Phenylpropanoid Biosynthesis Research Articles

6-BA Reduced Yield Loss under Waterlogging Stress by Regulating the Phenylpropanoid Pathway in Wheat.

Waterlogging stress causes substantial destruction to plant growth and production under climatic fluctuations globally. Plants hormones have been widely explored in numerous crops, displaying an imperative role in crop defense and growth mechanism. However, there is a paucity of research on the subject of plant hormones regulating waterlogging stress responses in wheat crop. In this study, we clarified the role of 6-BA in waterlogging stress through inducing phenylpropanoid biosynthesis in wheat. The application of 6-BA (6-benzyladenine) enhanced the growth and development of wheat plants under waterlogging stress, which was accompanied by reduced electrolyte leakage, high chlorophyll, and soluble sugar content. ROS scavenging was also enhanced by 6-BA, resulting in reduced MDA and H2O2 accumulation and amplified antioxidant enzyme activities. Additionally, under the effect of 6-BA, the acceleration of lignin content and accumulation in the cell walls of wheat tissues, along with the activation of PAL (phenylalanine ammonia lyase), TAL (tyrosine ammonia lyase), and 4CL (4-hydroxycinnamate CoA ligase) activities and the increase in the level of transcription of the TaPAL and Ta4CL genes, were observed under waterlogging stress. Also, 6-BA improved the root growth system under waterlogging stress conditions. Further qPCR analysis revealed increased auxin signaling (TaPR1) in 6-BA-treated plants under waterlogging stress that was consistent with the induction of endogenous IAA hormone content under waterlogging stress conditions. Here, 6-BA also reduced yield loss, as compared to control plants. Thus, the obtained data suggested that, under the application of 6-BA, phenylpropanoid metabolism (i.e., lignin) was stimulated, playing a significant role in reducing the negative effects of waterlogging stress on yield, as evinced by the improved plant growth parameters.

Sphingosine Promotes Fiber Early Elongation in Upland Cotton.

Sphingolipids play an important role in cotton fiber development, but the regulatory mechanism is largely unclear. We found that serine palmitoyltransferase (SPT) enzyme inhibitors, myriocin and sphingosine (dihydrosphingosine (DHS) and phytosphingosine (PHS)), affected early fiber elongation in cotton, and we performed a sphingolipidomic and transcriptomic analysis of control and PHS-treated fibers. Myriocin inhibited fiber elongation, while DHS and PHS promoted it in a dose-effect manner. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), we found that contents of 22 sphingolipids in the PHS-treated fibers for 10 days were changed, of which the contents of 4 sphingolipids increased and 18 sphingolipids decreased. The transcriptome analysis identified 432 differentially expressed genes (238 up-regulated and 194 down-regulated) in the PHS-treated fibers. Among them, the phenylpropanoid biosynthesis pathway is the most significant enrichment. The expression levels of transcription factors such as MYB, ERF, LBD, and bHLH in the fibers also changed, and most of MYB and ERF were up-regulated. Auxin-related genes IAA, GH3 and BIG GRAIN 1 were up-regulated, while ABPs were down-regulated, and the contents of 3 auxin metabolites were decreased. Our results provide important sphingolipid metabolites and regulatory pathways that influence fiber elongation.

Transcriptome mechanisms of dandelion under stress of polystyrene and dibutyl phthalate and quantitative tracing of nanoplastics

Polystyrene nanoplastics (PS NPs) and dibutyl phthalate (DBP) pollution pose significant risks to ecosystems and contribute to bioaccumulation in plants, yet uptake mechanisms and combined toxicity are poorly understood. We used fluorescent labeling and europium-doped PS NPs to reveal the absorption and translocation of NPs by dandelions and conducted a transcriptomic analysis under PS NPs and DBP exposure. The results indicated that NPs are transported horizontally through the intercellular gaps at the root tips and primary root-lateral root junctions via the apoplastic pathway, followed by longitudinal transport through the xylem vessels under the transpiration stream. Co-exposure significantly reduced the bioconcentration factors of dandelion seedlings by 113 % but increased the NP transfer factors by 33.8 %. Transcriptomic analysis confirmed that exposure to PS NPs and DBP activated gene expression in dandelion shoots and roots. The differentially expressed genes were primarily involved in the photosynthesis, plant hormone signal transduction, and phenylpropanoid biosynthesis pathways. Weighted gene co-expression network analysis identified key genes and hub transcription factors playing crucial roles in regulating dandelion's response to combined stress. Our study provides new insights into the plant toxicity mechanism underlying the interaction between PS NPs and DBP, highlighting the adverse effects of the combined pollution on plant health.

