Multimodal learning reveals plants’ hidden sensory integration logic

TL;DR

This paper shows how plants use complex networks to sense and respond to microbes, revealing new ways to improve crop resilience.

Contribution

The study introduces a novel multimodal approach to uncover how microbial effectors reprogram plant sensory systems.

Findings

Microbial effectors rewire iron homeostasis through citrate-mediated redox control.

Jasmonate defenses are specifically suppressed by microbial effectors.

Nuclear splicing programs remain isolated from metabolic noise.

Abstract

Plants integrate complex environmental signals through interconnected molecular networks, yet the fundamental rules governing this sensory integration remain unknown. Studying tomato roots interacting with fungal symbionts, we discovered how microbial effectors systematically reprogram plant sensory systems by coordinating transcriptional, metabolic, and phenotypic responses. Our multimodal analysis not only confirmed prior experimental findings through purely computational means, but also revealed novel integration hubs where sensory pathways converge. This dual validation approach revealed two key mechanisms: first, the rewiring of iron homeostasis through citrate-mediated redox control, and second, the targeted suppression of jasmonate defences. Furthermore, we demonstrate how nuclear splicing programs are isolated from metabolic noise. These findings establish a new paradigm for understanding plant-microbe communication by showing how symbionts exploit latent hubs where sensory pathways converge. The discovered integration logic provides both fundamental insights into plant perception and concrete targets for engineering stress-resilient crops.

The online version contains supplementary material available at 10.1186/s12864-026-12624-y.

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