Integrated Transcriptomic and Metabolomic Analysis of G. hirsutum and G. barbadense Responses to Verticillium Wilt Infection

<i>Verticillium</i> wilt (VW) caused by <i>Verticillium dahliae</i> (Vd) is a devastating fungal cotton disease characterized by high pathogenicity, widespread distribution, and frequent variation. It leads to significant losses in both the yield and quality of cotton. Identifying key non-synonymous single nucleotide polymorphism (SNP) markers and crucial genes associated with VW resistance in <i>Gossypium hirsutum</i> and <i>Gossypium barbadense</i>, and subsequently breeding new disease-resistant varieties, are essential for VW management. Here, we sequenced the transcriptome and metabolome of roots of TM-1 (<i>G. hirsutum</i>) and Hai7124 (<i>G. barbadense</i>) after 0, 1, and 2 days of V991 inoculation. Transcriptome analysis identified a total of 72,752 genes, with 5814 differentially expressed genes (DEGs) determined through multiple group comparisons. KEGG enrichment analysis revealed that the key pathways enriched by DEGs obtained from both longitudinal and transverse comparisons contained the glutathione metabolism pathway. Metabolome analysis identified 995 metabolites, and 22 differentially accumulated metabolites (DAMs), which were correlated to pathways including glutathione metabolism, degradation of valine, leucine, and isoleucine, and biosynthesis of terpenoids, alkaloids, pyridine, and piperidine. The conjoint analysis of transcriptomic and metabolomic sequencing revealed DAMs and DEGs associated with the glutathione metabolism pathway, and the key candidate gene <i>GH_D11G2329</i> (glutathione S-transferase, <i>GSTF8</i>) potentially associated with cotton response to VW infection was selected. These findings establish a basis for investigating the mechanisms underlying the cotton plant's resistance to VW.