Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Host-based markers for the early stage of infection by the grapevine trunk pathogen Neofusicoccum parvum

ABSTRACT: 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 pathogenâ??s presence with high specificity. Screening of genome-wide expression data revealed that this signature is not affected by many abiotic and biotic stresses. 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.

ORGANISM(S): Vitis vinifera

SUBMITTER: Stefan Czemmel

PROVIDER: E-GEOD-58653 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Genes expressed in grapevine leaves reveal latent wood infection by the fungal pathogen Neofusicoccum parvum.

Czemmel Stefan S Galarneau Erin R ER Travadon Renaud R McElrone Andrew J AJ Cramer Grant R GR Baumgartner Kendra K

PloS one 20150323 3

Some pathogenic species of the Botryosphaeriaceae have a latent phase, colonizing woody tissues while perennial hosts show no apparent symptoms until conditions for disease development become favorable. Detection of these pathogens is often limited to the later pathogenic phase. The latent phase is poorly characterized, despite the need for non-destructive detection tools and effective quarantine strategies, which would benefit from identification of host-based markers in leaves. Neofusicoccum p ...[more]

PMID: 25798871

Similar Datasets

Project description:Spinocerebellar ataxia type 6 (SCA6) is a dominantly inherited neurodegenerative disease caused by an expansion of a CAG repeat encoding a polyglutamine (PolyQ) tract in the Cav2.1 voltage-gated calcium channel. Pathologically, it is characterized by selective degeneration of cerebellar Purkinje cells (PCs), which are a common target for PolyQ-induced toxicity among several different SCAs. Mutant Cav2.1 confers toxicity mainly through a toxic gain-of-function mechanism, but subcellular site of expanded Cav2.1 toxicity is controversial and it remains elusive whether SCA6 shares pathogenic cascades with other SCAs. To gain insight into these problems, we studied the cerebellar gene expression patterns of young Sca6 MPI 118Q/118Q knockin (KI) mice, which express mutant Cav2.1 from endogenous locus and faithfully models human SCA6. Comparison of transcriptional changes with those of Sca1 154Q/2Q mice, a faithful KI mouse model of SCA1, revealed that transcriptional signatures in the MPI 118Q/118Q were distinct from those of Sca1 154Q/2Q. Examination of temporal profiles of candidate genes showed that upregulation of those associated with microglial activation was initiated before PC degeneration was apparent and augmented as the disease progressed. Histological analysis of the MPI 118Q/118Q cerebellum confirmed the presence of Iba-1 positive activated microglia. Moreover, predominance of M1-like pro-inflammatory microglia was observed and was concomitant with the increased expression of pro-inflammatory cytokines. These results suggest that the unique transcriptional response, which highlights upregulation of neuroinflammatory genes possibly associated with lysosomal involvement, may play a pivotal role in the pathogenesis. Modulation of innate immune system could pave the way for slowing the progression of SCA6. We used MPI 118Q/118Q and MPI 11Q/11Q mice for Sca6 KI model at six weeks old. Statistical analysis of differently expressed genes was performed using the Linear Models for Microarray Data (limma) package in R/Bioconductor.

Project description:Systems responses of mature leaves from 4 reference cultivars of a larger collection of European potato cultivars (Solanum tuberosum L.) are investigated by metabolome profiling and RNA-Sequencing. The chosen reference cultivars, Milva, Alegria, Desiree, and Saturna, vary in ascending order in regard to drought tolerance. Systems analyses are based on 3 independent field trials and 3 paralleled greenhouse trials. Robust responses across all cultivars and conditions to natural seasonal drought stress comprise proline, raffinose, galactinol, arabitol, arabinonic acid, chlorogenic acid, and 102 transcripts which consist to a high proportion of heat shock proteins and genes with signaling or regulatory functions, such as a homolog of abscisic acid receptor PYL4. Constitutive differences of the tolerant cultivars, Desiree and Saturna, compared to the sensitive cultivars include arbutin (hydroquinone-beta-D-glucopyranoside), octopamine (p-hydroxyphenylethanolamine), ribitol and 248 differential transcripts. Many of these transcripts are disease related, receptor kinases, or regulatory genes, for example a homolog of the Arabidopsis FOUR LIPS MYB-regulator of stomatal cell proliferation. Functional enrichment analyses imply that heat stress is a major acclimation component of potato leaves to agronomical relevant drought stress. Enhanced leaf heat stress is a result of drought caused by loss of transpiration cooling. This effect and CO2-limitation are the main dilemmas of drought- or ABA-induced stomatal closure. Constitutive differences between tolerant and sensitive cultivars indicate partially synergistic interactions of drought and biotic stress responses. We suggest that drought tolerance of the potato reference cultivars may be caused by general resistance mechanisms which are part of previously selected pathogen tolerance. Transcriptome profiling by RNA-sequencing of 48 leaf samples from 4 potato cultivars grown under control or drought stress conditions in 6 independent experiments

Dataset Information

Host-based markers for the early stage of infection by the grapevine trunk pathogen Neofusicoccum parvum

Publications

Genes expressed in grapevine leaves reveal latent wood infection by the fungal pathogen Neofusicoccum parvum.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets