Transcriptome Reprogramming of Tomato Orchestrate the Hormone Signaling Network of Systemic Resistance Induced by Chaetomium globosum

Foliar infections by Botrytis cinerea modulate the tomato root volatilome and microbiome

The fungal pathogen Botrytis cinerea causes significant damage to aboveground plant parts, but its impact on root chemistry and microbiome composition is less understood. This study investigated how B. cinerea foliar infection influences the root volatilome and microbiome of two tomato genotypes: wild Solanum pimpinellifolium and domesticated Solanum lycopersicum var. Moneymaker. In the absence of infection, wild tomato roots emitted higher levels of monoterpenes such as α-pinene and terpinene compared to domesticated tomato roots. The fungal infection induced elevated levels of benzyl alcohol and benzofuran in the root headspace and/or rhizosphere of both genotypes, alongside genotype-specific changes. Multivariate analyses revealed that B. cinerea significantly altered bacterial and fungal community compositions in the rhizosphere and rhizoplane, with stronger bacterial community shifts in the rhizoplane. Taxa depletion and enrichment were observed, particularly among Proteobacteria and Ascomycota. Mantel tests showed significant correlations between rhizoplane bacterial community compositions and root-associated volatilome. Notably, enriched bacterial taxa such as Pelomonas and Comamonadaceae positively correlated with benzyl alcohol and benzofuran levels in the root volatilome. These findings demonstrate that B. cinerea foliar infection might induce profound changes in root-associated volatilome and microbiome composition, highlighting its systemic effects on plant root chemistry and microbiome composition.

Investigating the action model of the resistance enhancement induced by bacterial volatile organic compounds against Botrytis cinerea in tomato fruit

Introduction

Inducing natural resistance against pathogen infection in postharvest tomatoes is a sustainable strategy for reducing postharvest losses. The action model underlying the resistance enhancement of tomatoes induced by bacterial volatile organic compounds (VOCs) against Botrytis cinerea, however, have not been explored.

Methods

In this study, RNA-seq, metabolomics and physiological analysis were used to evaluate global change of defense response induced by VOCs in tomatoes.

Results

The application of VOCs inhibited the damage to tomatoes caused by B. cinerea. VOCs treatment had remarkable beneficial effects on the activities of the main defence-related enzymes, including chitinases, glucanases, peroxidases, ascorbate peroxidases, polyphenol oxidases, and phenylalanine ammonia-lyases. The expression of response genes involved in salicylic acid and jasmonic acid biosynthesis and signalling pathways was enhanced upon VOCs treatment. Metabolomics data demonstrated that VOC treatment triggered the accumulation of phenolic acids, including substrates in phenolic acid biosynthesis pathways, hydroxycinnamic acid, hydroxybenzoic acid, and their derivatives. Transcriptomics analysis and qRT-PCR verification revealed that VOCs treatment significantly upregulates the expression of core genes related to phenolic acid biosynthesis, specifically in shikimate pathway (SlDAHPS, SlSDH, SlCS, and SlADT3) and phenylalanine metabolic pathway (SlPAL, Sl4CL, SlBAHD1, SlCYP98A2 and SlCAP84A1).

Discussion

Results confirmed that VOCs enhanced tomatoes postharvest resistance against B. cinerea by regulating defence enzyme activity, SA/JA signalling, and phenolic acid biosynthesis pathway. This study provides new insights into the mechanisms by which VOCs fumigation manages postharvest grey mould in tomatoes.

Expression analysis of defense signaling marker genes in Capsicum annuum in response to phytohormones elicitation

BACKGROUND

To tolerate biotic stress, plants employ phytohormones such as jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) to regulate the immune response against different pathogens. Phytohormone-responsive genes, known as "Defense signaling marker genes," are used to evaluate plant disease resistance during pathogen infection. Most information on these marker genes derives from studies on the model plant Arabidopsis thaliana. The present study was aimed analyze the effect of hormonal elicitation at different concentrations at 24 h pos-treatment in the transcript level of 8 traditional genes selected for molecular studies plant-pathogen interactions in Capsicum.

METHODS AND RESULTS

Chemical treatment was achieved by spraying leaves of in vitro seedlings C. annuum L. with 0.1 mM, 1 mM or 2.5 mM ET; 1 mM, 2.5 mM, or 5 mM SA; 2.5 mM BABA; or 0.150 mM MeJA. Twenty-four hours after treatments were applied molecular analyses were carried out using qPCR to investigate the expression. Results revealed that 1 mM of ET or 0.15 mM of MeJA activated the expression CaPR1 (18--11.64-fold change), CaLOX2 (13.80-fold), CaAP2/ERF06 (22- 5.3- fold change), and CaPDF1.2 (2.3-1.5- fold). While, 5 mM of SA present effect of negative regulation on the expression in most of these genes.

CONCLUSIONS

Our results show that the expression profile induced by phytohormones in CaPR1 are particular in C. annuum, because were significantly induced for ET/MeJA, and dow-regulation with SA Contrary to Arabidopsis. Although, on both plants it is observed the cross talk between JA/ET and SA mediated signal pathways for the regulation of this gene.

