Transcriptomic and Metabolic Profiling Reveals 'Green Ring' and 'Red Ring' on Jujube Fruit upon Postharvest Alternaria alternata Infection

Transcriptomic responses of 'Huping jujube' (Zizyphus jujuba mill. cv. Huping) fruit to combined treatment of acidic electrolyzed water and high-voltage electrostatic field

The molecular mechanism underlying the preserving superior quality attributes of postharvest Huping jujube fruit by combining acidic electrolyzed water and high-voltage electrostatic field (AH) treatment remained unclear. The high-throughput sequencing analysis revealed a total of 3590 common differentially expressed genes (DEGs) in the T-W-CK0 vs T-W-CK75 and T-W-CK75 vs T-W-AH75 groups. AH treatment down-regulated most genes associated with respiratory metabolism, as well as lignin and anthocyanin biosynthesis, thereby maintaining lower physiological activities, improving taste and color quality of mature-white jujube. Additionally, AH treatment downregulated the genes involved in reactive oxygen species (ROS) generation and disease resistance, while simultaneously upregulating the genes associated with ROS elimination. This suggested that AH treatment could inhibit pathogen infection to prevent the activation of plants' active defense and reduce the ROS-induced damage. In sum, the present study provided a comprehension explanation that AH treatment improved the storage quality attributes of jujube fruit at the genetic level.

Fabrication and Characterization of Ag-Graphene Nanocomposites and Investigation of Their Cytotoxic, Antifungal and Photocatalytic Potential

In the present study, we aimed to synthesize (Ag)_1-x(GNPs)_x nanocomposites in variable ratios (25% GNPs-Ag, 50% GNPs-Ag, and 75% GNPs-Ag) via an ex situ approach to investigate the incremental effects of GNPs (graphene nanoparticles) on AgNPs (silver nanoparticles). The prepared nanocomposites were successfully characterized using different microscopic and spectroscopic techniques, including X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, ultraviolet spectroscopy, and Raman spectroscopic analysis. For the evaluation of morphological aspects, shape, and percentage elemental composition, SEM and EDX analyses were employed. The bioactivities of the synthesized nanocomposites were briefly investigated. The antifungal activity of (Ag)_1-x(GNPs)_x nanocomposites was reported to be 25% for AgNPs and 66.25% using 50% GNPs-Ag against Alternaria alternata. The synthesized nanocomposites were further evaluated for cytotoxic potential against U87 cancer cell lines with improved results (for pure AgNPs IC₅₀: ~150 µg/mL, for 50% GNPs-Ag IC₅₀: ~12.5 µg/mL). The photocatalytic properties of the nanocomposites were determined against the toxic dye Congo red, and the percentage degradation was recorded as 38.35% for AgNPs and 98.7% for 50% GNPs-Ag. Hence, from the results, it is concluded that silver nanoparticles with carbon derivatives (graphene) have strong anticancer and antifungal properties. Dye degradation strongly confirmed the photocatalytic potential of Ag-graphene nanocomposites in the removal of toxicity present in organic water pollutants.

Transcriptomics and gas chromatography-mass spectrometry metabolomics reveal the mechanism of heat shock combined with 1-methylcyclopropene to regulate the cuticle wax of jujube fruit during storage

Cuticle wax is closely related to fruit quality during storage. In this study, changes in epidermal wax morphology, composition, and genes regulation induced by heat shock (HT), 1-methylcyclopropene (1-MCP) or their combination (HT + 1-MCP) were investigated in jujube fruit during cold storage. HT, 1-MCP, or HT + 1-MCP caused a smoother wax layer and fewer micro-cracks compared to the control (CK) during cold storage. It was confirmed that acids and terpenoids were the main wax components by gas chromatography-mass spectrometry. HT + 1-MCP and 1-MCP treatments could significantly increase (p < 0.05) the wax content at 45 d of cold storage. The transcriptomics results indicated that HT + 1-MCP treatment up-regulated FATB, FATB, FAB2, FAD2 and CYP716A, and maintained the wax content of jujube fruit during cold storage. These results could provide new perspective for regulating the cuticle characteristics to extend the shelf life of jujube fruit.

Comparative transcriptome and metabolome analyses of cherry leaves spot disease caused by Alternaria alternata

Alternaria alternata is a necrotrophic fungal pathogen with a broad host range that causes widespread and devastating disease in sweet cherry (Prunus avium). We selected a resistant cultivar (RC) and a susceptible cultivar (SC) of cherry and used a combined physiological, transcriptomic, and metabolomic approach to investigate the molecular mechanisms underlying the plant's resistance to A. alternata, of which little is known. We found that A. alternata infection stimulated the outbreak of reactive oxygen species (ROS) in cherry. The responses of the antioxidant enzymes and chitinase to disease were observed earlier in the RC than in the SC. Moreover, cell wall defense ability was stronger in the RC. Differential genes and metabolites involved in defense responses and secondary metabolism were primarily enriched in the biosynthesis of phenylpropanoids, tropane, piperidine and pyridine alkaloids, flavonoids, amino acids, and α-linolenic acid. Reprogramming the phenylpropanoid pathway and the α-linolenic acid metabolic pathway led to lignin accumulation and early induction of jasmonic acid signaling, respectively, in the RC, which consequently enhanced antifungal and ROS scavenging activity. The RC contained a high level of coumarin, and in vitro tests showed that coumarin significantly inhibited A. alternata growth and development and had antifungal effect on cherry leaves. In addition, differentially expressed genes encoding transcription factors from the MYB, NAC, WRKY, ERF, and bHLH families were highly expressed, they could be the key responsive factor in the response of cherry to infection by A. alternata. Overall, this study provides molecular clues and a multifaceted understanding of the specific response of cherry to A. alternata.

