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BIOlogie et GEstion des Risques en agriculture - Champignons Pathogènes des Plantes

Different waves of effector genes with contrasted genomic location are expressed by Leptosphaeria maculans during cotyledon and stem colonisation of oilseed rape

Gervais's publication in Molecular Plant Pathology
BIOGER PhD student Julie GERVAIS and collab. from INRA and Génoscope published an article in which they analyzed, by RNA-seq, the expression profile of Leptosphaeria maculans genes during the early and late colonization stages of oilseed rape. The distinct waves of effectors expressed during these two stages correspond to genes with distinct genomic location: the early effector genes are located in gene-poor plastic regions whereas the late effector candidates are located in the core genome.

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 or 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 colonization compared to cotyledon colonization. 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 colonization 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 colonization, are located in gene-rich genomic regions, whereas the “early” effector genes, over-expressed in the early colonization stage, are located in gene-poor regions of the genome.


Julie Gervais is funded by a joint grant from the Santé des Plantes et Environnement (SPE) INRA department and the institute Terres Inovia (formely CETIOM).


Gervais, J., Plissonneau, C., Linglin, J., Meyer, M., Labadie, K., Cruaud, C., Fudal, I., Rouxel, T. and Balesdent, M.-H. (2016), Different waves of effector genes with contrasted genomic location are expressed by Leptosphaeria maculans during cotyledon and stem colonisation of oilseed rape. Molecular Plant Pathology. Accepted Author Manuscript. doi:10.1111/mpp.12464