggests that Ori has potential applications for the treatment of DED, provides potential novel therapeutic approaches to treat DED, and provides a theoretical foundation for treating DED using Ori.

Bismuth-Containing Quadruple Therapy for Helicobacter pylori Eradication: A Randomized Clinical Trial of 10 and 14 Days.

BACKGROUND: Bismuth-containing quadruple therapy is the first-line treatment for eradicating Helicobacter pylori (H. pylori). The optimal duration for H. pylori eradication using bismuth-containing quadruple therapy remains controversial. Therefore, we aimed to compare the clinical effects of the 10- and 14-day bismuth-containing quadruple treatment regimen to eradicate H. pylori. METHODS: Treatment-naïve patients with H. pylori infection (n = 1300) were enrolled in this multicenter randomized controlled study across five hospitals in China. They were randomized into 10- or 14-day treatment groups to receive bismuth-containing quadruple therapy as follows: vonoprazan 20 mg twice daily; bismuth 220 mg twice daily; amoxicillin 1000 mg twice daily; and either clarithromycin 500 mg twice daily or tetracycline 500 mg four times daily. At least 6 weeks after treatment, we performed a 13C-urea breath test to evaluate H. pylori eradication. RESULTS: The per-protocol eradication rates were 93.22% (564/605) and 93.74% (569/607) (p < 0.001) and the intention-to-treat eradication rates were 88.62% (576/650) and 89.38% (581/650) (p = 0.007) for the 10- and 14-day regimens, respectively. Incidence of adverse effects was lower in patients who received 10- vs. 14 days of treatment (22.59% vs. 28.50%, p = 0.016). We observed no significant differences in the compliance to treatment or the discontinuation of therapy because of severe adverse effects between the groups. CONCLUSION: Compared with the 14-day bismuth-containing quadruple regimens, the 10-day regimen demonstrated a non-inferior efficacy and lower incidence of adverse effects. Therefore, the 10-day regimen is safe and tolerated and could be recommended for H. pylori eradication (NCT05049902).

Diagnostic Significance of Ultrasound-Guided Fine-Needle Aspiration Biopsy and on-Site Assessment by Pathologists for Thyroid Micronodules.

Objective: Ultrasound-guided fine-needle aspiration biopsy (US-FNAB) is a safe and effective method for screening malignant thyroid nodules. The purpose of this study was to compare the diagnostic effectiveness of US-FNAB for nodules of different sizes. Methods: A total of 1085 patients with thyroid nodules who underwent US-FNAB between January 2021 and July 2023 were included in the study. The patients were divided into three groups based on the maximum diameter of the nodules: there were 324 patients with thyroid nodules ≤5 mm in Group A, 537 patients with thyroid nodules between 6 mm and 10 mm in Group B, and 224 patients with thyroid nodules >10 mm in Group C. The US-FNAB satisfactory specimen rate, biopsy time and cytopathological results for the three groups were collected and compared with the postoperative pathological results. Results: The US-FNAB satisfactory specimen rates for Groups A, B and C were 84.57% (274/324), 90.13% (484/537) and 94.64% (212/224), respectively. The average biopsy times for Groups A, B, and C were 100.84 ± 41.58 s, 91.20 ± 32.53 s, and 79.01 ± 29.62 s, respectively. In Groups A, B, and C, 103, 192 and 73 patients, respectively, underwent surgery, and the malignancy rates were 88.35%, 85.42% and 72.6%, respectively. The sensitivity, specificity, positive predictive value, and negative predictive value of US-FNAB in Group A were 78.26%, 81.82%, 97.30%, 31.03%; respectively; those in Group B were 73.78%,85.71%,96.80%, and 35.82%, respectively; and those in Group C were 75.47%, 85.00%, 93.02% and 56.67%, respectively. Conclusion: The US-FNAB satisfactory specimen rate for thyroid nodules ≤5 mm was relatively low, but the size of nodules had no effect on the diagnostic sensitivity of US-FNAB; additionally, nodules ≤5 mm had a higher probability of malignancy. Therefore, it is necessary to perform US-FNAB for thyroid nodules with a diameter ≤5 mm with malignant signs.

Case Report: A combination of chimeric CYP11B2/CYP11B1 and a novel p.Val68Gly CYP11B1 variant causing 11ß-Hydroxylase deficiency in a Chinese patient.

