The unusually long small subunit ribosomal RNA gene found in amitochondriate amoeboflagellate Pelomyxa palustris: its rRNA predicted secondary structure and phylogenetic implication

In order to ascertain a phylogenetic position of the freshwater amitochondr iate amoeboflagellate Pelomyxa palustris its small subunit (SSU) rRNA gene was amplified and sequenced. It was shown to be 3502 bp long. The predicted secondary structure of its rRNA includes at least 16 separate expansion zo nes located in ail the variable regions (Vl-V9), as well as in some conserv ative gene regions. Most insertions are represented by sequences of low com plexity that have presumably arisen by a slippage mechanism. Relatively con servative, uniformly positioned motifs contained in regions V4 and V7, as w ell as in some others, made it possible to perform folding. In maximum like lihood, maximum parsimony, and neighbor-joining trees, P. palustris tends t o cluster with amitochondriate and secondary lost mitochondria amoebae and amoeboflagellates Entamoeba, Endolimax nana, and Phreatamoeba balamuthi, co mprising together with them and aerobic lobose amoebae Vannella, Acanthamoe ba. Balamuthia, and Hartmannella a monophyletic cluster. Another pelobiont, Mastigamoeba invertens, does not belong to this cluster. No specific simil arity was discovered between the SSU rRNA of P. palustris and amitochondria te taxa of 'Archezoa': Diplomonada, Parabasalia, Microsporidia. Pelomyxa:a palustris SSU rRNA does not occupy a basal position in the phylogenetic tre es and could be ascribed to the so-called eukaryotic 'crown' group if the c omposition of the latter were not so sensitive to the methods of tree build ing. Thus, molecular and morphological data suggest that P. palustris repre sents a secondarily modified eukaryotic lineage. (C) 2001 Published by Else vier Science B.V. All rights reserved.