Integrated Metabolomics and Metagenomics Unveiled Biomarkers of Antioxidant Potential in Fermented Brewer's Grains.

About one-third of the global food supply is wasted. Brewers' spent grain (BSG), being produced in enormous amounts by the brewery industry, possesses an eminence nutritional profile, yet its recycling is often neglected for multiple reasons. We employed integrated metagenomics and metabolomics techniques to assess the effects of enzyme treatments and Lactobacillus fermentation on the antioxidant capacity of BSG. The biotreated BSG revealed improved antioxidant capability, as evidenced by significantly increased (p < 0.05) radical scavenging activity and flavonoid and polyphenol content. Untargeted metabolomics revealed that Lactobacillus fermentation led to the prominent synthesis (p < 0.05) of 15 novel antioxidant peptides, as well as significantly higher (p < 0.05) enrichment of isoflavonoid and phenylpropanoid biosynthesis pathways. The correlation analysis demonstrated that Lactiplantibacillus plantarum exhibited strong correlation (p < 0.05) with aucubin and carbohydrate-active enzymes, namely, glycoside hydrolases 25, glycosyl transferases 5, and carbohydrate esterases 9. The fermented BSG has potential applications in the food industry as a culture medium, a functional food component for human consumption, and a bioactive feed ingredient for animals.

Combined analysis of transcriptomics with metabolomics provides insights into the resistance mechanism in winter jujube using L-Methionine

Black rots lead to great economic losses in winter jujube industry. The objective of this research was to delve into the underlying mechanisms of enhanced resistance of winter jujube fruit to black rot by L-Methionine (Met) treatment. The findings revealed that the application of Met significantly curtailed lesion diameter and decay incidence in winter jujube fruit. The peroxidase (POD) activity in the Met-treated jujubes was 3.06-fold that in the control jujubes after 4 d of treatment. By day 8, the activities of phenylalanine ammonia-lyase (PAL), chitinase (CHI) and β-1,3-glucanase (GLU) in the Met-treated jujubes had surged to their zenith, being 1.39, 1.22, and 1.52 times in the control group, respectively. At the end of storage, the flavonoid and total phenol content remained 1.58 and 1.06 times than that of the control group. Based on metabolomics and transcriptomics analysis, Met treatment upregulated 6 key differentially expressed metabolites (DEMs) (succinic acid, trans-ferulic acid, salicylic acid, delphinium pigments, (S)-abscisic acid, and hesperidin-7-neohesperidin), 12 key differentially expressed genes (DEGs) (PAL, CYP73A, COMT, 4CL, CAD, POD, UGT72E, ANS, CHS, IAA, TCH4 and PR1), which were involved in phenylpropanoid biosynthesis pathway, flavonoid biosynthesis pathway and plant hormone signal transduction pathway. Further analysis revealed that the most of the enzymes, DEMs and DEGs in this study were associated with both antioxidant and disease resistance. Consequently, Met treatment enhanced disease resistance of winter jujube fruit by elevating antioxidant capacity and triggering defense response. This study might provide theoretical support for utilizing Met in the management and prevention of post-harvest black rot in winter jujube.

Comparative Analysis of Hulless Barley Transcriptomes to Regulatory Effects of Phosphorous Deficiency.

