Identify gene networks in maize and beneficial fungus Trichoderma virens that result in induced systemic resistance (ISR)
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ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE137826 | GEO | 2019/09/24
REPOSITORIES: GEO
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Project description:Combating the action of plant pathogenic microorganisms by antagonistic or mycoparasitic fungi has been announced as an attractive biological alternative to the use of chemical fungicides since more than 20 years, and gains additional importance in current trends to environmentally friendly agriculture. Taxa of the fungal genus Hypocrea/Trichoderma (Ascomycota, Hypocreales, Hypocreaceae) contain prominent examples of such biocontrol agents, because they not only antagonize plant-pathogenic fungi, but are also often rhizosphere competent and can enhance plant growth. Identification of the primary factors that regulate the mycoparasitic behaviour and metabolic activities related to it will therefore allow the full ecological significance of this trait to be explored. We performed the analysis of the genome sequence from two mycoparasitic and rhizosphere competent Trichoderma spp. – T. atroviride and T. virens – and compare it to that of the saprophyte T. reesei. The predicted gene inventory of the T. atroviride and T.virens genome, therefore, points to previously unknown mechanisms operating during biocontrol of plant pathogens. The availability of these genomes provides a unique opportunity to develop a deeper understanding of the processes fundamental to mycoparasitism and its application for the breeding of improved biocontrol strains for plant protection. To investigate the potential role in mycoparasitism, microarrays were used to examine T. virens transcript levels when confronted with a potential prey (the plant pathogen Rhizoctonia solani) before contact, during first physical contact and during overgrowth of the host. The study presented here is the result of this analysis.
2011-07-01 | GSE19832 | GEO
Project description:In this experiment we measured the transcriptional response of tomato plants (cv “Money maker”) when attacked belowground by the nematode M. inognita and, subsequently, aboveground by different (and common for this crop) biotic agents. Three weeks-old plants were exposed to nematodes for 5 days. At the fifth day the terminal leaflet of one of the first two true leaves was infected with the Cauliflower Mosaic Virus, or with the pathogen, or with the potato aphid Macrosiphum euphorbiae, or with the CMV-infected M. euphorbiae. For each belowground/aboveground combination treatment a set of control plants that received only the aboveground treatment was prepared. The infected leaflets of 5 biological replicates, each consisting of 1 plant, were collected 1, 2, 3, 4, 5 and 6 days after the onset of the aboveground treatment and flash frozen in liquid nitrogen. A different set of plants was used for every time point. Corresponding leaves from plants that did not receive any aboveground treatment (control) were selected and sampled as described above. Three biological replicates were selected among the five for RNA isolation. Total RNA was sent for sequencing to BGI Hong Kong.
2023-07-30 | E-MTAB-11956 | biostudies-arrayexpress
Project description:Combating the action of plant pathogenic microorganisms by antagonistic or mycoparasitic fungi has been announced as an attractive biological alternative to the use of chemical fungicides since more than 20 years, and gains additional importance in current trends to environmentally friendly agriculture. Taxa of the fungal genus Hypocrea/Trichoderma (Ascomycota, Hypocreales, Hypocreaceae) contain prominent examples of such biocontrol agents, because they not only antagonize plant-pathogenic fungi, but are also often rhizosphere competent and can enhance plant growth. Identification of the primary factors that regulate the mycoparasitic behaviour and metabolic activities related to it will therefore allow the full ecological significance of this trait to be explored. We performed the analysis of the genome sequence from two mycoparasitic and rhizosphere competent Trichoderma spp. – T. atroviride and T. virens – and compare it to that of the saprophyte T. reesei. The predicted gene inventory of the T. atroviride and T.virens genome, therefore, points to previously unknown mechanisms operating during biocontrol of plant pathogens. The availability of these genomes provides a unique opportunity to develop a deeper understanding of the processes fundamental to mycoparasitism and its application for the breeding of improved biocontrol strains for plant protection. To investigate the potential role in mycoparasitism, microarrays were used to examine T. virens transcript levels when confronted with a potential prey (the plant pathogen Rhizoctonia solani) before contact, during first physical contact and during overgrowth of the host. The study presented here is the result of this analysis. Two biological pools by condition against a common reference control each sample hybridized in dye switch. On the two biological replicates we apply on the pretreated results the linear modeling approach implemented by lmFit and the empirical Bayes statistics implemented by eBayes from the limma R package (Smyth 2004). For mycoparasitism confrontation assays T. virens was grown on potato dextrose agar plates (BD Dicfo, Franklin Lakes, NJ, USA), covered with cellophane, in constant light at 25°C and harvested when the mycelia were ca. 5 mm apart (before contact), at contact of the mycelia and after T. virens had overgrown the host fungus Rhizoctonia solani by ca. 5 mm (after contact). As control T. virens was confronted with itself and harvested at contact. Peripheral hyphal zones from each confrontation stage were harvested and shock frozen in liquid nitrogen. Mycelia were ground to a fine powder under liquid nitrogen and total RNA was isolated using the guanidinium thiocyanate method (Sambrook, 2001).
