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Tomato Root Transformation Followed by Inoculation with Ralstonia Solanacearum for Straightforward Genetic Analysis of Bacterial Wilt Disease

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Decoding stage-specific symbiotic programs in the Rhizophagus irregularis-tomato interaction using single-nucleus

Naomi Stuer¹, Toon Leroy¹, Thomas Eekhout²

¹Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium.

Current Biology : CB

|June 19, 2026

Summary

This summary is machine-generated.

This study reveals stage-specific gene expression in tomato roots during arbuscular mycorrhizal fungi (AMF) colonization. It identifies key transcription factors crucial for establishing this plant-fungal symbiosis.

Keywords:

AMF MINI-EX Rhizophagus irregularis Solanum lycopersicum arbuscular mycorrhiza single-cell transcriptomics snRNA-seq symbiosis tomato transcription factor

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Area of Science:

Plant biology
Mycology
Genomics

Background:

Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with most land plants.
Understanding the molecular mechanisms of AMF root colonization is complex due to spatial and temporal dynamics.

Purpose of the Study:

To generate a high-resolution single-nucleus RNA-sequencing dataset of tomato roots colonized by AMF.
To identify stage-specific transcriptional signatures during arbuscule formation.
To discover candidate transcription factors involved in symbiosis establishment.

Main Methods:

Single-nucleus RNA-sequencing (snRNA-seq) of *Solanum lycopersicum* roots colonized by *Rhizophagus irregularis*.
Unsupervised subclustering to resolve cell populations and developmental stages.
Motif-informed network inference (MINI-EX) for identifying regulatory factors.

Main Results:

Resolved AM-responsive root epidermal and cortical cells across arbuscule formation stages.
Unveiled stage-specific transcriptional signatures during AMF colonization.
Identified candidate transcription factors orchestrating symbiotic transcriptional programs.

Conclusions:

The dataset provides novel insights into plant developmental and physiological coordination during symbiosis.
Supports hypotheses on cell-cycle reactivation and nutritional cue integration.
Serves as a resource for prioritizing genes for future studies on plant-fungal interactions.