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Series GSE58653 Query DataSets for GSE58653
Status Public on Mar 24, 2015
Title Host-based markers for the early stage of infection by the grapevine trunk pathogen Neofusicoccum parvum
Organism Vitis vinifera
Experiment type Expression profiling by high throughput sequencing
Summary In the vineyard, symptoms of the grapevine trunk disease Botryosphaeria dieback do not appear until 1 or 2 years after the causal fungus Neofusicoccum parvum establishes a necrotic canker in the permanent woody structure of the vine. There are preventative management practices, but growers tend to wait until symptoms are widespread, at which point prevention has limited efficacy.
Toward development of an early detection tool, we examined the leaves of inoculated vs. non-inoculated plants for differential gene expression via RNASeq. Stems were examined to monitor spread of the infection, and its spatial and temporal relationship to anatomical changes via light microscopy and high resolution computed tomography (HRCT).
The early stage of infection occurred prior to 2 months post-inoculation (MPI), at which point spread of the pathogen beyond the inoculation site was greatest. This incubation period was also characterized by the largest stem lesions, the highest levels of fungal colonization and xylem vessels fully-occluded by gels, and the lowest starch content of xylem fibers and rays.
Prior to 2 MPI, RNASeq and validative qPCR analysis identified eight candidate markers, which are transcriptionally activated by infection, but not by wounding alone. Our best marker genes, a dehydrin, a BURP domain containing protein and an abscissic acid-induced wheat plasma membrane polypeptide 19 (AWPM-19), identified the pathogen’s presence with high specificity. Screening of genome-wide expression data revealed that this signature is not affected by many abiotic and biotic stresses.
 
Overall design Asymptomatic leaf mRNA profiles of Neofusicoccum parvum infected wounded plants (IW) and non-infected wounded plants (NIW) at two different time points post inoculation (0 MPI, 0.5-1.5 MPI) were generated by deep sequencing in biological triplicates using Illumina HiSeq2500 technology.
 
Contributor(s) Czemmel S, Galarneau ER, Travadon R, McElrone AJ, Cramer GR, Baumgartner K
Citation(s)
  • Czemmel S, Galarneau ER, Travadon R, McElrone AJ et al. Genes expressed in grapevine leaves reveal latent wood infection by the fungal pathogen Neofusicoccum parvum. PLoS One 2015;10(3):e0121828. PMID: 25798871
Submission date Jun 19, 2014
Last update date May 15, 2019
Contact name Stefan Czemmel
Organization name Quantitative Biology Center (QBiC)
Department University of Tuebingen
Street address Auf der Morgenstelle 10
City Tuebingen
ZIP/Postal code 72076
Country Germany
 
Platforms (1)
GPL18580 Illumina HiSeq 2500 (Vitis vinifera)
Samples (12)
GSM1416452 IW_0_MPI_1
GSM1416453 IW_0_MPI_2
GSM1416454 IW_0_MPI_3
Relations
BioProject PRJNA253108
SRA SRP043418

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE58653_normalized.read.counts.txt.gz 2.1 Mb (ftp)(http) TXT
GSE58653_raw.read.counts.txt.gz 628.0 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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