Introduction: 11ß-Hydroxylase deficiency (11ß-OHD, OMIM#202010) is the second most common form of congenital adrenal hyperplasia (CAH) caused by pathogenic variants in the CYP11B1 gene. Both single nucleotide variations (SNV)/small insertion and deletion and genomic rearrangements of CYP11B1 are important causes of 11ß-OHD. Among these variant types, pathogenic CYP11B2/CYP11B1 chimeras only contribute to a minority of cases. Heterozygote cases (chimera combined with SNV) are very rare, and genetic analysis of these cases can be challenging. Case presentation: We presented a suspected 11ß-OHD female patient with incomplete virilization, adrenal hyperplasia, and hypokalemia hypertension. Whole exome sequencing (WES) revealed that the patient carried both a chimeric CYP11B2/CYP11B1 and a novel missense variant, NM_000497.4: c.203T>G, p.Val68Gly (chr8:143961027) in CYP11B1, which were confirmed by CNVplex and Sanger sequencing, respectively. The patient's manifestations and genetic findings confirmed the diagnosis of 11ß-OHD, and oral dexamethasone was administered as a subsequent treatment. Conclusion: This report showed a rare CYP11B2/CYP11B1 chimera combined with a novel missense variant in a 11ß-OHD female patient. The result expands variant spectrum of CYP11B1 and suggests that both chimera and CYP11B1 variant screening should be performed simultaneously in suspected cases of 11ß-OHD. To our knowledge, this is the first report about CYP11B2/CYP11B1 chimera detected by WES analysis. WES combined with CNV analysis is an efficient method in the genetic diagnosis of this rare and complex disorder.

Promoter variations in a homeobox gene, BrLMI1, contribute to leaf lobe formation in Brassica rapa ssp. chinensis Makino.

Key message BrLMI1 is a positive regulatory factor of leaf lobe formation in non-heading Chinese cabbage, and cis-regulatory variations lead to the phenotype of lobed or entire leaf margins.Abstract Leaves are the main consumed organ in leafy non-heading Chinese cabbage (Brassica rapa L. ssp. chinensis Makino), and the shape of the leaves is an important economic trait. However, the molecular regulatory mechanism underlying the lobed-leaf trait in non-heading Chinese cabbage remains unclear. Here, we identified a stable incompletely dominant major locus, qLLA10, for lobed leaf formation in non-heading Chinese cabbage. Based on map-based cloning strategies, BrLMI1, a LATE MERISTEM IDENTITY1 (LMI1)-like gene, was predicted as the candidate gene for qLLA10. Genotyping analysis showed that promoter variations of BrLMI1 in the two parents are responsible for elevating the expression in the lobed-leaf parent and ultimately causing the difference in leaf shape between the two parents, and the promoter activity of BrLMI1 was significantly affected by the promoter variations. BrLMI1 was exclusively localized in the nucleus and expressed mainly at the tip of each lobe. Leaf lobe development was perturbed in BrLMI1-silenced plants produced by virus-induced gene silencing assays, and ectopic overexpression of BrLMI1 in Arabidopsis led to deeply lobed leaves never seen in the wild type, which indicates that BrLMI1 is required for leaf lobe formation in non-heading Chinese cabbage. These findings suggested that BrLMI1 is a positive regulatory factor of leaf lobe formation in non-heading Chinese cabbage and that cis-regulatory variations lead to the phenotype of lobed or entire leaf margins, thus providing a theoretical basis for unraveling the molecular mechanism underlying the lobed leaf phenotype in Brassica crops.

BrMYB108 confers resistance to Verticillium wilt by activating ROS generation in Brassica rapa.

Increasing plant resistance to Verticillium wilt (VW), which causes massive losses of Brassica rapa crops, is a challenge worldwide. However, few causal genes for VW resistance have been identified by forward genetic approaches, resulting in limited application in breeding. We combine a genome-wide association study in a natural population and quantitative trait locus mapping in an F2 population and identify that the MYB transcription factor BrMYB108 regulates plant resistance to VW. A 179 bp insertion in the BrMYB108 promoter alters its expression pattern during Verticillium longisporum (VL) infection. High BrMYB108 expression leads to high VL resistance, which is confirmed by disease resistance tests using BrMYB108 overexpression and loss-of-function mutants. Furthermore, we verify that BrMYB108 confers VL resistance by regulating reactive oxygen species (ROS) generation through binding to the promoters of respiratory burst oxidase genes (Rboh). A loss-of-function mutant of AtRbohF in Arabidopsis shows significant susceptibility to VL. Thus, BrMYB108 and its target ROS genes could be used as targets for genetic engineering for VL resistance of B. rapa.

