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Oilseed rape microbiome

ABSTRACT: Metagenomic analysis of oilseed rape microbiome under Irish agronomic conditions

PROVIDER: PRJEB13996 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1413143_1.fastq.gz	Fastqsanger.gz
	ERR1413143_2.fastq.gz	Fastqsanger.gz
	ERR1428068_1.fastq.gz	Fastqsanger.gz
	ERR1428068_2.fastq.gz	Fastqsanger.gz

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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.

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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.

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