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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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5'-Serial Analysis of Gene Expression of the transcriptomes of Coprinopsis cinerea during fruiting body initiation

ABSTRACT: Large scale assessment of the transcriptomes of the vegetative mycelium and primordium will facilitate the generation of a more comprehensive picture of the fruiting process in basidiomycetes. We coupled 5'-Serial Analysis of Gene Expression (5'-SAGE) to high-throughput pyrosequencing from 454 Life Sciences to analyze the transcriptomes and identify up-regulated genes (URGs) among vegetative mycelium (Myc) and stage 1 primordium (S1-Pri) of Coprinopsis cinerea during fruiting body development. We evaluated the expression of >3,000 genes in the two respective growth stages and demonstrated that almost one-third of these genes were preferentially expressed in either stage, which implicated a significant transcriptomic switch during fruiting body initiation. We annotated >34,000 and >45,000 transcription start sites (TSSs) in the transcriptomes of Myc and S1-Pri respectively. We identified a wealth of potential URGs related to early fruiting events, although their functions and roles are not exactly known. This study serves to advance our understanding of the molecular mechanisms of fruiting body development in the model mushroom C. cinerea. 5'-SAGE analysis of the transcriptomes of vegetative mycelium and primordium of C. cinerea by 454 GS20 high-throughput pyrosequencer

ORGANISM(S): Coprinopsis cinerea

SUBMITTER: CHI KEUNG CHENG

PROVIDER: E-GEOD-40722 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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5'-Serial Analysis of Gene Expression of the transcriptomes of Coprinopsis cinerea during fruiting body initiation

Project description:Large scale assessment of the transcriptomes of the vegetative mycelium and primordium will facilitate the generation of a more comprehensive picture of the fruiting process in basidiomycetes. We coupled 5'-Serial Analysis of Gene Expression (5'-SAGE) to high-throughput pyrosequencing from 454 Life Sciences to analyze the transcriptomes and identify up-regulated genes (URGs) among vegetative mycelium (Myc) and stage 1 primordium (S1-Pri) of Coprinopsis cinerea during fruiting body development. We evaluated the expression of >3,000 genes in the two respective growth stages and demonstrated that almost one-third of these genes were preferentially expressed in either stage, which implicated a significant transcriptomic switch during fruiting body initiation. We annotated >34,000 and >45,000 transcription start sites (TSSs) in the transcriptomes of Myc and S1-Pri respectively. We identified a wealth of potential URGs related to early fruiting events, although their functions and roles are not exactly known. This study serves to advance our understanding of the molecular mechanisms of fruiting body development in the model mushroom C. cinerea.

2013-01-10 | GSE40722 | GEO

Gene expression analysis of monokaryotic and dikaryotic 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 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.

2014-06-01 | E-MTAB-1993 | biostudies-arrayexpress

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

The infection cushion: a fungal weapon for plant-biomass destruction

Project description:Full transcriptomes of the Botrytis cinerea wild-type strain B0510, cultured in liquid medium or on cellophane sheets placed on PDB 1/4-agar plates, were compared to identify genes differentially expressed when infection cushions are formed from vegetative mycelium.

2020-12-31 | GSE141822 | GEO

Gene expression in protoapothecia from Ascodesmis nigricans

Project description:The aim of this analysis was to analyze gene expression in young fruiting bodies (protoapothecia) of the filamentous ascomycete Ascodesmis nigricans. Young fruiting bodies were isolated by laser microdissection, RNA was extracted, amplified and used for RNA-sequencing. The resulting data were compared to data from total vegetative and sexual mycelium.

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Gene expression in protoapothecia from Pyronema confluens

Project description:The aim of this analysis was to analyze gene expression in young fruiting bodies of the filamentous ascomycete Pyronema confluens. Young fruiting bodies were isolated by laser microdissection, RNA was extracted, amplified and used for RNA-sequencing. The resulting data were compared to data from total vegetative and sexual mycelium from a previous analysis.

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Homeobox transcription factors involved in fruiting body development of Volvariella volvacea

Project description:The genome of V. volvacea revealed 47 genes encoding homeobox transcription factors. Of them, 8 differentially expressed homeobox transcription factors were obtained by comparing the gene expression during primordia and elongation formation. Furthermore, quantitative real-time PCR was performed on selected genes with different expression levels to demonstrate the utility of digital gene expression for gene expression profiles during fruiting body formation. The results showed that five homeobox transcription factors were up-regulated during primordia formation, and three homeobox transcription factors were down-regulated from the egg stage to elongation stage. Overall, a critical role for homeobox transcription factor was believed to contribute to the fruiting body formation. Using the 3'-tag digital gene expression (DGE), we compared the gene expression profiles in fruiting body development of V. volvacea.

2014-12-19 | E-GEOD-43297 | biostudies-arrayexpress

Developmental transcriptomics of the model caterpillar fungus Cordyceps militaris

Project description:The RNA-Seq technique was used to investigate the differentially transcribed genes of the caterpillar fungus Cordyces militaris. It was calculated that >63% of total annotated genes were expressed, including >55% of putative pathogen-host interaction genes. Overall, the fruiting-body development and mycelium growth by C. militaris activated high expression levels of genes in association with translation and post-translational modifications. Otherwise, there were many differentially expressed genes when the fungus was grown on insect pupae to different stages or in liquid medium. In general, the transcriptional profiles were more similar with each other during fungal fruiting-body developmental stages than during growth in a liquid culture. Examination of differential gene expressions by Cordyceps militaris during fruiting-body developments on silkmoth pupae and growth in a liquid medium.

2011-11-08 | E-GEOD-28001 | biostudies-arrayexpress

Combining laser microdissection and RNA-seq to chart the transcriptional landscape of fungal development

Project description:RNA-seq analysis of developmental stages from the filamenous ascomycete Sordaria macrospora. Using laser capture microdissection, we separated protoperithecia (young fruiting bodies) from the surrounding hyphae. RNA isolation and amplification from 150 protoperithecia yields enough material for RNA-seq analysis. The resulting data were compared to RNA-seq data from whole mycelial exctracts (total vegetative and total sexual mycelium) to characterize the genome-wide spatial distribution of gene expression during sexual development. We analyzed total vegetative mycelium, total sexual mycelium, and protoperithecia from the wild type as well as protoperithecia from the sterile mutant pro1. Additionally, we used the RNA-seq information to improve the predicted S. macrospora gene models, and annotated UTRs for more than 50 % of the genes.

2012-10-01 | GSE33668 | GEO

Mushroom development in S. commune

Project description:In order to study changes in gene expression during mushroom development in Schizophyllum commune, genome wide gene expression was analysed in 4 developmental stages: vegetative mycelium, stage I aggregates, stage II primordia and mature mushrooms 4 samples: - vegetative mycelium - stage I aggregates - stage II primordia - mature mushrooms RNA was obtained from 3 biological replicates and pooled

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