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

ABSTRACT: 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) 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 1.0; US Department of Energy Joint Genome Institute; http://genome.jgi.doe.gov/Mellp1/Mellp1.home.html; Duplessis et al. 2011a) using CLC Genomics Workbench 8.0.1

ORGANISM(S): Melampsora laricis-populina

PROVIDER: GSE106863 | GEO | 2018/01/15

SECONDARY ACCESSION(S): PRJNA418247

REPOSITORIES: GEO

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Transcriptome of Melampsora larici-populina sexual stages [JGI version 2 genome]

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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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. We performed 9 hybridizations (Nimblegen) with samples derived from urediniospores, germlings and infected Poplar leaves (three replicates each). Samples from infected leaves were harvested 96 hours post infection. All samples were labeled with Cy3.

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Project description:Microarray expression profiling was carried out in poplar leaves upon infection with rust in order to identify genes expressed during tree defense response. For this purpose, we inoculated detached leaves of the interamerican hybrid poplar Populus trichocarpa x Populus deltoides 'Beaupré' grown in greenhouse with spores of avirulent strain 93ID6 of the pathogenic rust fungus Melampsora larici-populina (incompatible interaction, I48). Besides, we mock-inoculated 'Beaupré' leaves with water (control condition, T48). Detached leaves were maintained in vitro in controled conditions to allow fungal infection and colonization of plant tissue. Leaves were sampled 48 hours post-inoculation after that the fungus attempt to penetrate plant cells in mesophyll. Competitive hybridization between transcripts of incompatible interaction (I48) and control condition (T48) was done on Populus PICME 28K cDNA microarray. Keywords: Time-course infection of plant tissue, defense response, cDNA microarray

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