Transcriptional analysis of Coccidioides immitis mycelia and spherules by RNA sequencing

Coccidioides immitis and posadasii are dimorphic fungi that transform from mycelia with internal arthroconidia in the soil to a tissue form known as a spherule. Genes that were highly up-regulated in young spherules include a spherule surface protein and iron and copper membrane transporters. Genes that are unique to Coccidioides spp. are also over-represented in this group, suggesting that they may be important for spherule differentiation. Enriched GO terms in up-regulated genes in young spherules include oxidation/reduction, response to stress and membrane proteins. Down-regulated genes are enriched for transcription factors, especially helix-loop-helix and C2H2 type zinc finger domain-containing proteins which is consistent with the dramatic change in transcriptional profile. Almost all genes that are up-regulated in young spherules remain up-regulated in mature spherules, but a small number of genes are differentially expressed in those two stages of spherule development. Mature spherules express more Hsp31, and amylase than young spherules and less tyrosinase. Some expression of transposons was detected and most of the differentially expressed transposons were up-regulated in spherules. RNA was harvested from C. immitis RS mycelia, young spherules or mature spherules grown in vitro. rRNA was depeted and biological duplicate strand-specific, paired-end libraries were made and 100 bases sequenced from both ends using an Novaseq 6000 instrument according to the manufacturer's instructions (Illumina). Paired reads were mapped to predicted CDS or transposons using Kallisto. The count tables were normalized and adjusted p values and fold change values were determined in DESeq2.