Secondary structure model for the ITS-2 precursor rRNA of strongyloid nematodes of equids: implications for phylogenetic inference

In order to maximise the positional homology in the primary sequence alignm ent of the second internal transcribed spacer for 30 species of equine stro ngyloid nematodes, the secondary structures of the precursor ribosomal RNA were predicted using an approach combining an energy minimisation method an d comparative sequence analysis. The results indicated that a common second ary structure model of the second internal transcribed spacer of these nema todes was maintained despite significant interspecific differences (2-56%) in primary sequences. The secondary structure model was then used to refine the primary second internal transcribed spacer sequence alignment. The 'ma nual' and 'structure' alignments were both subjected to phylogenetic analys is to compare the effect of using different sequence alignments on phylogen etic inference. The topologies of the phylogenetic trees inferred from the manual second internal transcribed spacer alignment were usually different to those derived from the structure second internal transcribed spacer alig nment. The results suggested that the positional homology in the second int ernal transcribed spacer primary sequence alignment was maximised when the secondary structure model was taken into consideration. (C) 1999 Australian Society for Parasitology Inc. Published by Elsevier Science Ltd. All right s reserved.