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Dichomitus squalens

ABSTRACT: The molecular response of the white-rot fungus Dichomitus squalens to wood and non-woody biomass as examined by transcriptome and exoproteome analyses

PROVIDER: PRJNA316680 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3309180.fastq.gz	Fastqsanger.gz
	SRR3309181.fastq.gz	Fastqsanger.gz
	SRR3309172.fastq.gz	Fastqsanger.gz
	SRR3309182.fastq.gz	Fastqsanger.gz
	SRR3309173.fastq.gz	Fastqsanger.gz

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Similar Datasets

The molecular response of the white-rot fungus Dichomitus squalens to wood and non-woody biomass as examined by transcriptome and exoproteome analyses

Project description: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. In this study we evaluated how well the white-rot fungus Dichomitus squalens has adapted to degrade its natural wood substrate. The transcriptome and exoproteome of D. squalens were analysed after cultivation on two natural substrates, aspen and spruce wood, and two non-woody substrates, wheat bran and cotton seed hulls. D. squalens produced ligninolytic enzymes mainly at the early time point of the wood cultures, indicating the need to degrade lignin to get access to wood polysaccharides. Surprisingly, the response of the fungus to the non-woody polysaccharides was nearly as good match to the substrate composition as observed for the wood polysaccharides. This indicates that D. squalens has preserved its ability to efficiently degrade plant polysaccharides not present in its natural habitat.

2017-01-05 | GSE79674 | GEO

Widespread glucose-mediated repression of plant biomass utilization in the white-rot fungus Dichomitus squalens

Project description:Carbon catabolite repression (CCR) occurs in the presence of sufficient concentrations of easy metabolizable carbon sources (e.g. glucose), down-regulating the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. The extent of CCR at a global level is unknown in wood-rotting fungi – and was investigated in Dichomitus squalens with transcriptomics and exo-proteomics. Approximately 10% of expressed genes had lower expression in presence of glucose compared to Avicel or xylan alone. The glucose repressed genes included key components for utilization of plant biomass – CAZymes, sugar transporters and carbon catabolic genes. The majority of polysaccharide degrading CAZymes were repressed and included activities towards all major polymers. The repression found in the transcriptome was strongly supported by exo-proteomics – there was repression of almost all of the CAZymes whose transcripts were repressed on Avicel. The clear CCR-mediated effects indicate biotech production of CAZymes by D. squalens would benefit from de-repressed or constitutively expressing strains. The extent of CCR is surprising given that D. squalens rarely experiences high sugar concentrations in its woody environment.

2019-10-07 | PXD014774 | Pride

Dichomitus squalens

Project description:Transcriptional response of the white-rot fungus Dichomitus squalens to polysaccharides

| PRJNA1416411 | ENA

Dichomitus squalens

Project description:Dichomitus squalens Raw sequence reads

| PRJNA378592 | ENA

Analyses of long-term fungal degradation of spruce bark reveals varying potential for catabolism of polysaccharides and extractive compounds

Project description:The bark represents the outer protective layer of trees. It contains high concentrations of antimicrobial extractives, in addition to regular wood polymers. It represents a huge underutilized side stream in forestry, but biotechnological valorization is hampered by a lack of knowledge on microbial bark degradation. Many fungi are efficient lignocellulose degraders, and here, spruce bark degradation by five species, Dichomitus squalens, Rhodonia placenta, Penicillium crustosum, Trichoderma sp. B1, and Trichoderma reesei, was mapped, by continuously analyzing chemical changes in the bark over six months. The study reveals how fungi from different phyla degrade bark using diverse strategies, regarding both wood polymers and extractives, where toxic resin acids were degraded by Basidiomycetes but unmodified/tolerated by Ascomycetes. Proteome analyses of the white-rot D. squalens revealed several proteins, with both known and unknown functions, that were specifically upregulated during growth on bark. This knowledge can accelerate improved utilization of an abundant renewable resource.

2024-05-04 | PXD043339 | Pride

Dichomitus squalens strain:OM18370.1

Project description:Dichomitus squalens OM18370.1 Transcriptome

| PRJNA459691 | ENA

Early response of the fungus Pycnoporus coccineus to softwood and hardwood feedstocks

Project description: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. The Polyporale fungus Pycnoporus coccineus CIRM-BRFM310 grows well on both coniferous and deciduous wood. In the present study we analyzed the early response of the fungus to softwood (pine) and hardwood (aspen) feedstocks.

2016-10-10 | GSE74234 | GEO

The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown.

Project description: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.

2017-05-21 | GSE94878 | GEO

Dichomitus squalens strain:CBS463.89 | isolate:CBS463.89

Project description:Dichomitus squalens CBS463.89 Transcriptome

| PRJNA459689 | ENA

Dichomitus squalens strain:OM18370.1

Project description:Dichomitus squalens OM18370.1 Standard Draft genome sequencing

| PRJNA334681 | ENA