Comparative transcriptome analysis reveals regulatory networks and key genes of microsclerotia formation in the cotton vascular wilt pathogen

•Melanin synthesis-related DEGs are preferentially up-regulated during microsclerotia formation.•The C2H2, Zn2Cys6, bZIP, and fungal-specific transcription factors regulated microsclerotia formation.•G-protein receptors, Ca2+, small GTPases, and cAMP were very important for the process.•VDAG_06474 and VDAG_05314 gene were negatively and positively influence microsclerotia formation, respectively. Verticillium dahliae is a soil-borne, hemibiotrophic phytopathogenic fungus that causes Verticillium wilt in a broad range of economic crops. The microsclerotia (MS), which act as the main host inoculum, can survive long-term in soil resulting in uncontrollable disease. In order to clarify the mechanism of MS formation, we sequenced the whole genome-wide expression profile of V. dahliae strain V991. Compared with M1 (no MS formation), during the process of MS formation and maturation, 1354, 1571, and 1521 unique tags were significantly regulated in M2, M3, and M4 library, respectively. During MS formation, melanin synthesis-related genes were preferentially upregulated. The process is more likely to regulated by transcription factors (TFs) including C2H2, Zn2Cys6, bZIP, and fungal-specific TF domain-containing proteins; additionally, G-protein coupled receptors, Ca2+, small GTPases, and cAMP were involved in signalling transduction. Protein kinase-encoding (VDAG_06474) and synthase-encoding (VDAG_05314) genes were demonstrated to negatively and positively influence MS production, respectively. The gene expression dynamics revealed during MS formation provide comprehensive theoretical knowledge to further understanding of the metabolism and regulation of MS development in V. dahliae, potentially providing targets to control Verticillium wilt through interfering MS formation.