Phenylalanine Promotes Biofilm Formation of Meyerozyma caribbica to Improve Biocontrol Efficacy against Jujube Black Spot Rot

During storage and transportation after harvest, the jujube fruit is susceptible to black spot rot, which is caused by Alternaria alternata. The present study aimed to evaluate the effectiveness of the yeast Meyerozyma caribbica in controlling A. alternata in postharvest jujube fruits, and to explore the biofilm formation mechanism. The results showed that M. caribbica treatment significantly reduced the A. alternata decay in jujube fruits. M. caribbica could rapidly colonize jujube fruit wounds, adhering tightly to hyphae of A. alternata, and accompanied by the production of extracellular secretions. In in vitro experiments, we identified that M. caribbica adhered to polystyrene plates, indicating a strong biofilm-forming ability. Furthermore, we demonstrated that M. caribbica can secrete phenylethanol, a quorum sensing molecule which can affect biofilm development. Phenylalanine (a precursor substance for phenylethanol synthesis) enhanced the secretion of phenylethanol and promoted the formation of M. caribbica biofilms. Meanwhile, phenylalanine enhanced the biological control performance of M. caribbica against jujube black spot rot. Our study provided new insights that enhance the biological control performance of antagonistic yeast.

DeLTa-Seq: direct-lysate targeted RNA-Seq from crude tissue lysate

BACKGROUND

Quantification of gene expression such as RNA-Seq is a popular approach to study various biological phenomena. Despite the development of RNA-Seq library preparation methods and sequencing platforms in the last decade, RNA extraction remains the most laborious and costly step in RNA-Seq of tissue samples of various organisms. Thus, it is still difficult to examine gene expression in thousands of samples.

RESULTS

Here, we developed Direct-RT buffer in which homogenization of tissue samples and direct-lysate reverse transcription can be conducted without RNA purification. The DTT concentration in Direct-RT buffer prevented RNA degradation but not RT in the lysates of several plant tissues, yeast, and zebrafish larvae. Direct reverse transcription on these lysates in Direct-RT buffer produced comparable amounts of cDNA to those synthesized from purified RNA. To maximize the advantage of the Direct-RT buffer, we integrated Direct-RT and targeted RNA-Seq to develop a cost-effective, high-throughput quantification method for the expressions of hundreds of genes: DeLTa-Seq (Direct-Lysate reverse transcription and Targeted RNA-Seq). The DeLTa-Seq method could drastically improve the efficiency and accuracy of gene expression analysis. DeLTa-Seq analysis of 1056 samples revealed the temperature-dependent effects of jasmonic acid and salicylic acid in Arabidopsis thaliana.

CONCLUSIONS

The DeLTa-Seq method can realize large-scale studies using thousands of animal, plant, and microorganism samples, such as chemical screening, field experiments, and studies focusing on individual variability. In addition, Direct-RT is also beneficial for gene expression analysis in small tissues from which it is difficult to purify enough RNA for the experiments.

Time Is of the Essence—Early Activation of the Mevalonate Pathway in Apple Challenged With Gray Mold Correlates With Reduced Susceptibility During Postharvest Storage

Apple is typically stored under low temperature and controlled atmospheric conditions to ensure a year round supply of high quality fruit for the consumer. During storage, losses in quality and quantity occur due to spoilage by postharvest pathogens. One important postharvest pathogen of apple is Botrytis cinerea. The fungus is a broad host necrotroph with a large arsenal of infection strategies able to infect over 1,400 different plant species. We studied the apple-B. cinerea interaction to get a better understanding of the defense response in apple. We conducted an RNAseq experiment in which the transcriptome of inoculated and non-inoculated (control and mock) apples was analyzed at 0, 1, 12, and 28 h post inoculation. Our results show extensive reprogramming of the apple’s transcriptome with about 28.9% of expressed genes exhibiting significant differential regulation in the inoculated samples. We demonstrate the transcriptional activation of pathogen-triggered immunity and a reprogramming of the fruit’s metabolism. We demonstrate a clear transcriptional activation of secondary metabolism and a correlation between the early transcriptional activation of the mevalonate pathway and reduced susceptibility, expressed as a reduction in resulting lesion diameters. This pathway produces the building blocks for terpenoids, a large class of compounds with diverging functions including defense. 1-MCP and hot water dip treatment are used to further evidence the key role of terpenoids in the defense and demonstrate that ethylene modulates this response.

