Project description:Co-occurrence analysis of root-associated fungi in roots of oak species reveals the positive association among ectomycorrhizal and non-ectomycorrhizal fungi and the levels of associations among root-associated fungi are different between host species.
Project description:Laccaria bicolor transcript profiles of different tissues and mycorrhizal root tips from different host trees were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) Laccaria bicolor genome sequence version 1. One goal was to compare gene expression profiles from ectomycorrhizal root tips with different host plants.
Project description:Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production. Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Hebeloma cylindrosporum ectomycorrhizal root tips compared to free-living mycelium . Ectomycorrhizal root tips were harvested after 6 months and used for RNA extraction. Reads of 100 bp were generated and aligned to Hebeloma cylindrosporum transcripts (http://genome.jgi-psf.org/Hebcy2) using CLC Genomics Workbench 6.
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Hebeloma cylindrosporum ectomycorrhizal root tips compared to free-living mycelium . Ectomycorrhizal root tips and control mycelium were harvested after 3 weeks and used for RNA extraction. Reads of 150 bp were generated and aligned to Hebeloma cylindrosporum transcripts (http://genome.jgi-psf.org/Hebcy2) using CLC Genomics Workbench 7.
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.
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Hebeloma cylindrosporum ectomycorrhizal root tips compared to free-living mycelium . Ectomycorrhizal root tips were harvested after 6 months and used for RNA extraction. Reads of 100 bp were generated and aligned to Hebeloma cylindrosporum transcripts (http://genome.jgi-psf.org/Hebcy2) using CLC Genomics Workbench 6. mRNA profiles from Hebeloma cylindrosporum ectomycorrhizal root tips and free-living mycelium were generated by Illumina HiSeq2000 sequencing (100bp). Ttwo 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:Illumina HiSeq technology was used to generate mRNA profiles from Hebeloma cylindrosporum ectomycorrhizal root tips compared to free-living mycelium . Ectomycorrhizal root tips and control mycelium were harvested after 3 weeks and used for RNA extraction. Reads of 150 bp were generated and aligned to Hebeloma cylindrosporum transcripts (http://genome.jgi-psf.org/Hebcy2) using CLC Genomics Workbench 7. mRNA profiles from Hebeloma cylindrosporum ectomycorrhizal root tips and free-living mycelium were generated by Illumina HiSeq2000 sequencing (150bp). Three biological replicates were sequenced for mycorrhizal and mycelium samples.
Project description:Complex community structure of ectomycorrhizal, arbuscular-mycorrhizal and root-endophytic fungi in a mixed subtropical forest of ectomycorrhizal and arbuscular-mycorrhizal plants