Hulless barley is a cold-resistant crop widely planted in the northwest plateau of China. It is also the main food crop in this region. Phosphorus (P), as one of the important essential nutrient elements, regulates plant growth and defense. This study aimed to analyze the development and related molecular mechanisms of hulless barley under P deficiency and explore the regulatory genes so as to provide a basis for subsequent molecular breeding research. Transcriptome analysis was performed on the root and leaf samples of hulless barley cultured with different concentrations of KH2PO4 (1 mM and 10 μM) Hoagland solution. A total of 46,439 genes were finally obtained by the combined analysis of leaf and root samples. Among them, 325 and 453 genes had more than twofold differences in expression. These differentially expressed genes (DEGs) mainly participated in the abiotic stress biosynthetic process through Gene Ontology prediction. Moreover, the Kyoto Encyclopedia of Genes and Genomes showed that DEGs were mainly involved in photosynthesis, plant hormone signal transduction, glycolysis, phenylpropanoid biosynthesis, and synthesis of metabolites. These pathways also appeared in other abiotic stresses. Plants initiated multiple hormone synergistic regulatory mechanisms to maintain growth under P-deficient conditions. Transcription factors (TFs) also proved these predictions. The enrichment of ARR-B TFs, which positively regulated the phosphorelay-mediated cytokinin signal transduction, and some other TFs (AP2, GRAS, and ARF) was related to plant hormone regulation. Some DEGs showed different values in their FPKM (fragment per kilobase of transcript per million mapped reads), but the expression trends of genes responding to stress and phosphorylation remained highly consistent. Therefore, in the case of P deficiency, the first response of plants was the expression of stress-related genes. The effects of this stress on plant metabolites need to be further studied to improve the relevant regulatory mechanisms so as to further understand the importance of P in the development and stress resistance of hulless barley.

Selenium Nanoparticle and Melatonin Treatments Improve Melon Seedling Growth by Regulating Carbohydrate and Polyamine.

Bio-stimulants, such as selenium nanoparticles and melatonin, regulate melon growth. However, the effects of individual and combined applications of selenium nanoparticles and melatonin on the growth of melon seedlings have not been reported. Here, two melon cultivars were sprayed with selenium nanoparticles, melatonin, and a combined treatment, and physiological and biochemical properties were analyzed. The independent applications of selenium nanoparticles, melatonin, and their combination had no significant effects on the plant heights and stem diameters of Jiashi and Huangmengcui melons. Compared with the controls, both selenium nanoparticle and melatonin treatments increased soluble sugars (6-63%) and sucrose (11-88%) levels, as well as the activity of sucrose phosphate synthase (171-237%) in melon leaves. The phenylalanine ammonia lyase (29-95%), trans cinnamate 4-hydroxylase (32-100%), and 4-coumaric acid CoA ligase (26-113%), as well as mRNA levels, also increased in the phenylpropanoid metabolism pathway. Combining the selenium nanoparticles and melatonin was more effective than either of the single treatments. In addition, the levels of superoxide dismutase (43-130%), catalase (14-43%), ascorbate peroxidase (44-79%), peroxidase (25-149%), and mRNA in melon leaves treated with combined selenium nanoparticles and melatonin were higher than in controls. The results contribute to our understanding of selenium nanoparticles and melatonin as bio-stimulants that improve the melon seedlings' growth by regulating carbohydrate, polyamine, and antioxidant capacities.

Morphological, anatomical, and transcriptomics analysis reveals the regulatory mechanisms of cassava plant height development

BackgroundCassava is one of three major potato crops and the sixth most important food crop globally. Improving yield remains a primary aim in cassava breeding. Notably, plant height significantly impacts the yield and quality of crops; however, the mechanisms underlying cassava plant height development are yet to be elucidated.ResultsIn this study, we investigated the mechanisms responsible for cassava plant height development using phenotypic, anatomical, and transcriptomic analyses. Phenotypic and anatomical analysis revealed that compared to the high-stem cassava cultivar, the dwarf-stem cassava cultivar exhibited a significant reduction in plant height and a notable increase in internode tissue xylem area. Meanwhile, physiological analysis demonstrated that the lignin content of dwarf cassava was significantly higher than that of high cassava. Notably, transcriptome analysis of internode tissues identified several differentially expressed genes involved in cell wall synthesis and expansion, plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis between the two cassava cultivars.ConclusionsOur findings suggest that internode tissue cell division, secondary wall lignification, and hormone-related gene expression play important roles in cassava plant height development. Ultimately, this study provides new insights into the mechanisms of plant height morphogenesis in cassava and identifies candidate regulatory genes associated with plant height that can serve as valuable genetic resources for future crop dwarfing breeding.

Spotlight on Secondary Metabolites Produced by an Early-Flowering Apulian Artichoke Ecotype Sanitized from Virus Infection by Meristem-Tip-Culture and Thermotherapy.

