ArticleMolecular plant pathology2018
Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk disease complex.
Article in Molecular plant pathology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Esca disease triggers local transcriptomic response and DNA methylation changes in grapevine.Journal of experimental botany · 2026Article
- From Traditional to Omics-Driven: Emerging Strategies for Isolation, Cultivation, and Identification of Plant Endophytes.Plants (Basel, Switzerland) · 2026Review
- Beyond Koch's postulates: the pathobiome paradigm in grapevine esca disease.FEMS microbiology ecology · 2026Review
- Transcriptome profiling of symptomatic vs. asymptomatic grapevine plants reveals candidate genes for plant improvement against trunk diseases.BMC plant biology · 2025Article
- Pathogenicity Factors of Botryosphaeriaceae Associated with Grapevine Trunk Diseases: New Developments on Their Action on Grapevine Defense Responses.Pathogens (Basel, Switzerland) · 2022Review
- Characterization of Grapevine Wood Microbiome Through a Metatranscriptomic Approach.Microbial ecology · 2022Article
- Population genomics of the grapevine pathogen Eutypa lata reveals evidence for population expansion and intraspecific differences in secondary metabolite gene clusters.PLoS genetics · 2022Article
- Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review.International journal of molecular sciences · 2022Review
- The Grapevine Microbiome to the Rescue: Implications for the Biocontrol of Trunk Diseases.Plants (Basel, Switzerland) · 2022Review
- Fungal species associated with grapevine trunk diseases in Washington wine grapes and California table grapes, with novelties in the generaFrontiers in fungal biology · 2022Article
- The road to molecular identification and detection of fungal grapevine trunk diseases.Frontiers in plant science · 2022Review
- The Mycorrizal Status in Vineyards Affected by Esca.Journal of fungi (Basel, Switzerland) · 2021Article
- Evaluating the lettuce metatranscriptome with MinION sequencing for future spaceflight food production applications.NPJ microgravity · 2021Article
- Phylogenomics of Plant-AssociatedFrontiers in microbiology · 2021Article
- Exploring the Hydraulic Failure Hypothesis of Esca Leaf Symptom Formation.Plant physiology · 2019Article
- Profiling grapevine trunk pathogens in planta: a case for community-targeted DNA metabarcoding.BMC microbiology · 2018Article
- Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca PathogenFrontiers in microbiology · 2018Article
- Current Knowledge and Computational Techniques for Grapevine Meta-Omics Analysis.Frontiers in plant science · 2017Review
- Fungal Pathogen Activity and Stress-Dependent Responses of Grapevine Wood to Esca and Drought.Physiologia plantarumArticle
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Grapevines, like other perennial crops, are affected by so-called 'trunk diseases', which damage the trunk and other woody tissues. Mature grapevines typically contract more than one trunk disease and often multiple grapevine trunk pathogens (GTPs) are recovered from infected tissues. The co-existence of different GTP species in complex and dynamic microbial communities complicates the study of the molecular mechanisms underlying disease development, especially under vineyard conditions. The objective of this study was to develop and optimize a community-level transcriptomics (i.e. metatranscriptomics) approach that could monitor simultaneously the virulence activities of multiple GTPs in planta. The availability of annotated genomes for the most relevant co-infecting GTPs in diseased grapevine wood provided the unprecedented opportunity to generate a multi-species reference for the mapping and quantification of DNA and RNA sequencing reads. We first evaluated popular sequence read mappers using permutations of multiple simulated datasets. Alignment parameters of the selected mapper were optimized to increase the specificity and sensitivity for its application to metagenomics and metatranscriptomics analyses. Initial testing on grapevine wood experimentally inoculated with individual GTPs confirmed the validity of the method. Using naturally infected field samples expressing a variety of trunk disease symptoms, we show that our approach provides quantitative assessments of species composition, as well as genome-wide transcriptional profiling of potential virulence factors, namely cell wall degradation, secondary metabolism and nutrient uptake for all co-infecting GTPs.
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