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Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza development

ABSTRACT: 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.

ORGANISM(S): Laccaria bicolor Populus trichocarpa

PROVIDER: GSE54789 | GEO | 2014/02/08

SECONDARY ACCESSION(S): PRJNA237653

REPOSITORIES: GEO

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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.

2014-02-08 | E-GEOD-54789 | biostudies-arrayexpress

Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza

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Poplar-Laccaria: A Timecourse of Mycorrhizal Root Tip Development

Project description:This study characterizes the transcriptomic alterations of P. trichocarpa during interaction with the ectomycorrhizal fungus Laccaria bicolor S238N. Four time-points were analyzed, two weeks, four weeks , six weeks and twelve weeks after inoculation. We performed 32 hybridizations (NimbleGen) with samples derived from Populus trichocarpa control roots and P.trichocarpa mycorrhizal root tips. Samples were taken after 2,4,6 and 12 weeks of interaction (four biological replicates). All samples were labeled with Cy3.

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Comparison of gene expression in roots from Populus trichocarpa and Populus deltoides colonized with Laccaria bicolor

Project description:The majority of trees live in association with symbiotic fungi, which facilitate their access to soil nutrients. The ectomycorrhizal symbiosis represents a complex biological system involving multifaceted interactions between the two partners. The establishment of the symbiosis depends on various conditions (e.g. climate), but also on the genetic traits of the partners. To evaluate the impact of the genetic predisposition on the development and functioning of ectomycorrhizas, we compared the transcriptome of roots from Populus trichocarpa and Populus deltoides colonized with Laccaria bicolor.

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Time Course of Laccaria bicolor S238N and Populus tremula x alba 717-1B4 in vitro ectomycorrhizal development

Project description:Illumina technology was used to generate mRNA profiles of a time course of Laccaria bicolor S238N and Populus tremula x alba 717-1B4 in vitro ectomycorrhizal development. Total RNA was extracted, TruSeq mRNA Stranded libraries were constructed and and sequenced in triplicates (2 x 150 bp Illumina HiSeq3000) at the Genotoul sequencing facilities (Toulouse, France). Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the L. bicolor v2 reference transcripts available at the JGI database https://mycocosm.jgi.doe.gov/Lacbi2/Lacbi2.home.html using CLC Genomics Workbench v8.

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The transcriptome of poplar roots incubated with MiSSP7, a secreted effector protein of Laccaria bicolor

Project description:To investigate which genes are affected by MiSSP7, a secreted effector protein of Laccaria bicolor, we analyzed the transcriptomes of poplar roots incubated with MiSSP7 protein. The Populus trichocarpa custom-exon expression array (12x135K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products/exp/index.html) contained three independent, nonidentical, 60-mer probes per gene model coding sequence. Included in the oligoarray were 43,929 annotated gene models (Populus trichocarpa genome v2 ; Phytozome 5.0), 5,859 random 60-mer control probes and labelling controls. We performed six hybridizations, three biological replicates from poplar roots inoculated with MiSSP7 peptide for one hour and three biological replicates from control roots.

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Project description:This study characterizes the transcriptomic alterations of Laccaria bicolor S238N during interaction with P. trichocarpa. Four time-points were analyzed, two weeks, four weeks , six weeks and twelve weeks after inoculation and compared to the transcriptome of free-living mycelium from Laccaria bicolor S238N We performed 16 hybridizations (NimbleGen) with samples derived from P.trichocarpa/L.bicolor mycorrhizal root tips. Samples were taken after 2,4,6 and 12 weeks of interaction (four biological replicates). These samples were compared to free-living mycelium from Laccaria bicolor S238N (three biological replicates). All samples were labeled with Cy3.

2014-10-10 | E-GEOD-62225 | biostudies-arrayexpress

Gene expression changes in leaves, roots and Laccaria bicolor mycorrhiza of Poplar treated with ozone or stopped watering.

Project description:Illumina technology was used to generate mRNA profiles of leaves, roots and Laccaria bicolor mycorrhiza of Poplar treated with ozone or stopped watering. Total RNA was extracted separately from each plant and pooled to 4 biological replicates per condition.TruSeq mRNA Stranded libraries were constructed and and sequenced using Illumina HiSeq 3000 at the Genotoul sequencing facilities (Toulouse, France). Raw reads were filtered and trimmed using erne-filter command. Filtered reads from each library were aligned to P. trichocarpa (https://phytozome-next.jgi.doe.gov/info/Ptrichocarpa_v4_1) using TopHat2 v2.12.

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