Wall-associated kinase BrWAK1 confers resistance to downy mildew in Brassica rapa.

The plant cell wall is the first line of defence against physical damage and pathogen attack. Wall-associated kinase (WAK) has the ability to perceive the changes in the cell wall matrix and transform signals into the cytoplasm, being involved in plant development and the defence response. Downy mildew, caused by Hyaloperonospora brassicae, can result in a massive loss in Chinese cabbage (Brassica rapa L. ssp. pekinensis) production. Herein, we identified a candidate resistant WAK gene, BrWAK1, in a major resistant quantitative trait locus, using a double haploid population derived from resistant inbred line T12-19 and the susceptible line 91-112. The expression of BrWAK1 could be induced by salicylic acid and pathogen inoculation. Expression of BrWAK1 in 91-112 could significantly enhance resistance to the pathogen, while truncating BrWAK1 in T12-19 increased disease susceptibility. Variation in the extracellular galacturonan binding (GUB) domain of BrWAK1 was found to mainly confer resistance to downy mildew in T12-19. Moreover, BrWAK1 was proved to interact with BrBAK1 (brassinosteroid insensitive 1 associated kinase), resulting in the activation of the downstream mitogen-activated protein kinase (MAPK) cascade to trigger the defence response. BrWAK1 is the first identified and thoroughly characterized WAK gene conferring disease resistance in Chinese cabbage, and the plant biomass is not significantly influenced by BrWAK1, which will greatly accelerate Chinese cabbage breeding for downy mildew resistance.

PTT/ PDT-induced microbial apoptosis and wound healing depend on immune activation and macrophage phenotype transformation.

Antibiotics show unsuccessful application in biofilm destruction, which induce chronic infections and emergence of antibiotic resistant bacteria. Photodynamic therapy (PDT) and photothermal therapy (PTT), as widely accepted antimicrobial tools of phototherapy, could effectively activate the immune system and promote the proliferation of wound tissue, thus becoming the most promising therapeutic strategy to replace antibiotics and avoid drug-resistant strains. However, there is no consensus on whether antibacterial and wound healing achieved by PDT/PTT depend not only on the cytotoxic effect of the treatment itself, but also on the activation of host immune system. In this study, CaSiO3-ClO2@PDA-ICG nanoparticles (CCPI NPs) were designed as PDT/PTT antimicrobial model material. With the comparison of healing effect between wide-type mice and severely immunodeficient (C-NKG) mice, the dependence of PDT/PTT-induced microbial apoptosis and wound healing on immune activation and macrophage phenotype transformation was explored and verified. Furthermore, the induced phenotypic transformation of macrophages during PDT/PTT treatment was demonstrated to play crucial role in the improvement of epithelial-mesenchymal transformation (EMT). In summary, this study represents great significance for further identifying the role of immune system activation in antibacterial phototherapy and developing new treatment strategies for biofilm-infected wound healing. STATEMENT OF SIGNIFICANCE: A PDT/PTT combination therapy model nanoparticle was established for biofilm-infected wounds. Both microbial apoptosis and wound healing achieved by PDT/PTT combination therapy were highly dependent on the activated immune system, especially the M2 macrophage phenotype. PDT/PTT could promote the polarization of monocytes to the phenotype of M2 macrophages, which promotes EMT behavior of the tissue at the edge of the wound through the secretion of TGF-ß1, thus accelerating wound healing.

Three-dimension chitosan hydrogel loading melanin composite nanoparticles for wound healing by anti-bacteria, immune activation and macrophage autophagy promotion.

