# Integrated RNA-seq and snRNA-seq analysis identifies PR10 tandem gene cluster governing early defense against Fusarium wilt in sea island cotton

## TL;DR

This study identifies a gene cluster in cotton that helps defend against a harmful fungus, using RNA sequencing and single-cell analysis.

## Contribution

The study identifies a PR10 tandem gene cluster in cotton that governs early defense against Fusarium wilt using integrated RNA-seq and snRNA-seq analysis.

## Key findings

- A PR10 gene cluster on chromosome 10 of the D sub-genome is significantly involved in defense against Fusarium wilt.
- GbD_PR10.11 is specifically activated in the root epidermis during infection.
- The study links genome-wide patterns to a single gene in a specific cell type for cotton resistance.

## Abstract

Fusarium wilt, caused by Fusarium oxysporum f. sp. vasinfectum 7 (FOV7), poses a major threat to the production of elite Sea Island cotton (Gossypium barbadense). To uncover the molecular basis of defense FOV7 in cotton, we employed RNA sequencing to identify numerous differentially expressed genes across various stages of infection. Subsequent K-means clustering and weighted gene co-expression network analysis revealed a core module significantly enriched in defense response and abscisic acid-activated signaling pathways. A detailed examination of the gene distribution within these pathways identified 10 out of 50 genes as members of the Pathogenesis-Related 10 (PR10) gene family. Evolutionary analysis of these PR10 genes uncovered a tandemly-expanded gene cluster located on chromosome 10 of the D sub-genome. In addition, root cell type maps constructed via single-nucleus RNA sequencing (snRNA-seq) enabled pinpointing FOV7 response in the root epidermis, where GbD_PR10.11 was identified as a specifically activated sentinel. Our work, by logically progressing from genome-wide patterns to a single gene in a single cell type, not only deciphers a key component of the cotton-pathogen arms race but also delivers a high-confidence target for engineering frontline resistance.