GEO DataSets

(Submitter supplied) Expression of genes encoding plant biomass degrading enzymes in ascomycetes is controlled by transcriptional activators that respond to the presence of monomeric components of plant polymers. It can be expected that a similar system exists in basidiomycetes, but no homologs of the ascomycete regulators could be identified in basidiomycetes.

Organism:

Dichomitus squalens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24128

6 Samples

Download data: GFF3, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Dichomitus squalens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24128

20 Samples

Download data: TXT

(Submitter supplied) The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of plant biomass substrates. Which genes need to be activated in certain environmental conditions depends on the composition of the available substrate. Previous studies have demonstrated the involvement of a number of transcriptional regulators in plant biomass degradation and have identified sets of target genes for each regulator. more...

Organism:

Aspergillus niger; Aspergillus niger CBS 513.88

Type:

Expression profiling by array

Platform:

GPL6758

59 Samples

Download data: CEL

(Submitter supplied) Expression of genes encoding plant biomass degrading enzymes in ascomycetes is controlled by transcriptional activators that respond to the presence of monomeric components of plant polymers. It can be expected that a similar system exists in basidiomycetes, but no homologs of the ascomycete regulators could be identified in basidiomycetes.

Organism:

Dichomitus squalens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24128

14 Samples

Download data: TXT

(Submitter supplied) The ability to obtain carbon and energy is a major requirement to exist in any environment. For several ascomycete fungi (post-)genomic analyses have shown that species that occupy a large variety of habitats possess a diverse enzymatic machinery, while species with a specific habitat have a more focused enzyme repertoire that is well-adapted to the prevailing substrate. White-rot basidiomycete fungi also live in a specific habitat, as they are found exclusively in wood. more...

Organism:

Dichomitus squalens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21661

16 Samples

Download data: TXT

(Submitter supplied) The basidiomycete white-rot fungus Obba rivulosa, a close relative of Gelatoporia (Ceriporiopsis) subvermispora, is an efficient degrader of softwood. The dikaryotic O. rivulosa strain T241i (FBCC949) has been shown to selectively remove lignin from spruce wood prior to depolymerization of plant cell wall polysaccharides, thus possessing potential in biotechnological applications such as pretreatment of wood in pulp and paper industry. more...

Organism:

Obba rivulosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23564

6 Samples

Download data: TXT

(Submitter supplied) Wood-degrading fungi play a critical role in global carbon cycling, and their varied mechanisms for deconstruction offer pathways for industrial bioconversion. In this study, we used comparative genomics to isolate upregulation patterns among fungi with brown rot (carbohydrate-selective) or white rot (lignin-degrading) nutritional modes. Specifically, we used whole-transcriptome profiling to compare early, middle, and late decay stages on wood wafers, matching differentially-expressed gene (DEG) patterns with fungal growth and enzyme activities. more...

Organism:

Pleurotus ostreatus; Gloeophyllum trabeum; Trametes versicolor; Postia placenta

Type:

Expression profiling by high throughput sequencing

4 related Platforms

36 Samples

Download data: GTF, TXT, XLSX

(Submitter supplied) Cre1 is an important transcription factor that regulates carbon catabolite repression (CCR) and is widely conserved across fungi. This gene has been extensively studied in several Ascomycota species, whereas its role in gene expression regulation in the Basidiomycota remains poorly understood. Here, we identified and investigated the role of cre1 in Coprinopsis cinerea, a basidiomycete model mushroom that can efficiently degrade lignocellulosic plant wastes. more...

Organism:

Coprinopsis cinerea AmutBmut pab1-1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32332

7 Samples

Download data: GTF, TSV

(Submitter supplied) White-rot basidiomycete fungi are potent degraders of plant biomass with the ability to mineralize all lignocellulose components. Recent comparative genomics studies showed that these fungi use a wide diversity of enzymes for wood degradation. In order to improve our understanding on the enzymatic mechanisms leading to lignocellulose breakdown, we analysed the early response of the white-rot fungus Pycnoporus coccineus CIRM-BRFM310 to various lignocellulosic substrates at two time points; Day 3 and Day 7.

Organism:

Trametes coccinea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23066

22 Samples

Download data: TXT

(Submitter supplied) Transcript profiles of Serpula lacrymans grown on different substrates were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) Serpula lacrymans genome sequence version 1. One aim of this study was to verify the expression of the automatically annotated gene models under various conditions. Another goal was to compare gene expression profiles from Serpula lacrymans grown on liquid MMN medium and on wood.

