Table 1_Integrated RNA-seq and snRNA-seq analysis identifies PR10 tandem gene cluster governing early defense against Fusarium wilt in sea island cotton.xlsx

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.

由尖孢镰刀菌萎蔫专化型7号小种（Fusarium oxysporum f. sp. vasinfectum 7, FOV7）引发的棉花枯萎病，对优质海岛棉（Gossypium barbadense）的生产构成重大威胁。为解析棉花抵御FOV7的分子机制，本研究通过RNA测序（RNA sequencing）鉴定了不同侵染阶段的大量差异表达基因（differentially expressed genes）。后续通过K均值聚类（K-means clustering）与加权基因共表达网络分析，发现一个显著富集于防御反应及脱落酸激活信号通路的核心模块。对这些通路内基因分布的详细分析显示，50个基因中有10个属于病程相关蛋白10（Pathogenesis-Related 10, PR10）基因家族。对这些PR10基因的进化分析揭示，D亚基因组（D sub-genome）第10号染色体上存在一个串联扩增基因簇（tandemly-expanded gene cluster）。此外，通过单细胞核RNA测序（single-nucleus RNA sequencing, snRNA-seq）构建的根细胞类型图谱，精准定位了根表皮中的FOV7响应位点，并鉴定出GbD_PR10.11为特异性激活的哨兵基因。本研究从全基因组模式逐步聚焦至单一细胞类型中的单个基因，不仅解析了棉花-病原菌军备竞赛的关键组分，同时为创制前沿抗病性提供了高可信度的靶点。