 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 |
| E-mail(s) |
dcullen@wisc.edu
|
| 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)
|
|
| Relations |
| BioProject |
PRJNA230883 |
| SRA |
SRP033587 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE53112_RPKM_all.txt.gz |
544.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...