GEO Logo
   NCBI > GEO > Accession DisplayHelp Reviewer access | Sign OutHelp
GEO help: Mouse over screen elements for information.
Series GSE53112 Query DataSets for GSE53112
Status Public on Oct 01, 2014
Title Comparisons of Phlebiopsis gigantea transcript profiles when cultured different substrates
Organism Phlebiopsis gigantea
Experiment type Expression profiling by high throughput sequencing
Summary 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. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of pitch were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea’s pitch metabolism. These results contribute to our fundamental understanding of conifer colonization and carbon cycling processes.
Overall design Phlebiopsis gigantea was cultivated in media containing one of three carbon sources: freshly harvested loblolly pine (3 replicates), acetone extracted lobollly pine (3 replicates), or glucose (2 replicates). RNA was extracted and processed for Illumina sequencing as described below.
Contributor(s) Cullen D
Citation(s) 25474575
Submission date Dec 08, 2013
Last update date May 15, 2019
Contact name Dan Cullen
Phone 608-231-9468
Organization name UW/FPL
Street address One Gifford Pinchot Dr
City Madison
State/province WI
ZIP/Postal code 53726
Country USA
Platforms (1)
GPL18039 Illumina HiSeq 2000 (Phlebiopsis gigantea)
Samples (8)
GSM1282521 NELP rep 1
GSM1282522 NELP rep2
GSM1282523 NELP rep3
BioProject PRJNA230883
SRA SRP033587

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE53112_RPKM_all.txt.gz 544.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap