Early transcriptome response of Trichoderma virens to colonization of maize roots
Ontology highlight
ABSTRACT:
ORGANISM(S): Trichoderma virens
PROVIDER: GSE181269 | GEO | 2021/08/03
REPOSITORIES: GEO
Similar Datasets
Project description:To test the hypothesis that gene expression by the fungal partner in this beneficial interaction is modulated by the plant host, Trichoderma virens was co-cultured with maize or tomato in a hydroponic system allowing interaction with the roots. The transcriptomes for T. virens alone were compared with fungus-inoculated tomato or maize roots by hybridization on oligonucleotide microarrays Based on the relevant role of Trichoderma virens as a biological control agent this study provides a better knowledge of its crosstalk with plants in a host-specific manner. Trichoderma virens was co-cultured for three days with maize or tomato in a hydroponic system allowing interaction with the roots. 3 experiments were performed for each treatment, and compared to 5 experiments with T. virens grown under the same conditions without plants.
2014-12-19 | E-GEOD-64344 | biostudies-arrayexpress
Project description:To test the hypothesis that gene expression by the fungal partner in this beneficial interaction is modulated by the plant host, Trichoderma virens was co-cultured with maize or tomato in a hydroponic system allowing interaction with the roots. The transcriptomes for T. virens alone were compared with fungus-inoculated tomato or maize roots by hybridization on oligonucleotide microarrays Based on the relevant role of Trichoderma virens as a biological control agent this study provides a better knowledge of its crosstalk with plants in a host-specific manner.
2014-12-19 | GSE64344 | GEO
Project description:The interactions of crops with root-colonizing endophytic microorganisms are highly relevant to agriculture, because endophytes can modify plant resistance to pests and increase crop yields. We investigated the interactions between the host plant <i>Zea mays</i> and the endophytic fungus <i>Trichoderma virens</i> at 5 days postinoculation grown in a hydroponic system. Wild-type <i>T. virens</i> and two knockout mutants, with deletion of the genes <i>tv2og1</i> or <i>vir4</i> involved in specialized metabolism, were analyzed. Root colonization by the fungal mutants was lower than that by the wild type. All fungal genotypes suppressed root biomass. Metabolic fingerprinting of roots, mycelia, and fungal culture supernatants was performed using ultrahigh performance liquid chromatography coupled to diode array detection and quadrupole time-of-flight tandem mass spectrometry. The metabolic composition of <i>T. virens</i>-colonized roots differed profoundly from that of noncolonized roots, with the effects depending on the fungal genotype. In particular, the concentrations of several metabolites derived from the shikimate pathway, including an amino acid and several flavonoids, were modulated. The expression levels of some genes coding for enzymes involved in these pathways were affected if roots were colonized by the ∆<i>vir4</i> genotype of <i>T. virens</i>. Furthermore, mycelia and fungal culture supernatants of the different <i>T. virens</i> genotypes showed distinct metabolomes. Our study highlights the fact that colonization by endophytic <i>T. virens</i> leads to far-reaching metabolic changes, partly related to two fungal genes. Both metabolites produced by the fungus and plant metabolites modulated by the interaction probably contribute to these metabolic patterns. The metabolic changes in plant tissues may be interlinked with systemic endophyte effects often observed in later plant developmental stages.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
2021-07-08 | MTBLS1964 | MetaboLights
Project description:Early transcriptome response of Trichoderma virens to colonization of maize roots
| PRJNA751374 | ENA
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:Trichoderma virens Gv29-8 isolate:Trichoderma virens | breed:fungi | cultivar:Trichoderma virens Raw sequence reads
| PRJNA715022 | ENA
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: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:Trichoderma virens is a well-known mycoparasitic fungal symbiont that is valued for its biocontrol capabilities. T. virens initiates a symbiotic relationship with a plant host through the colonization of its roots. To achieve colonization, the fungus must communicate with the host and evade its innate defenses. In this study, we explored the genes involved with the host communication and colonization process through transcriptomic profiling of the wild-type fungus and selected deletion mutants as they colonized maize roots. Transcriptome profiles of the T. virens colonization of maize roots over time revealed that 24 h post inoculation appeared to be a key time for plant-microbe communication, with many key gene categories, including signal transduction mechanisms and carbohydrate transport and metabolism, peaking in expression at this early colonization time point. The transcriptomic profiles of Sm1 and Sir1 deletion mutants in the presence of plants demonstrated that Sir1, rather than Sm1, appears to be the key regulator of the fungal response to maize, with 64% more unique differentially expressed genes compared to Sm1. Additionally, we developed a novel algorithm utilizing gene clustering and coexpression network analyses to select potential colonization-related gene targets for characterization. About 40% of the genes identified by the algorithm would have been missed using previous methods for selecting gene targets.
| S-EPMC10512331 | biostudies-literature
Project description:Trichoderma virens transcript levels during mycoparasitism
| PRJNA133071 | ENA