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RNA-seq of Basidiomycete fungi Laccaria bicolor

ABSTRACT: RNA-seq of Basidiomycete fungi Laccaria bicolor

PROVIDER: PRJNA769598 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16248484_1.fastq.gz	Fastqsanger.gz
	SRR16248484_2.fastq.gz	Fastqsanger.gz
	SRR16248485_1.fastq.gz	Fastqsanger.gz
	SRR16248485_2.fastq.gz	Fastqsanger.gz
	SRR16248486_1.fastq.gz	Fastqsanger.gz

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5mC oxidation products in the nucleic acids of the Basidiomycete fungi Laccaria bicolor and Coprinopsis cinerea

Project description:We analyzed oxidized 5-methylcytosine derivatives 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in nucleic acids of multicellular fungi Laccaria bicolor and Coprinopsis cinerea which have been used as models to study DNA methylation, developmental processes and symbiotic interactions. All three cytosine derivatives were detected in the genomes of both fungi, and importantly, we discovered 5carC in the RNA fractions, potentially including large non-coding, messenger RNAs and small RNA molecules, indicating gene regulatory functions of 5carC.

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Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza development

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Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza development

Project description:Illumina GAIIx technology was used to generate mRNA profiles from the ectomycorrhizal fungi Laccaria bicolor colonizing roots of Populus trichocarpa. Samples were taken after two, four and 12 weeks of contact in order to identify mycorrhiza-regulated transcripts. 37bp reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) and the Laccaria bicolor (http://genome.jgi-psf.org/Lacbi2/Lacbi2.home.html) reference genomes using CLC Genomics Workbench 6. mRNA profiles from Populus trichocarpa roots colonized by Laccaria bicolor for two, four and 12 weeks as well as from control roots and free-living mycelium were generated by using one lane of 37 bp Illumina GAIIx sequencing per sample.

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Project description:Illumina HiSeq2000 technology was used to generate mRNA profiles from the ectomycorrhizal fungi Laccaria bicolor colonizing roots of Populus trichocarpa. Samples were taken after 3 months of contact in order to identify mycorrhiza-regulated transcripts. 100bp reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) reference genome.

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Gene expression of Laccaria bicolor S238N free-living mycelium grown on different media

Project description:Transcript profiles of Laccaria bicolor S238N mycelium on various media 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 evaluate the effect of nutrient deprivation on the transcriptome of Laccaria bicolor.

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Dual transcriptomic analysis of the interaction between the ectomycorrhizal fungus Laccaria bicolor S238N and soil Pseudomonas fluorescens Pf29Arp

Project description:In order to get insights into the ability of ectomycorrhizal fungi to perceive their biotic environment as well as into the mechanisms of the interactions between ectomycorrhizal fungi and soil bacteria, we analysed the transcriptomic response of the ectomycorrhizal fungus L. bicolor and the strain Pseudomonas fluorescens Pf29Arp during their interactions in vitro. We performed six hybridizations (shotgun DNA microarray) with samples derived from Pseudomonas fluorescens Pf29Arp cultivated alone or with Laccaria bicolor S238N in vitro (3 control biological replicates and 3 biological replicates with L. bicolor)

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Dual transcriptomic analysis of the interaction between the ectomycorrhizal fungus Laccaria bicolor S238N and soil Collimonas fungivorans Ter331

Project description:In order to get insights into the ability of ectomycorrhizal fungi to perceive their biotic environment as well as into the mechanisms of the interactions between ectomycorrhizal fungi and soil bacteria, we analysed the transcriptomic response of the ectomycorrhizal fungus L. bicolor and one detrimental bacterial strain during their interactions in vitro. We performed hybridizations (whole genome array) with samples derived from Collimonas fungivorans Ter331cultivated alone or with Laccaria bicolor S238N in vitro (2 control biological replicates and 2 biological replicates with L. bicolor)

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