Organism:

Serpula lacrymans var. lacrymans S7.9

Type:

Expression profiling by array

Platform:

GPL13241

9 Samples

Download data: PAIR

(Submitter supplied) Brown rot fungi have great potential in biorefinery wood conversion systems, because they are the primary wood decomposers in coniferous forests and have an efficient lignocellulose degrading system. Their initial wood degradation mechanism is thought to consist of an oxidative radical-based system that acts sequentially with an enzymatic saccharification system, but the complete molecular mechanism of this system has not yet been elucidated. more...

Organism:

Gloeophyllum trabeum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28967

9 Samples

Download data: CSV

(Submitter supplied) We have studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA-sequencing we showed that, 24 hours after exposure to straw, gene expression of known plant cell wall degrading enzymes represents a huge investment for the cells (about 20 % of the total mRNA). Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal degradative arsenal. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14910

9 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling with next-generation sequencing methods demonstrated that a Neurospora crassa mutant with the three most highly expressed beta-glucosidase genes deleted had a transcriptional response to cellobiose similair to that of wild type N. crassa exposed to cellulose.

Organism:

Neurospora crassa OR74A

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15147 GPL15146

13 Samples

Download data: TXT

(Submitter supplied) Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high pitch content, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. more...

Organism:

Phlebiopsis gigantea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18039

8 Samples

Download data: TXT

(Submitter supplied) Transscript profiles of Ceriporiopsis subvermispora grown on different substrates were analyszed. Array design was based on the DoE's Joint Genome Institute's gene models for C. subvermispora version 1. The research goal is to identtify genes essential for lignocellulose depolymerization.

Organism:

Gelatoporia subvermispora

Type:

Expression profiling by array

Platform:

GPL15051

9 Samples

Download data: PAIR, XLS

(Submitter supplied) High throughput “omics technologies” such as transcriptomics and proteomics provide insights into the metabolic potential of an organism and have been used to understand the genetic and the central carbon metabolism mechanisms for the production of desired end products in various cellulolytic clostridia cultured on different substrates In this study, C. termitidis was cultured on lignocellulose derived simple and complex sugars: cellobiose, xylose, xylan and α–cellulose as sole carbon sources. more...

Organism:

Ruminiclostridium cellobioparum subsp. termitidis CT1112

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19810

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Trametes coccinea; Trametes cinnabarina; Trametes sanguinea

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21989 GPL21052 GPL21988

50 Samples

Download data

(Submitter supplied) White-rot basidiomycete fungi are potent degraders of plant biomass with the ability to mineralize all lignocellulose components. Recent comparative genomics studies showed that these fungi use a wide diversity of enzymes for wood degradation. Deeper functional analyses are however necessary to understand the enzymatic mechanisms leading to lignocellulose breakdown. In the present study we analyzed the early response of the Polyporales fungi Pycnoporus coccineus CIRM-BRFM310, Pycnoporus cinnabarinus CIRM-BRFM137 and Pycnoporus sanguineus CIRM-BRFM 1264 to various carbon sources including lignocellulosic biomass.

Organism:

Trametes sanguinea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21989

15 Samples

Download data: TXT

(Submitter supplied) White-rot basidiomycete fungi are potent degraders of plant biomass with the ability to mineralize all lignocellulose components. Recent comparative genomics studies showed that these fungi use a wide diversity of enzymes for wood degradation. Deeper functional analyses are however necessary to understand the enzymatic mechanisms leading to lignocellulose breakdown. In the present study we analyzed the early response of the Polyporales fungi Pycnoporus coccineus CIRM-BRFM310, Pycnoporus cinnabarinus CIRM-BRFM137 and Pycnoporus sanguineus CIRM-BRFM 1264 to various carbon sources including lignocellulosic biomass.

Organism:

Trametes cinnabarina

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21988

17 Samples

Download data: TXT

(Submitter supplied) White-rot basidiomycete fungi are potent degraders of plant biomass with the ability to mineralize all lignocellulose components. Recent comparative genomics studies showed that these fungi use a wide diversity of enzymes for wood degradation. Deeper functional analyses are however necessary to understand the enzymatic mechanisms leading to lignocellulose breakdown. In the present study we analyzed the early response of the Polyporales fungi Pycnoporus coccineus CIRM-BRFM310, Pycnoporus cinnabarinus CIRM-BRFM137 and Pycnoporus sanguineus CIRM-BRFM 1264 to various carbon sources including lignocellulosic biomass.

Organism:

Trametes coccinea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21052

18 Samples

Download data: TXT