Analysis of Transposable Elements in Coccidioides Species.

and are primary pathogenic fungi that cause disease in immunologically-normal animals and people. The organism is found exclusively in arid regions of the Southwestern United States, Mexico, and South America, but not in other parts of the world. This study is a detailed analysis of the transposable elements (TE) in spp. As is common in most fungi, Class I and Class II transposons were identified and the LTR superfamily is the most common. The minority of transposons contained regions highly homologous to polyprotein domains. Phylogenetic analysis of the integrase and reverse transcriptase sequences revealed that many, but not all, of the reverse transcriptase and integrase domains clustered by species suggesting extensive transposition after speciation of the two spp. The TEs were clustered and the distribution is enriched for the ends on contigs. Analysis of gene expression data from found that protein-coding genes within 1 kB of or TEs were poorly expressed. The expression of genes within 1 kB of TEs was also significantly lower compared to all genes but the difference in expression was smaller than . orthologs of -associated genes were also likely to be TE-associated. In both and the TEs were preferentially associated with genes annotated with protein kinase gene ontology terms. These observations suggest that TE may play a role in influencing gene expression in spp. Our hope is that these bioinformatic studies of the potential TE influence on expression and evolution of will prompt the development of testable hypotheses to better understand the role of TEs in the biology and gene regulation of spp.