Globe artichoke (Cynara cardunculus L. subsp. scolymus) is an important crop of the Mediterranean basin characterized by many properties, like hepatoprotective, anticarcinogenic, antioxidant, antibacterial, and beneficial to human health. The high bioactive compounds (BACs) content, as polyphenols, has attracted the research interest in artichoke extracts. We analysed the changes in polyphenol transcriptome profile between sanitized (S) virus-free and non-sanitized (NS) artichoke plants, focusing on genes involved in phenylpropanoid metabolic pathway and flavonoid biosynthesis. A total of 2458 upregulated and 2154 downregulated differentially expressed genes (DEGs) were functionally characterized. Among them, 31 and 35 KEGG orthology entries characterized by upregulated and downregulated DEGs, respectively, were involved in the biosynthesis of other secondary metabolites. A downregulation of PAL, C4H, 4CL, HST/HQT, C3'H, CCoAMT, CCR1, and F5H, was observed in S artichoke compared to NS one, whereas the CSE, CHS, and CHI genes were upregulated in S samples. Transcriptome results were compared to the polyphenols accumulation in S and NS artichoke leaves. A higher content of total polyphenols was observed in older leaves of NS samples, compared to extracts obtained from young leaves or from S plants, and this result was associated with the presence of viral infections in NS plants. In all the conditions tested, the most represented compound was chlorogenic acid, followed by luteolin-7-O-glucoside. The different composition of each extract was evaluated by a polyphenol dose-response treatment on the rodent hepatoma FaO cell line to the accumulation of reactive oxygen species (ROS). A significant reduction in ROS content ranging between -40% and -48% was observed when 10-20 mg/L of polyphenols from NS or S plants were used, characterized by a specific profile of compounds. To reduce MetOH residues in polyphenol extracts, a supercritical fluid CO2 extraction was evaluated to propose a sustainable green extraction.

Integrated transcriptomics and metabolomics provide insights into the biosynthesis of militarine in the cell suspension culture system of Bletilla striata

Militarine is a monomer molecule with abundant and distinctive biological properties, also the lead member of secondary metabolites in Bletilla striata, while its biosynthesis mechanism is still unknown. To improve the production efficiency of militarine, sodium acetate and salicylic acid (SA) were introduced as elicitors into the suspension-cultured callus of B. striata. Subsequently, samples were taken from callus at different culturing stages to investigate the synthesis mechanisms of militarine in B. striata through integrated metabolomics and transcriptomics. Metabolomics analysis revealed that acetate ions promoted militarine synthesis, while SA had an inhibitory effect. Additionally, regulators such as ferulic acid, 2-hydroxy-3-phenylpropionic acid, and cis-beta-D-Glucosyl-2-hydroxycinnamate were identified as influencing militarine synthesis. Transcriptomics analysis indicated that the expression levels of genes involved in phenylalanine metabolism, phenylpropanoid biosynthesis, and tyrosine metabolism were correlated with militarine content. This study sheds light on the regulatory mechanism of militarine biosynthesis in plants. The results suggested that acetate ions and SA impact militarine synthesis through specific metabolic pathways and gene expression changes. This knowledge serves as a foundation for future research on militarine biosynthesis and its industrial production.

Multi-Omics Analysis Reveals the Transcriptional Regulatory Network of Maize Roots in Response to Nitrogen Availability

Nitrogen (N) availability determines higher plant productivity and yield. However, the molecular mechanisms governing N acquisition and utilization remain largely unknown in maize. In this study, ATAC-seq, RNA-seq, and Ribo-seq analyses were conducted in maize roots under different N supply conditions. A set of differentially expressed genes enriched in N and phenylpropanoid metabolisms at both the transcription and translation levels were highlighted. Interestingly, less than half of low-N responsive genes were shared between transcription and translation. The alteration of translational efficiency (TE) is also an important mechanism by which maize responds to LN. In addition, we identified low-N-induced open chromatin regions (OCRs) and observed an enrichment of transcription factor (TF) binding motifs. Furthermore, we constructed a transcriptional regulatory network for maize roots subjected to low-N. These findings extend our understanding of N availability response and provide new insights for improving N use efficiency (NUE).

Dissection of Metabolome and Transcriptome-Insights into Capsaicin and Flavonoid Accumulation in Two Typical Yunnan Xiaomila Fruits.

