5.8s rrna sequence and secondary structure in parabronema skrjabini and related habronematidae species

Background: genomic dna was isolated from parabronema skrjabini. rrna region was amplified and sequenced. methods: the rna secondary structure was predicted using mfold software (http://mfold.rit.albany.edu). the secondary structure with bulge, hairpins, helices, interior, external and multi loops was predicted for 5.8srdna of our sequence of p. skrjabini and a sequence of p. skrjabini and two species of habronema (h. microstoma and h. muscae) in genbank. rna motifs were predicted by meme program version 4.10.2. results: the length of 5.8s rrna sequence for p. skrjabini#1, p. skrjabini#2, h. microstoma and h. muscae was 158, 156, 127 and 127bp, and the dg required for the formation of the secondary structure was -70.50, -56.40, -41.50 and -41.40 kcal/mol, respectively. common structural elements were initially recognized with the help of mfold by screening for thermodynamically optimal and suboptimal secondary structures (default settings, with t = 37 °c). the energy levels of the presumptive secondary structures were then calculated with mfold at the dna level. both motifs and the sequence of p. skrjabini#1 were completely different from the other analyzed samples. this difference might be due to the differences in host and geographical area. conclusion: this is the first molecular study of p. skrjabini in sheep, which could be further used in the structure modeling across habronematidae.