Single-nucleus RNA-sequencing reveals the cellular programs driving nematode-induced giant cell formation in tomato

Area of Science:

• Plant biology
• Nematology
• Molecular genetics

Background:

• Root-knot nematodes (Meloidogyne spp.) are major plant parasites.
• They induce galls by altering root cell identity to form giant cells for feeding.
• The molecular mechanisms of gall and giant cell development are largely unknown.

Purpose of the Study:

• To investigate the molecular events during giant cell formation and differentiation.
• To create a single-nucleus transcriptomic map of nematode-induced galls in tomato.
• To identify genes and regulatory networks involved in plant-parasite interactions.

Main Methods:

• Single-nucleus RNA sequencing (snRNA-seq) of tomato galls and root tissues infected by Meloidogyne incognita.
• Analysis of 35,393 nuclei to identify cell clusters and differentially expressed genes.
• Pseudotime and developmental trajectory analyses to trace gene activity changes.
• Promoter activity assays and gene silencing to validate gene function.

Main Results:

• Identified three stele-associated cell clusters representing developing giant cells.
• Discovered 772 preferentially expressed genes in giant cells.
• Revealed gradual activation of complex gene regulatory networks during giant cell development.
• Confirmed the role of giant cell-expressed genes in plant susceptibility to nematodes.
• Showed extensive transcriptome reprogramming in various root cell types (xylem, phloem, stele, endodermis, protophloem).

Conclusions:

• This study provides the first single-nucleus transcriptomic map of nematode-induced giant cells.
• Novel insights into the molecular basis of plant organ formation orchestrated by a parasite.
• Identified key genes and cellular processes mediating plant responses to nematode infection.