Nucleotide alterations in the D3 domain of the large subunit of ribosomal DNA among 21 species of equine strongyle

The expansion segments or divergent (D) domains in the large subunit (LSU) of the ribosomal DNA have been suggested as genetic markers for taxonomic and/or phylogenetic studies of parasites. In the present study, we assessed the degree of sequence variation in the D3 domain and flanking core regions of the LSU for 21 species of equine strongyles (Strongylida: Strongylidae) and determined which positions in the secondary structure of the LSU were associated with the nucleotide alterations. No intraspecific sequence variation was detected in 17 species, for which multiple individual worms were available. Mutations in sequence among species were detected at 19 nucleotide positions, most of which were located in the D3 domain. Fifteen alterations were transitions, three were transversions and one represented a site of multiple mutations. In relation to the secondary structure element of D3, 26% of these mutations were located in unpaired regions (i.e., end of loops, or in bulges of helices) and thus did not appear to alter the pairing arrangement in the helices of the secondary structure. Many of the other mutations represented partial or complete compensatory base pair changes. The magnitude of interspecific nucleotide variation in the D3 domain (0–4%) was considerably less than that recorded for some other nematode groups (enoplids and thelastomatoids), indicating that this region alone is of limited value for taxonomic and phylogenetic studies for strongyles of equids but is interesting in relation to the evolution of ribosomal DNA.