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First data on ribosome operon sequence (18S+ITS1+5.8S+ITS2+28S) of the archigregarine Selenidium sp., an intestine parasite of spionid polychetes Pygospio elegans and Polydora glycimerica, are obtained. Archigregarines are the most plesiomorphic group of sporozoan Apicomplexa: their mature gamonts and even syzygy retain a set of features, which are characteristic just for infection stages (sporo- and merozoites) of other sporozoans (apical complex of organelles consisting of conoid, polar ring, and rhoptry-micronemal system). According to molecular phylogenetic studies of archigregarine 18S rDNA performed by B.S. Leander et al., they form four branches (including two extremely long ones) hardly grouping to one another and keeping uncertain positions within Apicomplexa. We studied samples of Selenidium sp. from the White Sea (from P. elegans) and Sea of Japan (from P. glycimerica). A ribosome operon contig was obtained from the White Sea sample, but only 18S rDNA sequence from the Far East sample. Comparison of 18S rDNA of the two samples shows almost full identity (1 substitution /1602 sites, 0 indels), so these samples apparently represent the same species. ML and Bayesian analyses of 18S rDNA show this species belonging to one of the archigregarine long branches, which contains four other Selenidium species. The 28S and ribosome operon analyses show affinity of this species to gregarines; however the taxonomical sample is insufficient to make more certain conclusions. Funding: RFBR (10-04-90746, 11-04-90778), and Ministry of Education and Science of Russia (Federal Target Program "Scientific and scientific-pedagogical personnel of innovative Russia" for 2009 – 2013).