Trichoderma atroviride transcript levels during mycoparasitism
Ontology highlight
ABSTRACT:
ORGANISM(S): Trichoderma atroviride
PROVIDER: GSE23382 | GEO | 2011/07/01
SECONDARY ACCESSION(S): PRJNA133313
REPOSITORIES: GEO
Similar Datasets
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: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.
2011-07-01 | GSE23410 | GEO
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:Trichoderma atroviride is a fungus capable of establishing symbiotic relationships with plants, however, its main lifestyle is a saprophyte. Due to these characteristics, it must face a great quantity of microorganisms, and be able to compete for nutrients. T. atroviride is considered a necrotrophic mycoparasite and has developed the ability to kill other organisms and obtain nutrients from them. The object of this work is to explore the role of small RNAs in mycoparasitism. To this end, we obtained RNA-Seq libraries from the interactions of T. atroviride against Alternaria alternata and Rhizoctonia solani. The transcriptomes were obtained from three stages during mycoparasitsm: before contact (BC), contact (C), and after contact (AC).
2021-12-05 | GSE190033 | GEO
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 atroviride is a fungus capable of establishing symbiotic relationships with plants, however, its main lifestyle is a saprophyte. Due to these characteristics, it must face a great quantity of microorganisms, and be able to compete for nutrients. T. atroviride is considered a necrotrophic mycoparasite and has developed the ability to kill other organisms and obtain nutrients from them. The object of this work is to explore the role of small RNAs in mycoparasitism. To this end, we obtained small RNA-Seq libraries from the interactions of T. atroviride against Alternaria alternata. The libraries were obtained from three stages during mycoparasitsm: before contact (BC), contact (C), and after contact (AC).
2022-02-28 | GSE197448 | GEO
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.
2010-04-22 | E-GEOD-20516 | biostudies-arrayexpress
Project description:Trichoderma atroviride transcript levels during mycoparasitism
| PRJNA133313 | ENA
Project description:This SuperSeries is composed of the following subset Series: GSE19832: Trichoderma virens transcript levels during mycoparasitism GSE23382: Trichoderma atroviride transcript levels during mycoparasitism GSE23410: Trichoderma reesei transcript levels during mycoparasitism Refer to individual Series
2011-07-01 | E-GEOD-23438 | biostudies-arrayexpress