Application of Combined photodynamic therapy (PDT) and photothermal therapy (PTT) has become one of the most promising strategy to replace antibiotics and avoid the epidemic of drug-resistant strains during wound healing. However, high amount of reactive oxygen species (ROS) and high temperature cause severe stress response to normal tissues, leading to potential risks of wound healing. Herein, a three-dimension chitosan hydrogel melanin-glycine-C60 nanoparticles (MGC NPs) were prepared to realized effective anti-bacterial activity, immune activation and macrophage autophagy promotion in three-dimensional wound space without triggering stress response. MGC NP is a composite polymer material composed of natural melanin polymer, oligopeptide and carbon-based material, which showed excellent biological safety. By regulating the peptide length between melanin and C60 and nanoparticle content, a high ROS/heat environment at the upper wound site and a low ROS/heat environment at the lower region adjacent to the wound tissue were established to obtain a three-dimension hydrogel with precise PDT and PTT efficiency in different regions. Highly effective PDT/PTT was used to kill microorganisms in upper region, thus providing a barrier to reduce microbial infection. Mild PDT/PTT in lower region promoted the polarization of M1 macrophage to M2 macrophage and activated autophagy of M2 macrophages, regulating the immune microenvironment and promoting wound repair. In conclusion, the novel three-dimensional PDT/PTT therapy based on natural macromolecules proposed in this study accelerates wound healing through dual pathways on the premise of avoiding wound stress response, which is of great significance for the development of clinical strategies for phototherapy.

Recent Advancements and Biotechnological Implications of Carotenoid Metabolism of Brassica.

Carotenoids were synthesized in the plant cells involved in photosynthesis and photo-protection. In humans, carotenoids are essential as dietary antioxidants and vitamin A precursors. Brassica crops are the major sources of nutritionally important dietary carotenoids. Recent studies have unraveled the major genetic components in the carotenoid metabolic pathway in Brassica, including the identification of key factors that directly participate or regulate carotenoid biosynthesis. However, recent genetic advances and the complexity of the mechanism and regulation of Brassica carotenoid accumulation have not been reviewed. Herein, we reviewed the recent progress regarding Brassica carotenoids from the perspective of forward genetics, discussed biotechnological implications and provided new perspectives on how to transfer the knowledge of carotenoid research in Brassica to the crop breeding process.

Roles of ginsenosides in sepsis.

The herbal medication Panax ginseng Meyer has widespread use in China, Korea, and other parts of the world. The main constituents of ginseng are ginsenosides, which include over 30 different triterpene saponins. It has been found that ginsenosides and their metabolites including Rg1, compound K, Rb1, Re, Rg3, and Rg5 exert anti-inflammatory activities by binding to the glucocorticoid receptor, modulating inflammation-related signaling, including NF-κB and MAPK signaling, and reducing levels of pro-inflammatory cytokines. Here, we review the recent literature on the molecular actions of ginsenosides in sepsis, suggesting ways in which they may be used to prevent and treat the disease.

Role of flavonoids in age-related macular degeneration.

A common eye disorder known as age-related macular degeneration (AMD) eventually results in blindness and vision loss. AMD has a complicated and poorly understood aetiology. The main pathological processes associated with AMD include oxidative damage, inflammation, and neovascularization. Flavonoids are naturally occurring bioactive substances with extensive distribution and antioxidant, anti-inflammatory, and neovascularization inhibitory properties. Several in vitro and in vivo AMD-related models pertinent to vision and this ocular ailment have been used to assess the mechanisms of action of various flavonoids. This article will discuss the research progress of flavonoids in AMD, especially the characteristics and mechanism of flavonoids in treating AMD.

Na2S2O4@Co-metal organic framework (ZIF-67) @glucose oxidase for biofilm-infecting wound healing with immune activation.

In recent years, photodynamic therapy (PDT) or chemodynamic therapy (CDT) based on the antimicrobial property or anti-biofilm property of reactive oxygen species (ROS) have been widely recognized for their low susceptibility to microbial resistance. However, due to the complication of the three-dimensional structure of the biofilm at the wound site and the high quenching rate of common ROS, the treatment with traditional ROS could not achieve satisfactory wound healing effects. Here, Na2S2O8@ZIF-67/GOx nanoparticles (NZG NPs) were prepared as a new high-toxic ROS nanogenerator for application of biofilm-infecting wound healing with the assistance of glucose oxidase (GOx) for amplified CDT and immune activation. When the NZG NPs entered the biofilm, Co-based metal organic frame (ZIF-67) ruptured in the acidic microenvironment, which induced the release of GOx and the production of gluconic acid and H2O2, further promoting the decrease of pH of the biofilm microenvironment and in turn accelerating the cleavage of ZIF-67 and the release of Na2S2O8. Then, S2O82- could gradually transformed into high-toxic sulfate radical (SO4-), part of which further produced OH in situ with H2O, thereby inhibiting the proliferation of bacteria and biofilms. Interestingly, these two types of ROS not only caused direct damage to the biofilm, but also activated the immune system of the wound site as well as the body more effectively, which also played an indirect role in promoting biofilm destruction and wound healing. In vitro and in vivo results showed that, as a new high-toxic ROS nanogenerator, the NZG NPs supply amplified chemodynamic therapy and immune activation to destroy biofilms, but also achieve effective wound healing without causing bacterial tolerance, which provides a new strategy for the development of biofilm-infecting wound healing.

