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ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Publications at this Location » Publication #336134
Title: Closed reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk-disease complex

Author
item MORALES-CRUZ, ABRAHAM - University Of California
item ALLENBECK, GABRIELLE - University Of California
item FIGUEROA-BALDERAS, ROSA - University Of California
item ASHWORTH, VANESSA - University Of California
item Lawrence, Daniel
item TRAVADON, RENAUD - University Of California
item SMITH, RHONDA - University Of California - Cooperative Extension Service
item Baumgartner, Kendra
item ROLSHAUSEN, PHILIPPE - University Of California
item CANTU, DARIO - University Of California

Submitted to: Molecular Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/13/2017
Publication Date: 2/7/2018
Citation: Morales-Cruz, A., Allenbeck, G., Figueroa-Balderas, R., Ashworth, V.E., Lawrence, D.P., Travadon, R., Smith, R., Baumgartner, K., Rolshausen, P.E., Cantu, D. 2018. Closed reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk-disease complex. Molecular Plant Pathology. 19(2):490-503. https://doi.org/10.1111/mpp.12544.
DOI: https://doi.org/10.1111/mpp.12544

Interpretive Summary: Grapevines, like tree crops, are affected by so-called ‘trunk diseases’, which cause chronic infections of the trunk and other woody tissues. Mature grapevines typically contract more than one trunk disease. The presence of multiple fungi, which cause different trunk diseases (aka trunk pathogens), makes it difficult to understand how they interact with each other and how they collectively damage the grapevine wood. The objective of this study was to use a technique called ‘metatranscriptomics’ to compare gene expression of the trunk pathogens co-infecting the wood. Because we previously sequenced the genomes of the most widespread and aggressive trunk pathogens, we were able to map and quantify DNA and RNA sequencing reads. Initial testing on grapevine wood experimentally inoculated with individual trunk pathogens 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.

Technical 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 can 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 mapping and quantifying 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.