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Melampsora larici-populina gene expression in different tissues of uredinia

ABSTRACT: Laser Capture Microdissection (LCM) was used for expression analysis of three contrasted fungal tissues of uredinia corresponding respectively to spores and sporogenous hyphae, fungal structures in the spongy mesophyll and fungal infection structures in the palisade mesophyll. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Melampsora larici-populina genome sequence version 1. The aim of this study was to identify tissue-specific gene expression to gain insights into the genes specifically associated with the biotrophic phase and the sporulation phase of the rust fungus.

ORGANISM(S): Melampsora laricis-populina

PROVIDER: GSE21487 | GEO | 2010/07/22

SECONDARY ACCESSION(S): PRJNA126025

REPOSITORIES: GEO

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Melampsora larici-populina gene expression in different tissues of uredinia

Project description:Laser Capture Microdissection (LCM) was used for expression analysis of three contrasted fungal tissues of uredinia corresponding respectively to spores and sporogenous hyphae, fungal structures in the spongy mesophyll and fungal infection structures in the palisade mesophyll. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Melampsora larici-populina genome sequence version 1. The aim of this study was to identify tissue-specific gene expression to gain insights into the genes specifically associated with the biotrophic phase and the sporulation phase of the rust fungus. We performed 9 hybridizations (NimbleGen) with samples derived from Laser Capture Microdissection (LCM) of three contrasted fungal tissues of uredinia, corresponding respectively to spores and sporogenous hyphae, fungal structures in the spongy mesophyll and fungal infection structures in the palisade mesophyll. Three replicates per tissue. All samples were labeled with Cy3.

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Melampsora larici-populina gene expression in telia, uredinia, urediniospores and in planta

Project description:The transcriptome of Melampsora larici-populina was analysed in telia (in planta sample, early telia harvested before overwintering), uredinia (in planta sample, 168 hours post-inoculation, hpi), in planta during biotrophic growth (96 hpi) and in resting urediniospores. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Melampsora larici-populina genome sequence version 1. The aim of this study was to determine gene expression in early telia formed in decaying poplar leaves in autumn before the overwintering process and to compare this expression with other stages of the poplar rust life cycle that were previously described (i.e., resting urediniospores as pure fungal material, and uredinia and biotrophic growth stage as poplar leaf infecting fungal structures). This study should highlight telia-specific transcripts and contribute to the understanding of the poplar rust biological cycle.

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Project description:Illumina HiSeq2500 technology was used to generate mRNA-sequencing expression profiles of sexual stages of the poplar rust fungus M. larici-populina: - Basidia (BSD) were collected from rust-infected dead poplar leaves; - Pycnia (PYC) -also called spermogonia- were collected from rust-infected larch needles one week after inoculation with basidiospores and corresponded to different haploid fungal cell types such as in planta infection hyphae, receptive hyphae and pycniospores; - Aecia (AEC) were collected from rust-infected larch needles two weeks after inoculation, and corresponded to freshly produced aecia and dikaryotic aeciospores and remaining pycnia. Paired-end reads of 100bp were generated for three sets of biological replicates corresponding to each of the targeted stage and aligned to the genome of M. larici-populina isolate 98AG31 (version 2.0; US Department of Energy Joint Genome Institute; http://genome.jgi.doe.gov/Mellp2_3/Mellp2_3.home.html) using CLC Genomics Workbench 12.0

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Transcriptome of Melampsora larici-populina sexual stages [JGI version 1 genome]

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Project description:The transcriptome of Melampsora-larici-populina was analysed in urediniospores, germlings and infected Poplar leaves. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Melampsora larici-populina genome sequence version 1. One aim of this study was to verify the expression of the automatically annotated gene models in various tissues and development stages. Another goal was to monitor gene expression at different developmental stages and to highlight tissue-specific transcripts, e.g. in planta up-regulated transcripts for further analyses.

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Project description:The identification of early-expressed pathogen effectors and early-modulated host functions is currently a major goal to understand the molecular basis of biotrophic lifestyle. Melampsora larici-populina isolates 98AG31 and 93ID6, respectively virulent and avirulent on the hybrid P. trichocarpa x P. deltoides poplar cultivar M-bM-^@M-^XBeauprM-CM-)M-bM-^@M-^Y were used in this study. Inoculations were performed on 5 cm2 leaf disks. The following conditions were used for oligoarrays: Incompatible 18, 21 and 24 hpi, Compatible 18, 24 and 48hpi. One aim of this study was to compare RNA-Seq and hybridization-based approaches, therefore the cDNA templates were used for whole-genome poplar oligoarrays and 454-pyrosequencing. We performed 6 hybridizations (Nimblegen) with samples derived from incompatible (18, 21 and 24hpi) and compatible (18, 24 and 48hpi) interactions of Melampsora larici-populina with P. trichocarpa x P. deltoides poplar cultivar M-bM-^@M-^XBeauprM-CM-)M-bM-^@M-^Y leaves. All samples were labeled with Cy3.

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