ABSTRACT In the vast and diversified eukaryotic group Stramenopila we can find many different life strategies, one of them being parasitism. There are two groups of stramenopiles containing important parasites of vertebrates: the oomycetes (e.g. Saprolegnia) and the wholly parasitic group Slopalinida+its sister taxon—Blastocystis. The order Slopalinida comprises families Opalinidae and Proteromonadidae. The two families are considered related based on the structure of basal bodies and their appendages and the presence of subpelicular microtubules. However, a robust recognition of phylogenetic affinities of Opalinidae—the peculiar multinucleated intestine commensals of frogs—has been hindered by the absence of reliable molecular data. Up to now, all attempts to sequence opalinid genes failed, as the obtained sequences labeled as Protoopalina intestinalis, Cepedea virguloidea and Opalina ranarum in GenBank apparently originate from a zygomycete contamination. We present the first molecular data for the family Opalinidae—SSU rRNA gene of Protoopalina intestinalis. Our phylogenetic analyses undoubtedly show opalinids as a sister group to Proteromonas within the Stramenopila clade, confirming the monophyly of Patterson's order Slopalinida. The enigmatic genus Blastocystis is resolved with high statistical support as a sister group to Slopalinida. Our analyses clearly demonstrate that Cavalier–Smith's phylum Bigyra, which comprises Oomycetes and their relatives together with Slopalinida and Blastocystis, is not monophyletic. We also show, that Blastocystis sp. isolate obtained from the red-footed tortoise (Geochelone carbonaria), forms a sister group to all Blastocystis isolates from birds and mammals sequenced so far.
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