"We phenotyped 20 tomato genotypes for resistance against insects. We could show that whiteflies or thrips placed on leaves of this tomato collection exhibited differential survival rates.
We profiled volatiles and acylsugars from this tomato collection. I implemented an innovative Random Forest method to relate insect resistance to trichome metabolites. This approach yielded 17 metabolic candidates that putatively explain the toxicity of some tomato genotypes towards these herbivorous pests.
Upon identification of these metabolic candidates, an important goal is to ensure increased levels of natural insecticide pathways in cultivated tomatoes. To do so, one way is to find the transcriptional levers that can raise the expression levels of biosynthetic enzymes and other necessary genes. Therefore, trichomes from our set of 20 genotypes were also collected to isolate mRNA and small RNA (sRNA).
To be able to mine the built datasets, I developed the necessary bioinformatic pipelines and statistical methods to analyse mRNA expression levels, discover microRNA or sRNA clusters and perform reference-free de novo assembly of wild tomato transcriptomes. Regarding sRNAs, we developed a ""pangenome"" approach by relying on four genomic references from cultivated tomato (S. lycopersicum) and wild tomatoes (S. pennellii, S. arcanum and S. habrochaites) to discover a total of 123 unique microRNAs in the trichomes of our tomato collection.
Recently, I further developed tools allowing data mining and analyses for colleagues, such as a genome browser and a workflow engine (Snakemake) to improve the traceability and reproducibility of the genomic analyses.
In parallel to the main project we developed a new research on cross-kingdom transfer of small RNAs between tomato and whitefly. This work was a collaborative effort combining my expertise on sRNA-seq with the insect-effector expertise of a fellow post-doctoral researcher in the lab. We were the first to show that sap-feeding insects transfer sRNAs, a new type of interacting molecule (see results overview).
Results:
• Whitefly and thrips survivals
• Sequencing of trichome sRNA/mRNA transcriptomes
• Trichome volatile and acylsugar profiles
• Implementation of a Random Forest approach
• Bioinformatic pipelines on mRNA-Seq data
• Set-up of new bioinformatic tools to explore NGS results
Dissemination:
• User meetings: progress disseminated to 4 international seed/biotech companies twice a year.
• Lab, department and Institute meetings: weekly lab-meetings (Plant Physiology, Systems Biology departments).
• Conference: 2015/2016/2017. Attendance at the national yearly conference of the Dutch plant society (EPS), Lunteren, NL.
• Conference: November 2016: Attendance at the “Plant Omics for Human Health”, Gent, BE.
• Conference: April 2017: Poster at the Bioinformatics and Systems Biology conference (BioSB 2017): “Natural insecticides from wild tomatoes identified by regressions and Random Forest”.
• Invited Lecture: April 2017: sRNAs and their usability in breeding at seed company Enza Zaden, Enkhuizen, NL.
• Bioinformatics tool dissemination: sharing of RNA-Seq pipelines and animation of a Mozilla Study Group
• Publication: van Kleeff P*, Galland M*, Schuurink Rob, Bleeker PM. Front Plant Sci. 2016 7:1759.
• Workshop: October 2016. Presentation at the “11th Plant-Insect Interaction Workshop”, Leiden, NL. “Identification of natural insecticides from wild tomato relatives by combined regression and random forest analyses”.
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