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Background  Yeast-to-hypha transition is a major morphological change in fungi. Molecular regulators and pathways that are involved in this process have been extensively studied in model species, including  Saccharomyces cerevisiae . The Mitogen-Actived Protein Kinase (MAPK) cascade, for example, is known to be involved in the yeast-to-pseudohypha switch. Yet the conservation of mechanisms regulating such morphological changes in non-model fungi is still poorly understood. Here, we investigate cell remodeling and transcriptomic modifications that occur during this morphological switch in the highly aggressive ascomycete fungus  Ophiostoma novo-ulmi , the causal agent of Dutch elm disease.    Results  Using a combination of light microscopy, scanning electron microscopy and flow cytometry, we demonstrate that the morphological switch occurs in less than 27 h, with phenotypic cell modifications being detected within the first 4 h. Using RNAseq, we found that over 22% of the genome of  O. novo-ulmi  is differentially expressed during the transition. By performing clustering analyses of time series gene expression data, we identified several sets of genes that are differentially expressed according to distinct and representative temporal profiles. Further, we found that several genes that are homologous to  S. cerevisiae  MAPK genes are regulated during the yeast-to-hypha transition in  O. novo-ulmi  and mostly over-expressed, suggesting convergence in gene expression regulation.    Conclusions  Our results are the first report of a time-course experiment monitoring the morphological transition in a non-model Sordariomycota species and reveal many genes of interest for further functional investigations of fungal dimorphism.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3251-8) contains supplementary material, which is available to authorized users.

From yeast to hypha: defining transcriptomic signatures of the morphological switch in the dimorphic fungal pathogen Ophiostoma novo-ulmi