Filamentation involves two overlapping, but distinct, programs of filamentation in the pathogenic fungus Candida albicans

The ability of the human pathogenic fungus Candida albicans to switch between yeast-like and filamentous forms of growth has long been linked to pathogenesis. Numerous environmental conditions, including growth at high temperatures, nutrient limitation, and exposure to serum, can trigger this morphological switch and are frequently used in in vitro models to identify genes with roles in filamentation. Previous work has suggested that differences exist between the various in vitro models both in the genetic requirements for filamentation and transcriptional responses to distinct filamentation-inducing media. We compared 10 in vitro models for filamentation and found broad genetic and transcriptomic differences between model systems. Methods: Total RNA was extracted from yeast or filamentous cells grown in liquid media or on solid plates. Samples were tested in biological triplicates. RNASeq libraries were generated beginning with 1.8 ng of total RNA following standardized protocols with the TruSeq RNA v2 kit (Illumina, San Diego). Libraries were diluted to a concentration of 6.0 picomoles and sequenced on a HiSeq2500 and 100 bp single reads were generated. Two lanes were used for each sample. Overall design: Total RNA profiles of Candida albicans cells grown for 3 hours in inducing and non-inducing solid and liquid media were generated in triplicate on an Illumina HiSeq2500.