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New data on Protococcidia, a presumably plesiomorphic group of Apicomplexa, were obtained with help of molecular methods and electron microscopy. We have studied two species: Eleutheroschizon duboscqui and Coelotropha durchoni. E. duboscqui was studied by electron microscopy for the first time. As previously described (Chatton & Villeneuve, 1936), it has epicellular localization on the gut epithelium of the polychaete Scoloplos armiger. Our data show that E. duboscqui has an attachment apparatus similar to gregarines. Moreover the parasites enclosed within a thin membranous “sac” formed by the host cell. These morphological data liken E. duboscqui to Cryptosporidium. C. durchoni starts to develop as an intracellular parasite of coelomocytes of the polychaete Nereis diversicolor. However, during its growth, C. durchoni bursts the host cell from within and finalizes its life cycle extracellularly in coelom (Vivier & Hennere, 1965). We have sequenced ribosome operon (18S+ITS1+5,8S+ITS2+28S rRNA genes) of both species. The preliminary phylogenetic analysis was carried out by “Neighbor joining” (NJ) and “Bayesian inference” (BI) methods. According to the results, Protococcidia is a polyphyletic taxon. C. durchoni is associated with Coccidia, however it is not related to Eimeriida or Adeleida. C. durchoni and several unidentified environmental sequences form a basal branch to the Aggregata clade. E. duboscqui can not be unequivocally characterized by the molecular phylogenetic analysis used in this study. By NJmethod, E. duboscqui sequences create a basal branch to Coelotropha-Aggregata lineage. However, by BI method, which is more precise, this parasite is unexpectedly affined to colpodellids, not to Sporozoa. Thus, this species unite neither with Coccidia, nor with Cryptosporidia, as it could be inferred from their life cycle and parasitism mode. E. duboscqui appears more plesiomorphic than any other known organism with “sporozoan” life cycle.