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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 <jats:italic>Cryptosporidium<\/jats:italic> clinical isolates and reference strains.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The majority of the putative species-specific genes examined were in fact common to <jats:italic>C. parvum<\/jats:italic> and <jats:italic>C. hominis<\/jats:italic>. 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 <jats:italic>Cryptosporidium<\/jats:italic> species and subtypes.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Most of the genes identified as being species specific during bioinformatics in <jats:italic>Cryptosporidium<\/jats:italic> 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.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2180-10-213","type":"journal-article","created":{"date-parts":[[2010,8,10]],"date-time":"2010-08-10T06:15:46Z","timestamp":1281420946000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":33,"title":["Multi-locus analysis of human infective Cryptosporidium species and subtypes using ten novel genetic loci"],"prefix":"10.1186","volume":"10","author":[{"given":"Maha","family":"Bouzid","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kevin M","family":"Tyler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard","family":"Christen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rachel M","family":"Chalmers","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kristin","family":"Elwin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul R","family":"Hunter","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2010,8,9]]},"reference":[{"key":"1169_CR1","doi-asserted-by":"publisher","first-page":"1239","DOI":"10.1016\/j.ijpara.2008.03.006","volume":"38","author":"L Xiao","year":"2008","unstructured":"Xiao L, Fayer R: Molecular characterisation of species and genotypes of Cryptosporidium and Giardia and assessment of zoonotic transmission. 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