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Expression array for Trichoderma atroviride in mycoparasitic interaction with Rhizoctonia solani

ABSTRACT: 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 (Vizcaíno et al., 2006). The Trichochip1 EST database was generated in the TrichoEST project funded by the EU (QLK3-CT-2002-02032)

ORGANISM(S): Trichoderma atroviride Trichoderma virens Rhizoctonia solani

PROVIDER: GSE20516 | GEO | 2010/02/25

SECONDARY ACCESSION(S): PRJNA125239

REPOSITORIES: GEO

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Expression array for Trichoderma atroviride in mycoparasitic interaction with Rhizoctonia solani

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 25ÂºC 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

Expression array for Trichoderma harzianum T34 and nox1 overexpressed transformant Tnox5 strains in dual culture with Pythium ultimum

2010-10-13 | GSE24630 | GEO

Comparative study of transcriptomes from four Trichoderma strains gene expression in early interaction with tomato plants

2012-02-27 | GSE29171 | GEO

Expression array for Trichoderma harzianum T34 and nox1 overexpressed transformant Tnox5 strains in dual culture with Pythium ultimum

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). Confrontations were carried out between the T. harzianum T34 or nox1 overexpressed transformant Tnox5 and P. ultimum. Agar plugs cut from the growing edge of a 4-day colony of Trichoderma and Pythium were placed 2 cm from the border on the opposite side of the same petri plates containing PDA covered with sterile cellophane sheets. Dual cultures were allowed to grow at 25 ÂºC and mycelia were collected from the interaction zone in confrontations between P. ultimum and T. harzianum T34 or Tnox5 strains. Seven PDA plates were used for each condition considered and RNAs were extracted and the corresponding cDNAs were use to hybridize by triplicate the Trichoderma HDO microarray.

2010-10-13 | E-GEOD-24630 | biostudies-arrayexpress

Comparative study of transcriptomes from four Trichoderma strains gene expression in early interaction with tomato plants

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 14,081 EST-derived transcripts (Trichochip-1) and the genomes of T. reesei (9,129 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 (VizcaM-CM--no et al., 2006). This HDO microarray was used to analyze Trichoderma spp. transcriptomes after 20 h incubation in the presence of tomato plants. The Trichochip1 EST database was generated in the TrichoEST project funded by the EU (QLK3-CT-2002-02032). Eight samples were analyzed as follows: Strain T. reesei T6 grown in the presence or not of tomato plants, strain T. hamatum T7 grown in the presence or not of tomato plants, strain T. harzianum T34 grown in the presence or not of tomato plants and strain T. virens T87 grown in the presence or not of tomato plants. Three replicates for each samples were performed.

2012-02-27 | E-GEOD-29171 | biostudies-arrayexpress

Transcriptomic analysis of the biocontrol fungus Trichoderma atroviride overgrowing Verticilluim dahliae provides the identification of mycoparasitic candidate genes aganinst this plant pathogenic fungus

Project description:A Trichoderma microarrays composed of 385,000 probes, designed against the genomes of Trichoderma reesei (= Hypocrea jecorina), ID: 431241 (9,129 genes) + Trichoderma virens (= Hypocrea virens), ID: 413071 (11,643 genes) + Trichoderma atroviride (= Hypocrea atroviridis) ID: 197014A (11,643 genes), was constructed (Roche-NimbleGen, Inc., Madison, WI, USA). Probes contained entere transcript sequence. This microarray was used to analyze the transcriptomic changes of T. atroviride IMI 352941 (T11) in three conditions: T11 growing alone, T11 growing at ca 5 mm of V. dahliae V-138I and T11 overgrowing V-138I.

2018-03-09 | GSE66835 | GEO

Trichoderma sp. transcript levels during mycoparasitism

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

Gene expression response of the mycoparasite Trichoderma atroviride to confrontation with the host Rhizoctonia solani in the wild-type and tmk1 gene deletion mutants

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.

2024-04-24 | E-MTAB-13202 | biostudies-arrayexpress

Trichoderma atroviride

Project description:Trichoderma atroviride

| PRJEB33925 | ENA

Trichoderma atroviride small RNA1 targets the Arabidopsis PRIM2 gene to establish a mutualistic relationship

Project description:This study investigates the multifaceted defense mechanisms of plants in response to beneficial fungi Trichoderma atroviride. The researchers focus on a small RNA, Ta_sRNA1, produced by T. atroviride during its interaction with Arabidopsis thaliana.

2024-03-29 | GSE254275 | GEO

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