Insights into the effect of human civilization on Malus evolution and domestication

The evolutionary history of the Malus genus has not been well studied. In the current study, we presented genetic evidence on the origin of the Malus genus based on genome sequencing of 297 Malus accessions, revealing the genetic relationship between wild species and cultivated apples. Our results demonstrated that North American and East Asian wild species are closer to the outgroup (pear) than Central Asian species, and hybrid species including natural (separated before the Pleistocene, about 2.5 Mya) and artificial hybrids (including ornamental trees and rootstocks) are between East and Central Asian wild species. Introgressions from M. sylvestris in cultivated apples appeared to be more extensive than those from M. sieversii, whose genetic background flowed westward across Eurasia and eastward to wild species including M. prunifolia, M. × asiatica, M. × micromalus, and M. × robust. Our results suggested that the loss of ancestral gene flow from M. sieversii in cultivated apples accompanied the movement of European traders around the world since the Age of Discovery. Natural SNP variations showed that cultivated apples had higher nucleotide diversity than wild species and more unique SNPs than other apple groups. An apple ERECTA-like gene that underwent selection during domestication on 15^th chromosome was identified as a likely major determinant of fruit length and diameter, and an NB-ARC domain-containing gene was found to strongly affect anthocyanin accumulation using a genome-wide association approach. Our results provide new insights into the origin and domestication of apples and will be useful in new breeding programmes and efforts to increase fruit crop productivity.

A tomato receptor-like cytoplasmic kinase, SlZRK1, acts as a negative regulator in wound-induced jasmonic acid accumulation and insect resistance

Jasmonates accumulate rapidly and act as key regulators in response to mechanical wounding, but few studies have linked receptor-like cytoplasmic kinases (RLCKs) to wound-induced jasmonic acid (JA) signaling cascades. Here, we identified a novel wounding-induced RLCK-XII-2 subfamily member (SlZRK1) in tomato (Solanum lycopersicum) that was closely related to Arabidopsis HOPZ-ETI-DEFICIENT 1 (ZED1)-related kinases 1 based on phylogenetic analysis. SlZRK1 was targeted to the plasma membrane of tobacco mesophyll protoplasts as determined by transient co-expression with the plasma membrane marker mCherry-H+-ATPase. Catalytic residue sequence analysis and an in vitro kinase assay indicated that SlZRK1 may act as a pseudokinase. To further analyse the function of SlZRK1, we developed two stable knock-out mutants by CRISPR/Cas9. Loss of SlZRK1 significantly altered the expression of genes involved in JA biosynthesis, salicylic acid biosynthesis, and ethylene response. Furthermore, after mechanical wounding treatment, slzrk1 mutants increased transcription of early wound-inducible genes involved in JA biosynthesis and signaling. In addition, JA accumulation after wounding and plant resistance to herbivorous insects also were enhanced. Our findings expand plant regulatory networks in the wound-induced JA production by adding RLCKs as a new component in the wound signal transduction pathway.

Advances of Metabolomics in Fungal Pathogen-Plant Interactions

Plant disease caused by fungus is one of the major threats to global food security, and understanding fungus-plant interactions is important for plant disease control. Research devoted to revealing the mechanisms of fungal pathogen-plant interactions has been conducted using genomics, transcriptomics, proteomics, and metabolomics. Metabolomics research based on mass spectrometric techniques is an important part of systems biology. In the past decade, the emerging field of metabolomics in plant pathogenic fungi has received wide attention. It not only provides a qualitative and quantitative approach for determining the pathogenesis of pathogenic fungi but also helps to elucidate the defense mechanisms of their host plants. This review focuses on the methods and progress of metabolomics research in fungal pathogen-plant interactions. In addition, the prospects and challenges of metabolomics research in plant pathogenic fungi and their hosts are addressed.

Defense Responses, Induced by p-Coumaric Acid and Methyl p-Coumarate, of Jujube ( Ziziphus jujuba Mill.) Fruit against Black Spot Rot Caused by Alternaria alternata

The esterified fraction of jujube ( Ziziphus jujuba Mill.) peel extract showed strong antifungal activity on Alternaria alternata. p-Coumaric acid (pCA) was found to be the most predominant individual phenolic acid that was correlated highly with the antifungal activity of the esterified fraction. Thus, effects of postharvest treatments with pCA and its simplest esterified derivative methyl p-coumarate (MeCA) against black spot rot on jujube fruit caused by A. alternata were investigated. pCA and MeCA strongly suppressed in vitro growth of the fungus and significantly reduced postharvest Alternaria rot on fresh jujubes. Biochemical and transcriptional analysis revealed that pCA and MeCA regulated the expression of some genes encoding antioxidant enzymes and their enzymatic activities, enhanced the phenylpropanoid pathway metabolism, and activated the expression of genes encoding pathogenesis-related proteins. These results suggested that, apart from its direct antifungal activity, pCA and MeCA induced defense responses in jujube fruit against postharvest Alternaria rot.