5.8S rRNA Sequence and Secondary Structure in Parabronema skrjabini and Related Habronematidae Species
Abstract
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.Eslami A, Meydani M, Maleki S, Zargarzadeh A. Gastrointestinal nematodes of wild sheep (Ovis orientalis) from Iran. Iran. J wildl Dis. 1979;15(2):263-5.
Eslami A, Nabavi L. Species of gastro-intestinal nematodes of sheep from Iran. Bull Soc Pathol Exot Filiales. 1976;69(1):92-5.
Hasheminasab SS. Molecular characterization of the first internal transcribed spacer of rDNA of Parabronema skrjabini for the first time in sheep. Ann Parasitol. 2015;61(4):241-6.
Michot B, Qu Lh, Bachellerie Jp. Evolution of large‐subunit rRNA structure. Eur J Biochem. 1990;188(2):219-29.
Zwieb C, Glotz C, Brimacombe R. Secondary structure comparisons between small subunit ribosomal RNA molecules from six different species. Nucleic Acids Res. 1981;9(15):3621-40.
Crease TJ, Colbourne JK. The unusually long small-subunit ribosomal RNA of the crustacean, Daphnia pulex: sequence and predicted secondary structure. J Mol Evol. 1998;46(3):307-13.
Hwang UW, Ree HI, Kim W. Evolution of hypervariable regions, V4 and V7, of insect 18S rRNA and their phylogenetic implications. Zoolog Sci. 2000;17(1):111-21.
Zhang X, Jing C, Li Na L, Tong W, Jiang P, Wang ZQ. Phylogenetic location of the Spirometra sparganum isolates from China, based on sequences of 28S rDNA D1. Iran J Parasitol. 2014;9(3):319-28.
Zhang XD, Yang XY, Yang LR, Li LC, Zuo HT, Na RH, Zhao ZG, Wang JJ. Cloning and Sequence Analysis of the rDNA-ITS of Parabronema skrjabini . Chinese J Anim Vet Sci. 2009;5:026.
Jaeger JA, Turner DH, Zuker M. Improved predictions of secondary structures for RNA. Proc Natl Acad Sci. 1989;86(20):7706-10.
Zuker M, Mathews DH, Turner DH. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. RNA biochem biotechnol: Springer; 1999. p. 11-43.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725-9.
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| Issue | Vol 11 No 2 (2016) | |
| Section | Short Communication(s) | |
| Keywords | ||
| Parabronema skrjabini Secondary structure | ||
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