Project description:Illumina HiSeq technology was used to generate mRNA profiles from Pisolithus microcarpus basidiocarp compartments. Unconsolidated, young, and mature peridioles, as well as internal and free spores from three basidiocaps were harvested and used for RNA extraction. Paired-end reads of 100 bp were generated and aligned to Pisolithus microcarpus (http://genome.jgi.doe.gov/Pismi1/Pismi1.home.html) reference transcripts using CLC Genomics Workbench 7. Overall design: mRNA profiles from Pisolithus microcarpus basidiocarp compartments were generated by Illumina HiSeq2000 sequencing (2x100bp). Three biological replicates were sequenced from unconsolidated, young, and mature peridioles, as well as internal and free spores.
Project description:Pisolithus microcarpus (Cooke & Massee) G. Cunn is a gasteromycete that produces closed basidiocarps in symbiosis with eucalypts and acacias. The fungus produces a complex basidiocarp composed of peridioles at different developmental stages and an upper layer of basidiospores free of the hyphae and ready for wind dispersal upon the rupture of the basidiocarp pellis. During basidiosporogenesis, a process that takes place inside the basidiocarp peridioles, a conspicuous reserve of fatty acids is present throughout development. While several previous studies have described basidiosporogenesis inside peridioles, very little is known about gene expression changes that may occur during this part of the fungal life cycle. The objective of this work was to analyze gene transcription during peridiole and basidiospore development, while focusing specifically on cell cycle progression and lipid metabolism.Throughout different developmental stages of the peridioles we analyzed, 737 genes were regulated between adjacent compartments (>5 fold, FDR-corrected p-value?<?0.05) corresponding to 3.49% of the genes present in the P. microcarpus genome. We identified three clusters among the regulated genes which showed differential expression between the peridiole developmental stages and the basidiospores. During peridiole development, transcripts for proteins involved in cellular processes, signaling, and information storage were detected, notably those for coding transcription factors, DNA polymerase subunits, DNA repair proteins, and genes involved in chromatin structure. For both internal embedded basidiospores (hereto referred to as "Internal spores", IS) and external free basidiospores (hereto referred to as "Free spores", FS), upregulated transcripts were found to involve primary metabolism, particularly fatty acid metabolism (FA). High expression of transcripts related to ?-oxidation and the glyoxylate shunt indicated that fatty acids served as a major carbon source for basidiosporogenesis.Our results show that basidiocarp formation in P. microcarpus involves a complex array of genes that are regulated throughout peridiole development. We identified waves of transcripts with coordinated regulation and identified transcription factors which may play a role in this regulation. This is the first work to describe gene expression patterns during basidiocarp formation in an ectomycorrhizal gasteromycete fungus and sheds light on genes that may play important roles in the developmental process.
Project description:Illumina HiSeq technology was used to generate mRNA profiles from in vitro Eucalyptus grandis roots interacting with two different Pisolithus microcarpus strains (SI-9 and SI-12) and under two different CO2 concentrations (400 and 650 ppm) . Control roots or ectomycorrhizal root tips were harvested after 1 month and used for RNA extraction. Paired-end (2X150bp) reads were generated and aligned to Eucalyptus grandis transcripts (http://www.phytozome.net/; primarytranscripts only) using CLC Genomics Workbench 6. Overall design: mRNA profiles from in vitro Eucalyptus grandis roots interacting with two different Pisolithus microcarpus strains (SI-9 and SI-12) and under two different CO2 concentrations (400 and 650 ppm) were generated by paired-end (2X110bp) Illumina HiSeq1500 sequencing. Three biological replicates were sequenced for mycorrhizal samples, five for CO2 650ppm control roots and six for CO2 400ppm control roots.