Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

47 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression analysis of monokaryotic and dikaryotic mycelia from Coprinopsis cinerea

ABSTRACT: Sexual reproduction is an ancient trait that evolved shortly after the appearance of the first eukaryotic cell. In order to identify the set of genes differentially expressed in monokaryotic and dikaryotic mycelia, the poly(A)-positive transcriptomes of C. cinerea Okayama7 and C. cinerea A43mutB43mut were sequenced.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Coprinopsis cinerea

SUBMITTER: David Plaza

PROVIDER: E-MTAB-1993 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Coprinopsis cinerea transcriptome in response to hyphal damage, nematode predation or bacterial co-cultivation

Project description:We have recently shown that the coprophilous model mushroom Coprinopsis cinerea transcribes a broad array of genes encoding defense proteins in the vegetative mycelium and fruiting bodies that target bacterial competitors and animal predators challenging the respective tissues of this fungus. In addition, we have demonstrated in previous work that two nematotoxic defense proteins from Coprinopsis, CGL1 and CGL2, were induced in vegetative mycelium challenged with the predatory nematode Aphelenchus avenae; however, the specificity and broadness of this response remained unclear. In order to resolve these issues, we sequenced the poly(A)-positive transcriptome of vegetative mycelium of C. cinerea confronted with nematode predation, hyphal mechanical damage or bacterial co-culture.

2015-09-01 | E-MTAB-2763 | biostudies-arrayexpress

VIB1, a link between glucose signaling and carbon catabolite repression, is essential for plant cell wall degradation by Neurospora crassa

Project description:Purpose: To explore the function of VIB1 in regulating cellulase production in Neurospora crassa. Method: mRNA from vib-1 mutants were collected after a culture shift from sucrose to Avicel (crystaline cellulose) or carbon-free media. Expression profiles of vib-1 mutants were compared with published profiles of wild type created under the same conditions. Results: We found that many genes that specifically upregulated in wild type upon exposure to Avicel were expressed at low levels in M-bM-^HM-^Fvib-1 and many other genes involved in metabolism and energy were expressed at high levels compared to wild type. Conclusions: Our study shows that VIB1 is required for suppression of glucose response and carbon catabolite repression to allow proper expression of clr-2 and subsequent cellulase production in response to cellulosic induction. Biological triplicates of liquid culture N. crassa were harvested at 4 hours after a switch from sucrose media to media of interest. Global mRNA abundances were measured by sequencing on the Illumina Genome Analyzer Iix and HiSeq2000 platforms.

2014-07-08 | E-GEOD-52316 | biostudies-arrayexpress

Modifications of fungal membrane proteins profile under pathogenicity induction: a proteomic analysis of Botrytis cinerea membranome.

Project description:Botrytis cinerea is a model phytopathogenic fungus that infects more than 200 different relevant crops, thus being classified among the top ten fungal plant diseases. B. cinerea exhibits a wide arsenal of tools to infect plant tissues. Most of these factors are related to signal transduction cascades, in which membrane proteins play a key role as a bridge between environmental conditions and intracellular molecular processes. This work describes the first proteomic approach to study the membranome of B. cinerea under different pathogenicity condition induced by using different plant-based elicitors: Glucose and Tomato Cell Wall (TCW). A discovery proteomics analysis of membrane protein extracts was carried out by mass spectrometry. A total of 2,794 proteins were successfully identified, and approximately 46% of them could be classified as membrane proteins based on the presence of transmembrane regions and covalent post-translational modifications. Further analyses showed significant differences in the fungal membranome composition depending on the available carbon source: 804 proteins were exclusively identified when the fungus was cultured in the presence of glucose as sole carbon source, and 251 proteins were exclusively identified in the presence of TCW. Besides, among the 1737 common proteins, a subset of 898 proteins presented clear differences in their abundance and in order to clarify the specific changes produced in the membranome, proteins were categorized according to their gene ontology annotation shown different profiles. As a result of this work, we present here the first description of the membranome of B. cinerea, which will certainly provide a better understanding of this important subproteome in B. cinerea.

2016-07-11 | PXD003099 | Pride

vg120629 - Beyond plant defense: insights on the potential of salicylic and methylsalicylic acid to contain growth of the phytopathogen Botrytis cinerea

Project description:Using Botrytis cinerea we confirmed in the present work several previous studies showing that salicylic acid, a main plant hormone, inhibits fungal growth in vitro. Such an inhibitory effect was also observed for the two salicylic acid derivatives, methylsalicylic and acetylsalicylic acid. In marked contrast, 5-sulfosalicylic acid was totally inactive. Comparative proteomics from treated vs control mycelia showed that the intracellular proteome was markedly affected in the presence of salicylic acid or methylsalicylic acid, in a similar manner for the two compounds. These data suggest several mechanisms that could potentially account for the observed fungal growth inhibition, notably pH regulation, metal homeostasis, mitochondrial respiration, ROS accumulation and cell wall remodeling. The present observations document another facet of the role played by this phytohormone and derivatives in directly containing the pathogen.

