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

<i>Fusarium</i> wilt, caused by <i>Fusarium oxysporum f.</i> sp. <i>vasinfectum 7</i> (FOV7), poses a major threat to the production of elite Sea Island cotton (<i>Gossypium barbadense</i>). 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 <i>Pathogenesis-Related 10</i> (<i>PR10</i>) gene family. Evolutionary analysis of these <i>PR10</i> 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 <i>GbD_PR10.11</i> 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.