| Summary: | Cotton is often threatened by Verticillium wilt caused by <i>V. dahliae</i>. Understanding the molecular mechanism of <i>V. dahlia</i>–cotton interaction is important for the prevention of this disease. To analyze the transcriptome profiles in <i>V. dahliae</i> and cotton simultaneously, the strongly pathogenic strain Vd592 was inoculated into cotton, and the infected cotton roots at 36 h and 3 d post infection were subjected to dual RNA-seq analysis. For the <i>V. dahliae</i>, transcriptomic analysis identified 317 differentially expressed genes (DEGs) encoding classical secreted proteins, which were up-regulated at least at one time point during infection. The 317 DEGs included 126 carbohydrate-active enzyme (CAZyme) and 108 small cysteine-rich protein genes. A pectinesterase gene (VDAG_01782) belonging to CAZyme, designated as <i>VdPE1</i>, was selected for functional validation. <i>VdPE1</i> silencing by HIGS (host-induced gene silencing) resulted in reduced disease symptoms and the increased resistance of cotton to <i>V. dahliae</i>. For the cotton, transcriptomic analysis found that many DEGs involved in well-known disease resistance pathways (flavonoid biosynthesis, plant hormone signaling, and plant–pathogen interaction) as well as PTI (pattern-triggered immunity) and ETI (effector-triggered immunity) processes were significantly down-regulated in infected cotton roots. The dual RNA-seq data thus potentially connected the genes encoding secreted proteins to the pathogenicity of <i>V. dahliae</i>, and the genes were involved in some disease resistance pathways and PTI and ETI processes for the susceptibility of cotton to <i>V. dahliae</i>. These findings are helpful in the further characterization of candidate genes and breeding resistant cotton varieties via genetic engineering.
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