Primers for genotyping single nucleotide polymorphisms and microsatellites in the pathogenic fungus Coccidioides immitis

The pathogenic fungus Coccidioides immitis is endemic to semi-arid soils of southwestern United States, Central and South America (Pappagianis 1988) . Until recently, C. immitis had been considered a single species, however recent molecular analysis has shown that C. immitis consists of a species pair, now referred to as the Californian and non-California types (Zimmermann et al. 1994; Burtet al. 1997; Koufopanou et al. 1997). These species are estimated to have been reproductively isolated from one another for the past 11 million years (Koufopanou et al. 1997; Koufopanou et al. 1998). A study by Burt et al. (1997) used a panel of single nucleotide polymorphisms (SNPs) to infer the mode of reproduction and the amounts of gene flow between populations of the non-Californian species of C. immitis. However, due to the time of separation between the two species, these SNP markers had all gone to fixation within the California species and were uninformative in population genetic studies.

In this study, we describe the characterization and isolation of two classes of polymorphic genetic markers from the California species of C. immitis, (1) SNPs and (2) microsatellites. Due to their low mutation rates, SNP markers were isolated to test hypotheses about the mode of reproduction in California C. immitis. The multiallelic nature of microsatellites lends them to clinical diagnostic uses in both species of C. immitis simultaneously, and were isolated to this end.