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RNA-seq experiments of systemic colonization of oilseed rape by Leptosphaeria maculans

ABSTRACT: RNA-seq experiments of systemic colonization of oilseed rape by Leptosphaeria maculans

OTHER RELATED OMICS DATASETS IN: GSE81756

PROVIDER: PRJNA322501 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3571660.fastq.gz	Fastqsanger.gz
	SRR3571670_1.fastq.gz	Fastqsanger.gz
	SRR3571670_2.fastq.gz	Fastqsanger.gz
	SRR3571661.fastq.gz	Fastqsanger.gz
	SRR3571671_1.fastq.gz	Fastqsanger.gz

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Leptosphaeria maculans gene expression during in vitro growth and primary oilseed rape leaf infection

Project description:The transcriptome of Leptosphaeria maculans was analyzed in mycelium and during oilseed rape (Brassica napus) leaf infection. The array probes were designed from gene models from the L. maculans whole genome annotation. One aim of this study was to verify the expression of the automatically annotated gene models in various conditions. Another goal was to monitor gene expression profiles during oilseed rape leaf infection and to highlight tissue-specific transcripts, e.g. in plant up-regulated transcripts, for further analyses. We performed 9 hybridizations (NimbleGen) with samples derived from mycelium and infected oilseed rape leaves. Samples from infected oilseed rape leaves were harvested 7 and 14 days post infection. Three replicates each. All samples were labeled with Cy3.

2011-02-09 | E-GEOD-27152 | biostudies-arrayexpress

Leptosphaeria maculans gene expression during in vitro growth and primary oilseed rape leaf infection

2011-02-09 | GSE27152 | GEO

RNA-seq experiments of systemic colonization of oilseed rape by Leptosphaeria maculans

Project description:Leptosphaeria maculans, causal agent of stem canker disease, colonises oilseed rape (Brassica napus) in two stages: a short and early colonisation stage corresponding to cotyledon or leaf colonisation, and a late colonisation stage during which the fungus colonises systemically and symptomlessly the plant during several months before stem canker appears. To date, determinants of the late colonisation stage are poorly understood; L. maculans may either successfully escape plant defences leading to the stem canker development, or the plant can develop an “adult-stage” resistance reducing canker incidence. To get insight into these determinants, we performed an RNA-seq pilot project comparing fungal gene expression in infected cotyledons and in symptomless and necrotic stems. Despite the low fraction of fungal material in infected stems, enough fungal transcripts were detected and a large portion of fungal genes were expressed, thus validating the feasibility of the approach. Our analysis showed that all avirulence genes previously identified are under-expressed during stem colonisation compared to cotyledon colonisation. A validation RNA-seq experiment was then done to investigate the expression of candidate effector genes during systemic colonisation. 307 "late" effector candidates, under-expressed in the early colonisation stage and over-expressed in the infected stems, were identified. Finally our analysis revealed a link between regulation of expression of effectors and their genomic location: the late effector candidates, putatively involved in the systemic colonisation, are located in gene-rich genomic regions, whereas the "early" effector genes, over-expressed in the early colonisation stage, are located in gene-poor regions of the genome.

2016-12-30 | GSE81756 | GEO

Leptosphaeria maculans gene expression during in vitro growth and primary oilseed rape leaf infection

Project description:Leptosphaeria maculans gene expression during in vitro growth and primary oilseed rape leaf infection

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Regulation of effector gene expression as concerted waves in Leptosphaeria maculans: a two-players game

Project description:During infection, plant pathogenic fungi secrete a set of molecules collectively known as effectors, involved in overcoming the host immune defense system and in disease establishment. Effector genes are concertedly expressed as waves all along plant pathogenic fungi lifecycle. However, little is known about how coordinated expression of effector genes is regulated. Since many effector genes are located in repeat-rich regions, the role of chromatin remodeling in the regulation of effector expression was recently investigated. In Leptosphaeria maculans, causing stem canker of oilseed rape, we established that the repressive histone modification H3K9me3 (trimethylation of Lysine 9 of Histone H3), deposited by the histone methyltransferase KMT1, was involved in the regulation of expression of genes highly expressed during infection, including effectors. Nevertheless, inactivation of KMT1 did not induce expression of these genes at the same level as observed during infection of oilseed rape, suggesting that a second regulator, such as a transcription factor (TF), might be involved. Pf2, a TF belonging to the Zn2Cys6 fungal specific TF family, was described in several Dothideomycete species as essential for pathogenicity and effector gene expression. We identified the orthologue of Pf2 in L. maculans, LmPf2, and investigated the role of LmPf2 together with KMT1 in L. maculans, by inactivating and over-expressing LmPf2 in a wild type (WT) strain and a ∆kmt1 mutant. Functional analyses of the corresponding transformants highlighted an essential role of LmPf2 in the establishment of pathogenesis. Transcriptomic analyses during axenic growth showed that LmPf2 is involved in the control of effector gene expression. We observed an enhanced effect of the over-expression of LmPf2 on effector gene expression in a ∆kmt1 background, suggesting a synergic role between KMT1 and LmPf2.

2024-01-01 | GSE236510 | GEO

Gene expression profile in MS medium for the phytopathogenic fungus Leptosphaeria maculans brassicae (Lmb) and lepidii (Lml)

Project description:Full transcriptomes of Leptosphaeria maculans ‘brassicae’ v23.1.3 and Leptosphaeria maculans ‘lepidii’ IBCN84, grown in Fries medium, were studied.

2021-06-02 | GSE150126 | GEO

Comprehensive RNA profiling of susceptible and resistant (LepR1) Brassica napus to L. Maculans

Project description:The hemibiotrophic fungal pathogen Leptosphaeria maculans is the causal agent of blackleg disease in Brassica napus (canola, oilseed rape) and causes significant losses in crop yields worldwide. While genetic resistance has been used to mitigate the disease, little information about the genes and gene regulatory networks underlying blackleg resistance is currently available. High-throughput RNA sequencing and rigorous bioinformatics approaches revealed dynamic changes in the host transcriptome and identified plant defense pathways specific to the host-pathogen incompatible LepR1-AvrLepR1 interaction.

2016-04-01 | GSE77723 | GEO

Leptosphaeria maculans

Project description:Dual-RNAseq of Leptosphaeria maculans inoculated to canola

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Leptosphaeria maculans

Project description:Leptosphaeria maculans inoculated on Brassica napus host. Transcriptome

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Oilseed rape microbiome

Project description:Metagenomic analysis of oilseed rape microbiome under Irish agronomic conditions

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