| Summary: | <p>Abstract</p> <p>Background</p> <p><it>Cryptosporidium </it>is a protozoan parasite that causes diarrheal illness in a wide range of hosts including humans. Two species, <it>C. parvum </it>and <it>C. hominis </it>are of primary public health relevance. Genome sequences of these two species are available and show only 3-5% sequence divergence. We investigated this sequence variability, which could correspond either to sequence gaps in the published genome sequences or to the presence of species-specific genes. Comparative genomic tools were used to identify putative species-specific genes and a subset of these genes was tested by PCR in a collection of <it>Cryptosporidium </it>clinical isolates and reference strains.</p> <p>Results</p> <p>The majority of the putative species-specific genes examined were in fact common to <it>C. parvum </it>and <it>C. hominis</it>. PCR product sequence analysis revealed interesting SNPs, the majority of which were species-specific. These genetic loci allowed us to construct a robust and multi-locus analysis. The Neighbour-Joining phylogenetic tree constructed clearly discriminated the previously described lineages of <it>Cryptosporidium </it>species and subtypes.</p> <p>Conclusions</p> <p>Most of the genes identified as being species specific during bioinformatics in <it>Cryptosporidium </it>sp. are in fact present in multiple species and only appear species specific because of gaps in published genome sequences. Nevertheless SNPs may offer a promising approach to studying the taxonomy of closely related species of Cryptosporidia.</p>
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