Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Whole Genome sequence of white rot fungi Trametes flavida WTFP2

PROVIDER: PRJNA996515 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR25340711_1.fastq.gz	Fastqsanger.gz
	SRR25340711_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Project description:Whole Genome Sequence of Trametes flavida

| PRJNA1010726 | ENA

Intracellular pathways for lignin catabolism in white-rot fungi

Project description:White-rot fungi (WRF), considered the most efficient organisms at degrading organic carbon in the biosphere, are found in plant cell wall lignin biopolymer. We employ multi-omics to demonstrate that Trametes versicolor and Gelatoporia subvermispora funnel lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems.

2021-02-10 | PXD019839 | Pride

The transcriptomic response of two basidiomycetes to plant biomass is modulated by temperature to a different extent

Project description:In this study, we compared the transcriptomeic profiles of two recently sequenced white-rot wood-decaying mushrooms, Trametes pubescens and Phlebia centrifuga, during their growth on two common plant biomass substrates at different temperatures.

2023-02-03 | GSE213003 | GEO

Comparing gene expression timing and amplitude to delineate the unique pathways of brown and white rot wood-degrading fungi

Project description: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. This approach highlighted 34 genes uniquely upregulated in early brown rot stages, with notable candidates involved in generating reactive oxygen species (ROS) as a pretreatment mechanism during brown rot. This approach further isolated 18 genes in late brown rot stages that may be adapted to handle oxidatively-reacted lignocellulose components. By summing gene expression levels in functional classes, we also identified a broad and reliable distinction in glycoside hydrolase (GH) versus lignocellulose oxidative (LOX) transcript counts that may reflect the energy investment burden of lignin-degrading machinery among white rot fungi.

2018-01-05 | GSE108189 | GEO

Metabolic characterization of two white-rot fungi in diverse cultivation environments reveals biotechnologically relevant biosynthetic pathways

Project description:Two white-rot fungi, Trametes versicolor and Gelatoporia subvermispora, were cultivated in different environments - agitation and static incubation modes and variations in the level of antioxidants - during the conversion of a lignin-related aromatic compound and cellobiose. Both incubation mode and the presence of antioxidants impact sugars and aromatic catabolism, as well as lipid composition of the fungal mycelia, and the analyses reveal biosynthetic pathways for the production of extracellular fatty acids and phenylpropanoids by these fungi.

2024-08-05 | MSV000095519 | MassIVE

Catabolism of lignin-related methoxylated compounds in white-rot fungi utilizes a non-canonical extradiol dioxygenase

Project description:White-rot fungi (WRF) are the most effective lignin-degrading organisms in nature, making them essential to Earth’s carbon cycle. Lignin is a highly methoxylated, heterogeneous biopolymer derived from plants. However, the pathways WRF use to metabolize methoxylated aromatic compounds as carbon sources remain unidentified. Here, we employ a systems biology approach to elucidate the intracellular catabolism of vanillate – a monomethoxylated aromatic compound – in two white-rot fungi (WRF), Gelatoporia subvermispora and Trametes versicolor. We identified and biochemically validated a four-enzyme pathway that converts vanillate into β-ketoadipate – a metabolite that enters central carbon metabolism. This pathway deviates from typical bacterial pathways, where vanillate is initially demethylated and ring-cleaved by intradiol dioxygenases; instead, oxidative decarboxylation occurs prior to ring cleavage by extradiol dioxygenases. Thus, we conducted an in-depth investigation of ring cleavage and further downstream catabolism by the identified fungal enzymes using biochemical and structural approaches. This revealed non-canonical enzymes, including a highly substrate-specific extradiol dioxygenase and a metal-free, promiscuous reductase, the latter capable of acting on catabolic intermediates derived from both methoxylated and non-methoxylated aromatic compounds. This work emphasizes the potential of WRF and their enzymes to advance lignin valorization and enhance our understanding of their role during wood decay.

2026-04-01 | GSE300708 | 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

Intracellular pathways for lignin catabolism in white-rot fungi

Project description:Lignin is a biopolymer found in plant cell walls that accounts for 30% of the organic carbon in the biosphere. White-rot fungi (WRF) are considered the most efficient organisms at degrading lignin in Nature. While lignin depolymerization by WRF has been exhaustively studied, the possibility that WRF are able to utilize lignin as a carbon source is still a matter of controversy. Here we employ 13C-labeling and systems biology approaches to demonstrate that two WRF, Trametes versicolor and Gelatoporia subvermispora, funnel lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems, and furthermore establishes a foundation for employing WRF in simultaneous lignin depolymerization and bioconversion to bioproducts – a key step towards enabling a sustainable bioeconomy.

2021-01-15 | GSE151629 | GEO

Project description:Unique ability of basidiomycete white rot fungi to degrade all components of plant cell walls makes them indispensable organisms in global carbon cycle. In this study, we analyzed proteomes of two closely related white rot fungi, Obba rivulosa and Gelatoporia subvermispora, while growing on solid spruce wood, and defined a core set of CAZymes that was shared between these species including the orthologous enzymes. Similar production pattern of these CAZymes indicate their key role in plant biomass degradation and need for their further biochemical characterization. The obtained results give an insight into specific enzymes and enzyme sets that are produced during the degradation of solid spruce wood. These findings expand the knowledge on enzyme production in nature-mimicking conditions and may contribute to exploitation of white rot fungi and their enzymes in biotechnological applications.

2022-08-08 | PXD030609 | Pride

LongSAGE during the initiation of ligninolytic enzymes production in Phanerochaete chrysosporium

Project description:White rot fungi are able to degrade woody lignin and other persistent organic compounds including artificial chemicals (e.g. chlorinated dioxin) in secondary metabolism. This ability has potential in a wide range of biotechnological applications including remediation of organopollutants and the industrial processing of paper and textiles. Ligninolytic fungi secondarily secrete extracellular oxidative enzymes thought to play an important role in these compounds decay. However, detail of metabolic pathway and initiation signals of the degradation system is unclear. To investigate genes directly and indirectly related to it, we constructed long serial analysis of gene expression (Long SAGE) library from the most studied white rot fungus, Phanerochaete chrysosporium. Keywords: transcriptome profiling

2007-12-31 | GSE6649 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data