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| Status |
Public on Dec 30, 2016 |
| Title |
RNA-seq experiments of systemic colonization of oilseed rape by Leptosphaeria maculans |
| Organisms |
Brassica napus; Plenodomus lingam |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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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| Overall design |
Two RNA-seq-projects:
A pilot project RNA-seq with deep sequencing of L. maculans mRNA during early and late colonisation stages of oilseed rape, using Illumina HiSeq2000.
A validation RNA-seq experiment, with two biological replicates per condition, focused on two infection stages, infected cotyledons and early symptomless stem colonisation, as well as in vitro growth condition as a control.
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| Contributor(s) |
Gervais J, Plissonneau C, Linglin J, Meyer M, Labadie K, Cruaud C, Fudal I, Rouxel T, Balesdent M |
| Citation(s) |
27474899 |
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| Submission date |
May 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Julie Gervais |
| E-mail(s) |
julie.gerv@gmail.com
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| Phone |
0033130814573
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| Organization name |
INRA
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| Department |
BIOGER
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| Street address |
Avenue Lucien Brétignières
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| City |
Thiverval Grignon |
| ZIP/Postal code |
78850 |
| Country |
France |
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| Platforms (5)
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| GPL15579 |
Illumina HiSeq 2000 (Brassica napus) |
| GPL19731 |
Illumina HiSeq 2500 (Brassica napus) |
| GPL21409 |
Illumina HiSeq 2000 (Brassica napus; Leptosphaeria maculans) |
| GPL21443 |
Illumina HiSeq 2500 (Brassica napus; Leptosphaeria maculans) |
| GPL21935 |
Illumina HiSeq 2500 (Leptosphaeria maculans) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA322501 |
| SRA |
SRP075546 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE81756_RAW.tar |
2.1 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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