Probing the genetic population structure of Trypanosoma cruzi with polymorphic microsatellites

We describe here the identification of eight polymorphic microsatellite loci with (CA)(n) repeats in the Trypanosoma cruzi genome based on the affinity capture of fragments using biotinylated (CA)(12) attached to streptavidin-coated magnetic beads. The presence of two peaks in PCR amplification products from individual clones confirmed that T. cruzi is diploid. Hardy–Weinberg and linkage disequilibrium analyses suggested that sexual reproduction is rare or absent and that the population structure is clonal. Several strains, especially those isolated from nonhuman sources, showed more than two alleles in many loci demonstrating that they were multiclonal. The phylogenetic analysis of T. cruzi based on microsatellites revealed a great genetic distance among strains, although the strain dispersion profile in the Wagner network was in general agreement with the species dimorphism found by PCR amplification of the divergent region of the rRNA 24Sα gene.