2011-07-01 | E-GEOD-19832 | biostudies-arrayexpress
Project description:Trichoderma spp. are filamentous fungi that colonize plant roots conferring beneficial effects to plants, indirectly through the induction of their defense systems or directly through the suppression of phytopathogens in the rhizosphere. Transcriptomic analyses of Trichoderma emerged as a powerful method for identifying the molecular events underlying the establishment of this beneficial relationship. Here, we focus on the transcriptomic response of Trichoderma virens during its interaction with Arabidopsis seedlings. The main response of T. virens to co-cultivation with Arabidopsis was the repression of gene expression. The biological processes of transport and metabolism of carbohydrates were downregulated, including a set of cell-wall-degrading enzymes putatively relevant for root-colonization. Repression of such genes reached their basal levels at later times of the interaction when genes belonging to the biological process of copper ion transport were induced, a necessary process providing copper as a cofactor for cell-wall degrading enzymes with auxiliary activities (AAs) class. RNA-Seq analysis showed the induction of a member of the SNF2 family of chromatin remodelers/helicase-related proteins, which was named IPA-1 (Increased Protection of Arabidopsis-1). Sequence analyses of IPA-1 showed as its closest relatives members of the Rad5/Rad16- and SNF2-subfamilies; however, it grouped into a different clade. Although deletion of ipa-1 in T. virens did not affect its growth, the antibiosis of Δipa-1 culture filtrates showed a diminished effect against Rhizoctonia solani but remained unaltered against Botrytis cinerea. Triggering of the plant defense genes in plants treated with Δipa-1 was higher, showing enhanced resistance against Pseudomonas syringae but not against B. cinerea as compared to wild type.
2019-01-18 | GSE125225 | GEO
Project description:Identify gene networks in maize and beneficial fungus Trichoderma virens that result in induced systemic resistance (ISR)
| PRJNA573599 | ENA
Project description:Trichoderma virens (synonym, Gliocladium virens), a deuteromycete fungus, suppresses soilborne plant diseases caused by a number of fungi and is used as a biocontrol agent. Several traits that may contribute to the antagonistic interactions of T. virens with disease-causing fungi involve the production of peptide metabolites (e.g., the antibiotic gliotoxin and siderophores used for iron acquisition). We cloned a 5,056-bp partial cDNA encoding a putative peptide synthetase (Psy1) from T. virens using conserved motifs found within the adenylate domain of peptide synthetases. Sequence similarities with conserved motifs of the adenylation domain, acyl transfer, and two condensation domains support identification of the Psy1 gene as a gene that encodes a peptide synthetase. Disruption of the native Psy1 gene through gene replacement was used to identify the function of this gene. Psy1 disruptants produced normal amounts of gliotoxin but grew poorly under low-iron conditions, suggesting that Psy1 plays a role in siderophore production. Psy1 disruptants cannot produce the major T. virens siderophore dimerum acid, a dipetide of acylated N(delta)-hydroxyornithine. Biocontrol activity against damping-off diseases caused by Pythium ultimum and Rhizoctonia solani was not reduced by the Psy1 disruption, suggesting that iron competition through dimerum acid production does not contribute significantly to disease suppression activity under the conditions used.
| S-EPMC93271 | biostudies-literature
Project description:Trichoderma is a filamentous fungus that is widely distributed in nature. As a biological control agent of agricultural pests, Trichoderma species have been widely studied in recent years. This study aimed to understand the inhibitory mechanism of Trichoderma virens ZT05 on Rhizoctonia solani through the side-by-side culture of T. virens ZT05 and R. solani. To this end, we investigated the effect of volatile and nonvolatile metabolites of T. virens ZT05 on the mycelium growth and enzyme activity of R. solani and analyzed transcriptome data collected from side-by-side culture. T. virens ZT05 has a significant antagonistic effect against R. solani. The mycelium of T. virens ZT05 spirally wraps around and penetrates the mycelium of R. solani and inhibits the growth of R. solani. The volatile and nonvolatile metabolites of T. virens ZT05 have significant inhibitory effects on the growth of R. solani. The nonvolatile metabolites of T. virens ZT05 significantly affect the mycelium proteins of R. solani, including catalase (CAT), superoxide dismutase (SOD), peroxidase (POD), selenium-dependent glutathione peroxidase (GSH-Px), soluble proteins, and malondialdehyde (MDA). Twenty genes associated with hyperparasitism, including extracellular proteases, oligopeptide transporters, G-protein coupled receptors (GPCRs), chitinases, glucanases, and proteases were found to be upregulated during the antagonistic process between T. virens ZT05 and R. solani. Thirty genes related to antibiosis function, including tetracycline resistance proteins, reductases, the heat shock response, the oxidative stress response, ATP-binding cassette (ABC) efflux transporters, and multidrug resistance transporters, were found to be upregulated during the side-by-side culture of T. virens ZT05 and R. solani. T. virens ZT05 has a significant inhibitory effect on R. solani, and its mechanism of action is associated with hyperparasitism and antibiosis.
| S-EPMC7412022 | biostudies-literature
Project description:Trichoderma virens transcript levels during mycoparasitism
| PRJNA133071 | ENA
Project description:Host-specific transcriptomic pattern of Trichoderma virens during interaction with maize or tomato roots
| PRJNA270774 | ENA
Project description:Filamentous fungus (anamorph: Trichoderma virens; teleomorph: Hypocrea virens) that is a mycoparasite
| PRJNA19985 | ENA