Transcriptome-wide identification of WRKY transcription factors and their expression profiles under different stress in Cynanchum thesioides.

Cynanchum thesioides (Freyn) K. Schum. is an important economic and medicinal plant widely distributed in northern China. WRKY transcription factors (TFs) play important roles in plant growth, development and regulating responses. However, there is no report on the WRKY genes in Cynanchum thesioides. A total of 19 WRKY transcriptome sequences with complete ORFs were identified as WRKY transcriptome sequences by searching for WRKYs in RNA sequencing data. Then, the WRKY genes were classified by phylogenetic and conserved motif analysis of the WRKY family in Cynanchum thesioides and Arabidopsis thaliana. qRT-PCR was used to determine the expression patterns of 19 CtWRKY genes in different tissues and seedlings of Cynanchum thesioides under plant hormone (ABA and ETH) and abiotic stresses (cold and salt). The results showed that 19 CtWRKY genes could be divided into groups I-III according to their structure and phylogenetic characteristics, and group II could be divided into five subgroups. The prediction of CtWRKY gene protein interactions indicates that CtWRKY is involved in many biological processes. In addition, the CtWRKY gene was differentially expressed in different tissues and positively responded to abiotic stress and phytohormone treatment, among which CtWRKY9, CtWRKY18, and CtWRKY19 were significantly induced under various stresses. This study is the first to identify the WRKY gene family in Cynanchum thesioides, and the systematic analysis lays a foundation for further identification of the function of WRKY genes in Cynanchum thesioides.

Responses of transcriptome and metabolome in the roots of Pugionium cornutum (L.) Gaertn to exogenously applied phthalic acid.

BACKGROUND: The yield and quality of Pugionium cornutum (L.) Gaertn., a healthy, green vegetable with low sugar and high protein contents and high medicinal value, is severely affected by autotoxicity, which is a leading factor in the formation of plant disease. To help characterize the autotoxicity mechanism of P. cornutum (L.) Gaertn., we performed transcriptomic and metabolic analysis of the roots of P. cornutum (L.) Gaertn. response to phthalic acid, an autotoxin from P. cornutum (L.) Gaertn. RESULTS: In this study, high-throughput sequencing of nine RNA-seq libraries generated from the roots.of P. cornutum (L.) Gaertn. under different phthalic acid treatments yielded 37,737 unigenes. In total, 1085 (703 upregulated and 382 downregulated) and 5998 (4385 upregulated and 1613 downregulated) DEGs were identified under 0.1 and 10 mmol·L- 1 phthalic acid treatment, respectively, compared with the control treatment. Glutathione metabolism was among the top five important enriched pathways. In total, 457 and 435 differentially accumulated metabolites were detected under 0.1 and 10 mmol·L- 1 phthalic acid treatment compared with the control, respectively, of which 223 and 253, respectively, increased in abundance. With the increase in phthalic acid concentration, the accumulation of ten metabolites increased significantly, while that of four metabolites decreased significantly, and phthalic acid, dambonitol, 4-hydroxy-butyric acid, homocitrulline, and ethyl ß-D-glucopyranoside were 100 times more abundant under the 10 mmol·L- 1 phthalic acid treatment than under the control. Seventeen differentially expressed genes significantly associated with phthalic acid content were identified. In addition, the L-histidinol content was highest under 0.1 mmol·L- 1 phthalic acid, and a total of eleven differentially expressed genes were significantly positively correlated with the L-histidinol content, all of which were annotated to heat shock proteins, aquaporins and cysteine proteases. CONCLUSIONS: Accumulation of autotoxins altered the metabolic balance in P. cornutum (L.) Gaertn. and influenced water absorption and carbon and nitrogen metabolism. These important results provide insights into the formation mechanisms of autotoxicity and for the subsequent development of new control measures to improve the production and quality of replanted plants.

