title: RNAseq of pima roots under FOV4 inoculation
design: Three biological replicates were collected for each time point and treatment. Each replicate comprised roots pooled from two plants, flash-ground in liquid nitrogen for RNA isolation. Total RNA was extracted using a modified CTAB method with lithium chloride precipitation, following Kumar et al. [19]. mRNA libraries were prepared and sequenced at Novogene. Raw reads were trimmed with Trimmomatic and aligned to the Gossypium barbadense cultivar 3-79 reference genome (HAU_v1.1)  using Bowtie2. Because root tissue contained both host and fungal cells (Fusarium oxysporum f. sp. vasinfectum race 4), reads were binned to remove transcripts attributable to FOV4 prior to downstream host transcriptome analyses