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Emily joined the Taylor lab in April of 2008. On February 20 2008, Emily successfully passed her PhD qualifying exam.

The mammalian pathogens Coccidioides immitis and C. posadasii are the only dimorphic fungal pathogens that form spherules in the host. Furthermore, all of Coccidioides’ closest known relatives are non-pathogenic. In this project, we are interested in genome changes between the Coccidioides lineage and its relatives, and how these changes compare to recently published comparative and population genomics, and transcriptomics studies in Coccidioides. Coccidioides and its closest sequenced relative, Uncinocarpus reesii, are estimated to have diverged 75-80 million years ago. Here, we have sequenced the genomes of four species more closely related to Coccidioides than U. reesii: Byssoonygena ceratinophila, Chrysosporium queenslandicum, Amauroascus niger and A. mutatus. For each of these four species, we prepared genomic DNA Illumina sequencing libraries; the resulting genome assemblies ranged from 23-34Mb, with N50 of 90kb-205kb. Predicted genes were confirmed by RNAseq; the total number of genes ranged from 8,179-9,184. We assessed individual gene gain/loss, and gene family expansion/contraction in Coccioides using these new genomes and other recently published genomes from the Onygenales order, including the yeast-forming dimorphic pathogens Histoplasma and Paracoccidioides, and the dermatophytes Microsporum and Trichopyton. We have compared these results to genes identified in recently published Coccidioides “omics” studies that show evidence of positive selection, introgression and/or differential expression.