Transcriptional Response of Wolfberry to Infestation with the Endophytic Fusarium nematophilum Strain NQ8GII4

Fusarium nematophilum NQ8GII4 is an endophytic fungus isolated from the root of healthy wolfberry (Lycium barbarum). Previous studies have reported that NQ8GII4 could dwell in wolfberry roots and enhance the defense responses in wolfberry against root rot, which is caused by F. oxysporum. To further elucidate the molecular mechanism of wolfberry disease resistance induced by NQ8GII4, in the present study, we adopted RNA sequencing analysis to profile the transcriptome of wolfberry response to NQ8GII4 infestation over a time course of 3 and 7 days postinoculation. Gene ontology enrichment analysis revealed that differentially expressed genes (DEGs) were enriched in biological regulation, response to stimulus, signaling, detoxification, immune system process, transporter activity, electron carrier activity, transcription factor activity, nucleic acid binding transcription factor, and antioxidant activity. Through Kyoto Encyclopedia of Genes and Genomes analysis, it was found that many of these DEGs were enriched in pathways related to plant-pathogen interactions, hormone signal transduction, and the phenylpropanoid biosynthesis pathway in wolfberry. This result suggested that innate immunity, phytohormone signaling, and numerous phenylpropanoid compounds comprise a complex defense network in wolfberry. Chloroplast 50S ribosomal proteins were consistently located at the core position of the response in wolfberry following infestation with NQ8GII4 analyzed by the protein-protein interaction network. This study elucidated the molecular mechanism underlying the interaction between NQ8GII4 and wolfberry, clarified the wolfberry immune response network to endophytic fungi infestation, identified candidate resistance genes in wolfberry, and provided a fundamental date for subsequent work.

Structural diversity and stress regulation of the plant immunity-associated CALMODULIN-BINDING PROTEIN 60 (CBP60) family of transcription factors in Solanum lycopersicum (tomato)

Cellular signaling generates calcium (Ca2+) ions, which are ubiquitous secondary messengers decoded by calcium-dependent protein kinases, calcineurins, calreticulin, calmodulins (CAMs), and CAM-binding proteins. Previous studies in the model plant Arabidopsis thaliana have shown the critical roles of the CAM-BINDING PROTEIN 60 (CBP60) protein family in plant growth, stress responses, and immunity. Certain CBP60 factors can regulate plant immune responses, like pattern-triggered immunity, effector-triggered immunity, and synthesis of major plant immune-activating metabolites salicylic acid (SA) and N-hydroxypipecolic acid (NHP). Although homologous CBP60 sequences have been identified in the plant kingdom, their function and regulation in most species remain unclear. In this paper, we specifically characterized 11 members of the CBP60 family in the agriculturally important crop tomato (Solanum lycopersicum). Protein sequence analyses revealed that three CBP60 homologs have the closest amino acid identity to Arabidopsis CBP60g and SARD1, master transcription factors involved in plant immunity. Strikingly, AlphaFold deep learning-assisted prediction of protein structures highlighted close structural similarity between these tomato and Arabidopsis CBP60 homologs. Conserved domain analyses revealed that they possess CAM-binding domains and DNA-binding domains, reflecting their potential involvement in linking Ca2+ signaling and transcriptional regulation in tomato plants. In terms of their gene expression profiles under biotic (Pseudomonas syringae pv. tomato DC3000 pathogen infection) and/or abiotic stress (warming temperatures), five tomato CBP60 genes were pathogen-responsive and temperature-sensitive, reminiscent of Arabidopsis CBP60g and SARD1. Overall, we present a genome-wide identification of the CBP60 gene/protein family in tomato plants, and we provide evidence on their regulation and potential function as Ca2+-sensing transcriptional regulators.

Physiological and transcriptome profiling revealed defense networks during Cladosporium fulvum and tomato interaction at the early stage

Tomato leaf mold caused by Cladosporium fulvum (C. fulvum) is a serious fungal disease which results in huge yield losses in tomato cultivation worldwide. In our study, we discovered that ROS (reactive oxygen species) burst was triggered by C. fulvum treatment in tomato leaves. RNA-sequencing was used to identify differentially expressed genes (DEGs) induced by C. fulvum inoculation at the early stage of invasion in susceptible tomato plants. Gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to annotate functions of DEGs in tomato plants. Based on our comparative analysis, DEGs related to plant-pathogen interaction pathway, plant hormone signal transduction pathway and the plant phenylpropanoid pathway were further analyzed. Our results discovered that a number of core defense genes against fungal invasion were induced and plant hormone signal transduction pathways were impacted by C. fulvum inoculation. Further, our results showed that SA (salicylic acid) and ABA (abscisic acid) contents were accumulated while JA (jasmonic acid) content decreased after C. fulvum inoculation in comparison with control, and quantitative real-time PCR to detect the relative expression of genes involved in SA, ABA and JA signaling pathway further confirmed our results. Together, results will contribute to understanding the mechanisms of C. fulvum and tomato interaction in future.

