Project description:Illumina HiSeq technology was used to generate mRNA profiles from Oidiodendron maius mycorrhizal roots compared to free-living mycelium . Mycorrhizal roots and control mycelium were harvested after 45 days and used for RNA extraction. Reads of 2X100bp were generated and aligned to Oidiodendron maius transcripts (http://genome.jgi-psf.org/Oidma1) using CLC Genomics Workbench 6. mRNA profiles from Oidiodendron maius mycorrhizal roots and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Three biological replicates were sequenced for mycorrhizal and mycelium samples.
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Tulasnella calospora mycorrhizal protocorms compared to free-living mycelium . Protocorms and control mycelium were harvested after 30 days and used for RNA extraction. Reads of 2X100bp were generated and aligned to Tulasnella calospora transcripts (http://genome.jgi-psf.org/Tulca1) using CLC Genomics Workbench 6. mRNA profiles from Tulasnella calospora mycorrhizal protocorms and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Three biological replicates were sequenced for mycorrhizal and mycelium samples.
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Piloderma croceum ectomycorrhizal roots compared to free-living mycelium . Mycorrhizal roots were harvested after 8 weeks, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Piloderma croceum (http://genome.jgi-psf.org/Pilcr1/Pilcr1.home.html) using CLC Genomics Workbench 6. mRNA profiles from Piloderma croceum ectomycorrhizal roots and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Three biological replicates were sequenced for mycorrhizal and mycelium samples.
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Sebacina vermifera mycorrhizal roots compared to free-living mycelium . Mycorrhizal roots were harvested after 3, 7 and 14 days, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Sebacina vermifera (http://genome.jgi-psf.org/Sebve1/Sebve1.home.html) using CLC Genomics Workbench 6. mRNA profiles from Sebacina vermifera mycorrhizal roots and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Three biological replicates were sequenced for mycorrhizal and mycelium samples.
Project description:Decomposition of soil organic matter in forest soils is thought to be controlled by the activity of saprotrophic fungi, while biotrophic fungi including ectomycorrhizal fungi act as vectors for input of plant carbon. The limited decomposing ability of ectomycorrhizal fungi is supported by recent findings showing that they have lost many of the genes that encode hydrolytic plant cell-wall degrading enzymes in their saprophytic ancestors. Nevertheless, here we demonstrate that ectomycorrhizal fungi representing at least four origins of symbiosis have retained significant capacity to degrade humus-rich litter amended with glucose. Spectroscopy showed that this decomposition involves an oxidative mechanism and that the extent of oxidation varies with the phylogeny and ecology of the species. RNA-Seq analyses revealed that the genome-wide set of expressed transcripts during litter decomposition has diverged over evolutionary time. Each species expressed a unique set of enzymes that are involved in oxidative lignocellulose degradation by saprotrophic fungi. A comparison of closely related species within the Boletales showed that ectomycorrhizal fungi oxidized litter material as efficiently as brown-rot saprotrophs. The ectomycorrhizal species within this clade exhibited more similar decomposing mechanisms than expected from the species phylogeny in concordance with adaptive evolution occurring as a result of similar selection pressures. Our data shows that ectomycorrhizal fungi are potential organic matter decomposers, yet not saprotrophs. We suggest that the primary function of this decomposing activity is to mobilize nutrients embedded in organic matter complexes and that the activity is driven by host carbon supply. Comparative transcriptomics of ectomycorrhizal (ECM) versus brown-rot (BR) fungi while degrading soil-organic matter
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Paxillus involutus ectomycorrhizal roots compared to mycelium patches . Mycorrhizal roots were harvested after 4 weeks, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Paxillus involutus (http://genome.jgi-psf.org/Paxin1/Paxin1.home.html) using CLC Genomics Workbench 6. mRNA profiles from Paxillus involutus ectomycorrhizal roots and mycelium patches were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Two biological replicates were sequenced for mycorrhizal and mycelium samples.
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Amanita muscaria ectomycorrhizal root tips compared to free-living mycelium . Ectomycorrhizal root tips and control mycelium were harvested after 6 weeks and used for RNA extraction. Reads of 150 bp were generated and aligned to Amanita muscaria transcripts (http://genome.jgi-psf.org/Amamu1) using CLC Genomics Workbench 7. mRNA profiles from Amanita muscaria ectomycorrhizal root tips and free-living mycelium were generated by Illumina HiSeq2000 sequencing (150bp). Two biological replicates were sequenced for mycorrhizal and mycelium samples.
Project description:Fungi are an important source of enzymes for saccharification of plant polysaccharides and production of biofuels. Understanding of the regulation and induction of expression of genes encoding these enzymes is still incomplete. To explore the induction mechanism, we analysed the response of the industrially important fungus Aspergillus niger to wheat straw, with a focus on events occurring shortly after exposure to the substrate. RNA sequencing showed that over a third of the genes induced after 6 h of exposure to wheat straw were also induced during 6 h of carbon starvation, indicating that carbon starvation is probably an important factor in the early response to wheat straw. The up-regulation of the expression of a high number of genes encoding CAZymes that are active on plant-derived carbohydrates during early carbon starvation suggests that these enzymes could be involved in a scouting role during starvation, releasing inducing sugars from complex plant polysaccharides. Eight samples in total consisting of duplicate shake flask Aspergillus niger cultures from four conditions: 48h glucose, 6 h starvation, 6 h wheat straw, 24 h starvation
Project description:This study characterizes the transcriptomic alterations of Serpula lacrymans in contact with tree roots compared to the transcriptome of free-living mycelium. We performed 6 hybridizations (NimbleGen) with samples derived from Picea sylvestris root tips inoculated with Serpula lacrymans (three biological replicates). These samples were compared to free-living mycelium from Serpula lacrymans (three biological replicates). All samples were labeled with Cy3.