Subgenome dominance and its evolutionary implications in crop domestication and breeding.

Polyploidization or whole-genome duplication (WGD) is a well-known speciation and adaptation mechanism in angiosperms, while subgenome dominance is a crucial phenomenon in allopolyploids, established following polyploidization. The dominant subgenomes contribute more to genome evolution and homoeolog expression bias, both of which confer advantages for short-term phenotypic adaptation and long-term domestication. In this review, we firstly summarize the probable mechanistic basis for subgenome dominance, including the effects of genetic [transposon, genetic incompatibility, and homoeologous exchange (HE)], epigenetic (DNA methylation and histone modification), and developmental and environmental factors on this evolutionary process. We then move to Brassica rapa, a typical allopolyploid with subgenome dominance. Polyploidization provides the B. rapa genome not only with the genomic plasticity for adapting to changeable environments, but also an abundant genetic basis for morphological variation, making it a representative species for subgenome dominance studies. According to the 'two-step theory', B. rapa experienced genome fractionation twice during WGD, in which most of the genes responding to the environmental cues and phytohormones were over-retained, enhancing subgenome dominance and consequent adaption. More than this, the pangenome of 18 B. rapa accessions with different morphotypes recently constructed provides further evidence to reveal the impacts of polyploidization and subgenome dominance on intraspecific diversification in B. rapa. Above and beyond the fundamental understanding of WGD and subgenome dominance in B. rapa and other plants, however, it remains elusive why subgenome dominance has tissue- and spatiotemporal-specific features and could shuffle between homoeologous regions of different subgenomes by environments in allopolyploids. We lastly propose acceleration of the combined application of resynthesized allopolyploids, omics technology, and genome editing tools to deepen mechanistic investigations of subgenome dominance, both genetic and epigenetic, in a variety of species and environments. We believe that the implications of genomic and genetic basis of a variety of ecologically, evolutionarily, and agriculturally interesting traits coupled with subgenome dominance will be uncovered and aid in making new discoveries and crop breeding.

TMT-based proteomic analysis of liquorice root in response to drought stress.

BACKGROUND: Drought stress is a serious threat to land use efficiency and crop yields worldwide. Understanding the mechanisms that plants use to withstand drought stress will help breeders to develop drought-tolerant medicinal crops. Liquorice (Glycyrrhiza uralensis Fisch.) is an important medicinal crop in the legume family and is currently grown mostly in northwest China, it is highly tolerant to drought. Given this, it is considered an ideal crop to study plant stress tolerance and can be used to identify drought-resistant proteins. Therefore, to understand the effects of drought stress on protein levels of liquorice, we undertook a comparative proteomic analysis of liquorice seedlings grown for 10 days in soil with different relative water content (SRWC of 80%, 65%, 50% and 35%, respectively). We used an integrated approach of Tandem Mass Tag labeling in conjunction with LC-MS/MS. RESULTS: A total of 7409 proteins were identified in this study, of which 7305 total proteins could be quantified. There were 837 differentially expressed proteins (DEPs) identified after different drought stresses. Compared with CK, 123 DEPs (80 up-regulated and 43 down-regulated) were found in LS; 353 DEPs (254 up-regulated and 99 down-regulated) in MS; and 564 DEPs (312 up-regulated and 252 down-regulated) in SS.The number of differentially expressed proteins increased with increasing water stress, and the number of up-regulated proteins was higher than that of down-regulated proteins in the different drought stress treatments compared with the CK. Used systematic bioinformatics analysis of these data to identify informative proteins we showed that osmolytes such as cottonseed sugars and proline accumulated under light drought stress and improved resistance. Under moderate and severe drought stress, oxidation of unsaturated fatty acids and accumulation of glucose and galactose increased in response to drought stress. Under moderate and severe drought stress synthesis of the terpene precursors, pentacene 2,3-epoxide and ß-coumarin, was inhibited and accumulation of triterpenoids (glycyrrhetinic acid) was also affected. CONCLUSIONS: These data provide a baseline reference for further study of the downstream liquorice proteome in response to drought stress. Our data show that liquorice roots exhibit specific response mechanisms to different drought stresses.