Temporal transcriptome of tomato elucidates the signaling pathways of induced systemic resistance and systemic acquired resistance activated by Chaetomium globosum

C. globosum is an endophytic fungus, which is recorded effective against several fungal and bacterial diseases in plants. The exclusively induce defense as mechanism of biocontrol for C. globosum against phyto-pathogens is reported. Our pervious study states the effectiveness of induced defense by C. globosum (Cg), in tomato against Alternaria solani. In this study the temporal transcriptome analysis of tomato plants after treatment with C. globosum was performed for time points at 0 hpCi, 12 hpCi, 24 hpCi and 96 phCi. The temporal expression analysis of genes belonging to defense signaling pathways indicates the maximum expression of genes at 12 h post Cg inoculation. The sequential progression in JA signaling pathway is marked by upregulation of downstream genes (Solyc10g011660, Solyc01g005440) of JA signaling at 24 hpCi and continued to express at same level upto 96 hpCi. However, the NPR1 (Solyc07g040690), the key regulator of SA signaling is activated at 12 h and repressed in later stages. The sequential expression of phenylpropanoid pathway genes (Solyc09g007920, Solyc12g011330, Solyc05g047530) marks the activation of pathway with course of time after Cg treatment that results in lignin formation. The plant defense signaling progresses in sequential manner with time course after Cg treatment. The results revealed the involvement of signaling pathways of ISR and SAR in systemic resistance induced by Cg in tomato, but with temporal variation.

Comprehensive Biochemical, Physiological, and Transcriptomic Analyses Provide Insights Into Floral Bud Dormancy in Rhododendron delavayi Franch

Due to a scarcity of relevant data, the ornamental woody flower Rhododendron delavayi Franch. is examined in the current study for its low temperature-induced floral bud dormancy (late October-end December) aspect. This study used transcriptome data profiling and co-expression network analyses to identify the interplay between endogenous hormones and bud dormancy phases such as pre-dormancy, para-dormancy, endo-dormancy, eco-dormancy, and dormancy release. The biochemical and physiological assays revealed the significance of the abundance of phytohormones (abscisic acid, auxin, zeatin, and gibberellins), carbohydrate metabolism, oxidative species, and proteins (soluble proteins, proline, and malondialdehyde) in the regulatory mechanism of floral bud dormancy. The transcriptome sequencing generated 65,531 transcripts, out of which 504, 514, 307, and 240 expressed transcripts were mapped uniquely to pre-, para-, endo-, and eco-phases of dormancy, showing their roles in the stimulation of dormancy. The transcripts related to LEA29, PGM, SAUR family, RPL9e, ATRX, FLOWERING LOCUS T, SERK1, ABFs, ASR2, and GID1 were identified as potential structural genes involved in floral bud dormancy. The transcription factors, including Zinc fingers, CAD, MADS-box family, MYB, and MYC2, revealed their potential regulatory roles concerning floral bud dormancy. The gene co-expression analysis highlighted essential hub genes involved in cold stress adaptations encoding proteins, viz, SERPIN, HMA, PMEI, LEA_2, TRX, PSBT, and AMAT. We exposed the connection among low temperature-induced dormancy in floral buds, differentially expressed genes, and hub genes via strict screening steps to escalate the confidence in selected genes as being truly putative in the pathways regulating bud dormancy mechanism. The identified candidate genes may prove worthy of further in-depth studies on molecular mechanisms involved in floral bud dormancy of Rhododendron species.

Biostimulant Effects of Chaetomium globosum and Minimedusa polyspora Culture Filtrates on Cichorium intybus Plant: Growth Performance and Metabolomic Traits

In this study, we investigated the biostimulant effect of fungal culture filtrates obtained from Chaetomium globosum and Minimedusa polyspora on growth performance and metabolomic traits of chicory (Cichorium intybus) plants. For the first time, we showed that M. polyspora culture filtrate exerts a direct plant growth-promoting effect through an increase of biomass, both in shoots and roots, and of the leaf area. Conversely, no significant effect on morphological traits and biomass yield was observed in C. intybus plants treated with C. globosum culture filtrate. Based on ¹H-NMR metabolomics data, differential metabolites and their related metabolic pathways were highlighted. The treatment with C. globosum and M. polyspora culture filtrates stimulated a common response in C. intybus roots involving the synthesis of 3-OH-butyrate through the decrease in the synthesis of fatty acids and sterols, as a mechanism balancing the NADPH/NADP⁺ ratio. The fungal culture filtrates differently triggered the phenylpropanoid pathway in C. intybus plants: C. globosum culture filtrate increased phenylalanine and chicoric acid in the roots, whereas M. polyspora culture filtrate stimulated an increase of 4-OH-benzoate. Chicoric acid, whose biosynthetic pathway in the chicory plant is putative and still not well known, is a very promising natural compound playing an important role in plant defense. On the contrary, benzoic acids serve as precursors for a wide variety of essential compounds playing crucial roles in plant fitness and defense response activation. To the best of our knowledge, this is the first study that shows the biostimulant effect of C. globosum and M. polyspora culture filtrates on C. intybus growth and metabolome, increasing the knowledge on fungal bioresources for the development of biostimulants.