Pepper is an economically important vegetable worldwide, containing various specialized metabolites crucial for its development and flavor. Capsaicinoids, especially, are genus-specialized metabolites that confer a spicy flavor to Capsicum fruits. In this work, two pepper cultivars, YB (Capsicum frutescens L.) and JC (Capsicum baccatum L.) pepper, showed distinct differences in the accumulation of capsaicin and flavonoid. However, the molecular mechanism underlying them was still unclear. Metabolome analysis showed that the JC pepper induced a more abundant accumulation of metabolites associated with alkaloids, flavonoids, and capsaicinoids in the red ripening stages, leading to a spicier flavor in the JC pepper. Transcriptome analysis confirmed that the increased expression of transcripts associated with phenylpropanoid and flavonoid metabolic pathways occurred in the JC pepper. Integrative analysis of metabolome and transcriptome suggested that four structural genes, 4CL7, 4CL6, CHS, and COMT, were responsible for the higher accumulation of metabolites relevant to capsaicin and flavonoids. Through weighted gene co-expression network analyses, modules related to flavonoid biosynthesis and potential regulators for candidate genes were identified. The promoter analysis of four candidate genes showed they contained several cis-elements that were bonded to MYB, bZIP, and WRKY transcription factors. Further RT-qPCR examination verified three transcription factors, MYB, bZIP53, and WRKY25, that exhibited increased expression in the red ripening stage of the JC pepper compared to YB, which potentially regulated their expression. Altogether, our findings provide comprehensive understanding and valuable information for pepper breeding programs in the future.

Sugar Accumulation Patterns and Transcriptome Analysis during the Developmental Stage of Small-Fruit Watermelon (Citrullus lanatus L.)

The sugar content in watermelon significantly influences its flavor. To understand the sugar accumulation pattern in small-fruited watermelon and identify candidate genes involved in sugar synthesis and conversion, we measured the sugar content (sucrose, fructose, and glucose) at five developmental stages: 10d, 16d, 22d, 28d, and 34d post-pollination. Two watermelon varieties with the largest sugar content difference at 28d post-pollination (high-sugar G38-28 and low-sugar 482276-28) were selected for transcriptome sequencing. Differentially expressed genes (DEGs) were validated using RT-qPCR. Additionally, the sugar contents of three commercial varieties (‘Su Meng NO.5’, ‘Su Meng NO.6’, ‘Su Meng NO.7’) and their parents were compared at five stages. Results showed glucose and fructose levels peaked between 22d and 28d, followed by a decrease, while sucrose content continuously increased. F1 hybrids exhibited glucose and sucrose trends similar to their paternal parent and fructose trends similar to their maternal parent. Transcriptome sequencing identified 9337 DEGs (5072 upregulated and 4265 downregulated). Gene Ontology analysis highlighted overrepresentation in categories such as pectinase and oxidoreductase activity. KEGG analysis identified 12 DEGs involved in sugar synthesis and conversion pathways, including phenylpropanoid biosynthesis and pentose and glucuronate interconversions. RT-qPCR validation corroborated the transcriptome data. These findings explain the distinct sugar accumulation patterns in G38-28 and 482276-28 at the transcriptional level, offering insights for genetic breeding and regulation of key sugar-related genes in watermelon.

Identification of tomato F-box proteins functioning in phenylpropanoid metabolism.

Phenylpropanoids, a class of specialized metabolites, play crucial roles in plant growth and stress adaptation and include diverse phenolic compounds such as flavonoids. Phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS) are essential enzymes functioning at the entry points of general phenylpropanoid biosynthesis and flavonoid biosynthesis, respectively. In Arabidopsis, PAL and CHS are turned over through ubiquitination-dependent proteasomal degradation. Specific kelch domain-containing F-Box (KFB) proteins as components of ubiquitin E3 ligase directly interact with PAL or CHS, leading to polyubiquitinated PAL and CHS, which in turn influences phenylpropanoid and flavonoid production. Although phenylpropanoids are vital for tomato nutritional value and stress responses, the post-translational regulation of PAL and CHS in tomato remains unknown. We identified 31 putative KFB-encoding genes in the tomato genome. Our homology analysis and phylogenetic study predicted four PAL-interacting SlKFBs, while SlKFB18 was identified as the sole candidate for the CHS-interacting KFB. Consistent with their homolog function, the predicted four PAL-interacting SlKFBs function in PAL degradation. Surprisingly, SlKFB18 did not interact with tomato CHS and the overexpression or knocking out of SlKFB18 did not affect phenylpropanoid contents in tomato transgenic lines, suggesting its irreverence with flavonoid metabolism. Our study successfully discovered the post-translational regulatory machinery of PALs in tomato while highlighting the limitation of relying solely on a homology-based approach to predict interacting partners of F-box proteins.

