P-021 - Deciphering the mechanisms of molecular reprogramming in plants upon interaction with biotic agents using multi-omics integration, knowledge graph and topological data analysis

Global population is rapidly increasing, representing a major challenge for food supply, exacerbated by climate change and environmental degradation. Most of those depend on agriculture, however plants health is threatened by various stressors. Although how plants respond to each of these individual stresses is well studied, little is known about how they respond to a combination of many of these bio-aggressors occurring together.

To tackle this question, we analyzed the transcriptome response of tomato to six distinct pathogens with our novel integrative approach, HIVE. Then we used TomTom, a knowledge graph which we developed gathering molecular interactions from nine databases, to extract a comprehensive gene regulatory network (GRN) to study how multi-pathogens stress response is coordinated.  By estimating the transcription factor activity, we identified 43 TFs responding either specifically to one bio-aggressor or to multiple ones. The analysis of the GRN with a topological data analysis approach, allowed to identify 18 clusters of transcription factors hierarchically organized in four main configurations depending on TF activity and shared targets. Finally, we found four ERF hubs which cooperatively orchestrate the tomato response to multiple pests.

Our tools allowed to study the complex molecular reprogramming in tomato upon interaction with wide-different biotic agents, providing methods scalable to other phyto-pathosystems.