2015-11-06 | PXD002873 | Pride

Next Generation Sequencing Facilitates Quantitative Analysis of Cucumber and Botrytis cinerea Transcriptome Changes During Infection

Project description:Purpose: The goals of this study are using RNA-seq to obtain cucumber and Botrytis cinerea transcriptome changes during infection Methods: mRNA profiles of anti-infection samples and interaction sample were generate by deep sequencing,using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: BurrowsâWheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRTâPCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow,In total, 248,908,688 raw reads were generated; after removing low-quality reads and those containing adapter and poly-N, 238,341,648 clean reads remained to map the reference genome. There were 3,512 cucumber (differential expression genes) DEGs and 1,735 B. cinerea DEGs. GO enrichment and KEGG enrichment analysis were performed on these DEGs to study the interaction between cucumber and B. cinerea. To verify the reliability and accuracy of our transcriptome data, 5 cucumber DEGs and 5 B. cinerea DEGs were chosen for RT-PCR verification. Conclusions:To the best of our knowledge, this is the first analysis of large-scale transcriptome changes of cucumber during the infection of Botrytis cinerea. These results will increase our understanding of the molecular mechanisms of the cucumber defense Botrytis cinerea and may be used to protect plants against disasters caused by necrotrophic fungal pathogens. mRNA profiles of infection and anti-infection cucumber were generated by deep sequencing, using Illumina Hiseq 2500 .

2016-08-01 | E-GEOD-72191 | biostudies-arrayexpress

Inducer Free Cellulase Secretion in Neurospora Crassa and comparitive analysis of cellulase induction in Aspergillus nidulans

Project description:Purpose: To explore conservation of gene regulation by the transcription factor clr-2/clrB in Neurospora crassa and Aspergillus nidulans Methods: mRNA from wild type and clr-2/clrB mutants were collected after a culture shift from sucrose/glucose to Avicel (crystaline cellulose) or no carbon media Results: We show that N. crassa and A. nidulans have similair global transcriptional responses to Avicel, with several hundred genes showing specific induction, though the induced genes are more specifically targeted at cellulose for N. crassa and more targeted at hemicellulose and pectin for A. nidulans. clr-2/clrB has a conserved fundamental function in cellulose induction, though the mechanism has diverged. Misexpression of clr-2 is sufficeint for inducer free cellulase secretion in N. crassa, but neither clrB or heterologous clr-2 is sufficient for inducer free cellulase secretion in A. nidulans. Conclusions: Our study demonstrates a conserved and essential role in cellulose utilization for the transcription factor clr-2 in filamentous ascomycetes and demonstrates that manipulation of clr-2 expression can be used to control cellulase expression in some species. Biological triplicates of liquid culture N. crassa and A. nidulans were harvested at 4 hours and 6 hours, respectively, after a switch to media of interest. Global mRNA abundances from liquid cultures of N. crassa and A. nidulans were measured by sequencing on the Illumina Genome Analyzer IIx and HiSeq2000 platforms.

2013-09-01 | E-GEOD-44100 | biostudies-arrayexpress

Proteome-wide Analysis of Lysine 2-hydroxyisobutyrylation in the Phytopathogenic Fungus Botrytis cinerea

Project description:Lysine 2-hydroxyisobutyrylation , a recently discovered post-translational modification, plays a key role in the regulation of diverse cellular processes. Botrytis cinerea is a destructive necrotrophic fungal pathogen distributed worldwide with broad ranging hosts. However, the functions of Lysine 2-hydroxyisobutyrylation are unknown in B. cinerea or any other plant fungal pathogens

2020-09-07 | PXD021059 | Pride

Transcriptional response to hypoxia in the rice blast fungus, M. oryzae

Project description:Transcriptional analysis using RNA-Seq to low oxygen Samples from wild type mycelia with and without oxygen (21% and 1% Oxygen)

2015-05-18 | E-GEOD-51597 | biostudies-arrayexpress

Gene expression analysis of stage 1 primordia and vegetative mycelia from Coprinopsis cinerea

Project description:Sexual reproduction is an ancient trait that evolved shortly after the appearance of the first eukaryotic cell. In order to study the transcriptional circuitries driving sexual reproduction in basidiomycota, we sequenced the poly(A)-positive transcriptome of stage 1 primordia and vegetative mycelia from the self-compatible dikaryotic basidiomycete Coprinopsis cinerea A43mutB43mut. Please note Okayama7 samples not included in this submission.

2014-06-01 | E-MTAB-1968 | biostudies-arrayexpress

Elucidation of FOXP1 target genes in DLBCL by RNA-Seq

Project description:Elucidation of FOXP1 target genes by RNA-Seq of DLBCL cell lines transfected with siRNAs targeting FOXP1 expression

2015-11-30 | E-MTAB-3740 | biostudies-arrayexpress