Genome assembly of Hibiscus sabdariffa L. provides insights into metabolisms of medicinal natural products.

Hibiscus sabdariffa L. is a widely cultivated herbaceous plant with diverse applications in food, tea, fiber, and medicine. In this study, we present a high-quality genome assembly of H. sabdariffa using more than 33 Gb of high-fidelity (HiFi) long-read sequencing data, corresponding to ∼20× depth of the genome. We obtained 3 genome assemblies of H. sabdariffa: 1 primary and 2 partially haplotype-resolved genome assemblies. These genome assemblies exhibit N50 contig lengths of 26.25, 11.96, and 14.50 Mb, with genome coverage of 141.3, 86.0, and 88.6%, respectively. We also utilized 26 Gb of total RNA sequencing data to predict 154k, 79k, and 87k genes in the respective assemblies. The completeness of the primary genome assembly and its predicted genes was confirmed by the benchmarking universal single-copy ortholog analysis with a completeness rate of 99.3%. Based on our high-quality genomic resources, we constructed genetic networks for phenylpropanoid and flavonoid metabolism and identified candidate biosynthetic genes, which are responsible for producing key intermediates of roselle-specific medicinal natural products. Our comprehensive genomic and functional analysis opens avenues for further exploration and application of valuable natural products in H. sabdariffa.

Regulatory Peptide Encoded by the Primary Transcript of miR396a Influences Gene Expression and Root Development in Solanum lycopersicum.

MicroRNAs (miRNAs) are the processing products of primary miRNAs (pri-miRNAs) that regulate the expression of target genes. Recent studies have demonstrated that some pri-miRNAs can encode small peptides (miPEPs) that perform significant biological functions. The function of miPEPs in tomatoes, an important model horticultural crop, remains to be investigated. Here, we characterized the primary sequence of tomato miR396a using 5' RACE and confirmed the presence of miPEP396a in tomato by verifying the translational activity of the start codon. It primarily resides in the nucleus to exert its function and additionally regulates the expression of pri-miR396a, miR396a, and its target genes. Transcriptomic and metabolomic analyses showed that in vitro synthesis of miPEP396a significantly increased the expression of genes related to phenylpropanoid biosynthesis and hormones in tomato. Meanwhile, our in vitro application of miPEP396a in tomato significantly inhibited the elongation of tomato primary roots. In conclusion, our results indicate that miPEP396a regulates root growth in tomato by specifically promoting miR396a expression, provide insight into the function of miPEPs in tomato and potential applications.

Transcriptomic and Metabolomic Insights into ABA-Related Genes in Cerasus humilis under Drought Stress.

Cerasus humilis, a small shrub of the Cerasus genus within the Rosaceae family, is native to China and renowned for its highly nutritious and medicinal fruits, robust root system, and remarkable drought resistance. This study primarily employed association transcriptome and metabolome analyses to assess changes in abscisic acid (ABA) levels and identify key regulatory genes in C. humilis subjected to varying degrees of drought stress. Notably, we observed distinct alterations in transcription factors across different drought intensities. Specifically, our transcriptome data indicated noteworthy shifts in GATA, MYB, MYC, WRKY, C2H2, and bHLH transcription factor families. Furthermore, combined transcriptomic and metabolomic investigations demonstrated significant enrichment of metabolic pathways, such as 'Carbon metabolism', 'Biosynthesis of amino acids', 'Biosynthesis of cofactors', 'Phenylpropanoid biosynthesis', 'Starch and sucrose metabolism', and 'Plant hormone signal transduction' under moderate (Mod) or severe (Sev) drought conditions. A total of 11 candidate genes involved in ABA biosynthesis and signaling pathways were identified. The down-regulated genes included secoisolariciresinol dehydrogenase-like and PYL2. Conversely, genes including FAD-dependent urate hydroxylase-like, cytochrome P450 97B2, carotenoid cleavage dioxygenase 4 (CCD4), SnRK2.2, ABI 5-like protein 5, PP2C 51, and SnRK2.3, were up-regulated under Mod or Sev drought stress. This study lays the genetic foundation for ABA biosynthesis to enhance drought tolerance and provides genetic resources for plant genetic engineering and breeding efforts.

