Bioinformatic methods for the investigation of cross-kingdom RNA communication

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Technological advances in terms of high-throughput RNA sequencing and bioinformatics data processing enable cost effective experiments for the investigation of cross-kingdom RNA communication (ckRNAi) in host-microbe interactions. In addition, the effects on the transcriptome of plants and their interacting microbes (viz. pathogens and beneficials) can be studied at an unprecedented level of detail by dual RNA sequencing approaches. With the establishment of many of these data sets, it becomes feasible to implement a comparative perspective to evaluate the effects of different RNA species (e.g. small (s)RNA and mRNA) in different plant-microbe interactions. Within this project, we will automate and standardize the existing analysis protocols and incorporate comparative analyses. We will apply the FAIR (Findable, Accessible, Interoperable, Reusable) principles on data and results. Participation in the consortium facilitates access to the required large-scale data sets and the comparative investigation of ckRNAi effects, whereas the RU5116 and each member of the consortium will benefit from our analysis capabilities for their own projects and for a more comprehensive view on RNA communication in plant-microbe interactions.More specifically, we will support our collaborating partners within this research group by implementing automated analysis workflows that are easy to use, that process, visualize, and compare the results, and that can be scaled-out efficiently in cloud computing environments. Finally, we will also evaluate open-source tools for comparative co-expression network analyses for the extension of our pipelines.