Microsclerotia developmental process of the smoke tree vascular wilt fungus, V. dahliae . and the transcriptome analysis pipeline. A. Micrographs showing microsclerotial development processes from conidia to microsclerotia in Verticillium dahliae. The panels represent different developmental stages of smoke tree wilt fungus cultured in CM broth and BM, respectively. Scale bar = 10 μm. MS1-MS4 represent four typical stages during the entire process of microsclerotia formation at 60 h, 72 h, 96 h and 14 d represent four stages of microsclerotia formation used for RNA-Seq. B. Flowcharts of the RNA-Seq method employed in this study. Tophat was used to align RNA-Seq reads to the genome of V. dahliae VdLs.17 (Broad Institute) and Cufflinks package was used to assemble and find differentially expressed genes and transcripts.