Transcriptome of Melampsora larici-populina sexual stages [JGI version 1 genome]
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ABSTRACT:
PROVIDER: PRJNA418247 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6288030_1.fastq.gz | Fastqsanger.gz | |||
| SRR6288030_2.fastq.gz | Fastqsanger.gz | |||
| SRR6288031_1.fastq.gz | Fastqsanger.gz | |||
| SRR6288031_2.fastq.gz | Fastqsanger.gz | |||
| SRR6288023_1.fastq.gz | Fastqsanger.gz |
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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
2021-07-24 | GSE180724 | GEO
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) 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
2018-01-15 | GSE106863 | GEO
Project description:The transcriptome of Melampsora-larici-populina was analysed in urediniospores, germlings and during poplar leaf infection. 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 profiles during poplar leaf infection and to highlight tissue-specific transcripts, e.g. in planta up-regulated transcripts for further analyses.
2011-06-10 | GSE21624 | GEO
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.
2011-04-30 | GSE23097 | GEO
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.
2011-04-30 | E-GEOD-23097 | biostudies-arrayexpress
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.
2013-11-01 | GSE49099 | GEO
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.
2010-07-22 | GSE21487 | GEO
Project description:Transcriptome of Melampsora larici-populina sexual stages [JGI version 2 genome]
| PRJNA749283 | ENA
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. We performed 12 hybridizations (NimbleGen) with samples derived from resting urediniospores (3 biological replicates), infected poplar leaves harvested at 96 and 168 hpi (3 biological replicates each) and Telia (3 biological replicates). All samples were labeled with Cy3.
2013-11-01 | E-GEOD-49099 | biostudies-arrayexpress
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.
2012-09-01 | E-GEOD-34802 | biostudies-arrayexpress