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.