Chitosan boosts ginger disease resistance: Insights from transcriptomic and metabolomic analyses

Chitosan exhibits efficacy in controlling ginger diseases, yet its systemic regulatory mechanisms remain unknown. This study explored the potential mechanisms underlying chitosan-regulated resistance by conducting physiological, comparative transcriptome, and metabolome analyses in Fusarium solani-inoculated ginger rhizomes with and without chitosan treatment. Chitosan treatment decreased decay severity and water loss, and reduced reactive oxygen species accumulation by enhancing antioxidant enzyme activities. Chitosan increased PAL, C4H, and CHI activities, along with elevated levels of lignin, total phenolic, total flavonoid, and the accumulation of suberin polyphenolic. RNA-seq analysis identified 1158 differentially expressed genes, predominantly involved in active oxygen and phenylpropanoid metabolism. Metabolomics identified 226 differential metabolites, including numerous phenylpropanoids and flavonoids. Integrated RNA-seq and metabolome analyses revealed chitosan's regulatory impact on gene expression and metabolite accumulation in the phenylpropanoid metabolism. These findings provide novel insights into chitosan's mechanisms against Fusarium solani.

Multi-omics analysis of Populus simonii × P. nigra leaves under Hyphantria cunea stress.

Poplar is an important greening and timber tree species in China, which has great economic and ecological values. However, the spread of Hyphantria cunea has become increasingly serious in recent years, resulting in huge economic loss of poplar production. Exploring the molecular mechanism of poplar reponse to H. cunea stress has significant implications for future development of new insect-resistant poplar varieties using genetic engineering technology. In this study, a total of 1039 differentially expressed genes (DEGs), 106 differentially expressed proteins (DEPs) and 212 differentially expressed metabolites (DEMs) were screened from Populus simonii × P. nigra leaves under H. cunea stress by transcriptome, proteomics and metabolomics analysis, respectively. GO and KEGG analysis showed that the DEGs and DEPs are associated with endopeptidase inhibitor activity, stress response, α-linolenic acid metabolism, phenylpropanoid biosynthesis and metabolic pathways, cysteine and methionine metabolism pathways and MAKP signaling pathway. Metabolomics analysis showed the most of DEMs were lipids and lipid molecules, and the pathways associated with transcriptome mainly include plant hormone signal transduction, α-linolenic acid metabolic pathway, amino sugar and nucleotide sugar metabolism, and phenylpropanoid biosynthesis. In particular, multi-omics analysis showed that several pathways such as α-linolenic acid metabolic, phenylpropanoid biosynthesis and metabolic pathway and cysteine and methionine metabolic pathway were significantly enriched in the three omics, which may play an important role in the resistance to pests in poplar.

Transcriptome sequencing of garlic reveals key genes related to the heat stress response

With global warming, heat stress has become an important factor that seriously affects crop yield and quality. Therefore, understanding plant responses to heat stress is important for agricultural practice, but the molecular mechanism of high-temperature tolerance in garlic remains unclear. In this study, ‘Xusuan No. 6’ was used as the experimental material. After heat stress for 0 (CK), 2 and 24 h, transcriptome sequencing was used to screen metabolic pathways and differentially expressed genes (DEGs) closely related to heat stress and was further verified by quantitative real-time polymerase chain reaction (qRT-PCR). A total of 86,110 unigenes obtained from the raw transcriptome sequencing data were spliced. After 2 h of heat treatment, the expression levels of 8898 genes increased, and 3829 genes were decreased in leaves. After 24 h, the expression levels of 7167 genes were upregulated, and 3176 genes were downregulated. Gene Ontology enrichment analysis showed that DEGs were mainly enriched in seven categories: cellular processes, metabolic processes, binging, catalytic activity, cellular anatomical entity and protein-containing complex response to stimulus. Kyoto Encyclopedia of Genes and Genomes pathway enrichment showed that DEGs are involved in protein processing in the endoplasmic reticulum, plant hormone signal transduction, phenylpropanoid biosynthesis, and photosynthetic antenna proteins. Six genes were selected and further verified by qRT-PCR. In this study, the full-length transcriptome of garlic was constructed, and the regulatory genes related to the heat resistance of garlic were studied. Taken together, these findings can provide a theoretical basis for the cloning of heat resistance genes in garlic and for the analysis of heat resistance mechanisms.