Trichoderma sp. transcript levels during mycoparasitism
Ontology highlight
ABSTRACT:
ORGANISM(S): Trichoderma atroviride
SUBMITTER: Stéphane LE CROM
PROVIDER: E-GEOD-23438 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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:To investigate the potential role in mycoparasitism, microarrays were used to examine T. reesei 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. 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).
2011-07-01 | E-GEOD-23410 | biostudies-arrayexpress
Project description:To investigate the potential role in mycoparasitism, microarrays were used to examine T. atroviride 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. Two biological poolw 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).
2011-07-01 | E-GEOD-23382 | biostudies-arrayexpress
Project description:Mycoparasitism is a key feature of Trichoderma biocontrol agents. Recent studies of intracellular signal transduction pathways of the potent mycoparasite Trichoderma atroviride revealed the involvement of Tmk1, a mitogen-activated protein kinase, in triggering the mycoparasitic response. We previously showed that mutants missing Tmk1 exhibit reduced mycoparasitic activity against several plant pathogenic fungi. In this study we identified the most robustly regulated targets governed by Tmk1 during mycoparasitism by whole transcriptome gene expression profiling using a custom microarray.
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2011-12-08 | E-GEOD-27471 | biostudies-arrayexpress
Project description:A self-designed Trichoderma high density oligonuclotide (HDO) microarray (Roche-NimbleGen, Inc., Madison, WI, USA) was constructed in a similar way than a previous Trichoderma HDO microarray (Samolski et al., 2009). The microarray was composed of 392,779 60-mer probes designed against 13,443 EST-derived transcripts (Trichochip-1) and the genomes of T. atroviride (11,100 genes) and T. virens (11,643 genes). The Trichochip-1 ESTs were obtained from 28 cDNA libraries from eight different species (representing the biodiversity of this genus: T. harzianum, T. atroviride, T. asperellum, T. viride, T. longibrachiatum, T. virens, T. stromaticum and T. aggresivum) under a wide range of growth conditions, including biocontrol-related conditions and different nutritional situations (VizcaÃno et al., 2006). The Trichochip1 EST database was generated in the TrichoEST project funded by the EU (QLK3-CT-2002-02032) T. atroviride P1 mycelium grown (approximately for 24h) at 25ºC on a cellophane sheet on PDA (Difco) plates before contact (at a distance of 5 mm) a R. solani colony grown under identical conditions in the same plate was compared with T. atroviride P1 mycelium after contact (5 mm) the above R. solani colony (mycoparasitic interaction). RNAs from both conditions were extracted and the corresponding cDNAs were use to hybridize by triplicate the Trichoderma HDO microarray.
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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.
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