Dataset Information

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.

SUBMITTER: Hasheminasab SS

PROVIDER: S-EPMC5236104 | biostudies-literature | 2016 Apr-Jun

REPOSITORIES: biostudies-literature

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5.8S rRNA Sequence and Secondary Structure in <i>Parabronema skrjabini</i> and Related Habronematidae Species.

Hasheminasab Seyed Sajjad SS

Iranian journal of parasitology 20160401 2

<h4>Background</h4>Genomic DNA was isolated from <i>Parabronema skrjabini</i>. rRNA region was amplified and sequenced.<h4>Methods</h4>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 <i>P. skrjabini</i> and a sequence <i>of P. skrjabini</i> and two species of <i>Habronema</i> (<i>H. microstoma</i> and <i>H. muscae< ...[more]

PMID: 28096861

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Project description:A comparative study of variable domains V4, V6, and V9 of the mitochondrial small-subunit (SSU) rRNA was carried out with the genus Agrocybe by PCR amplification of 42 wild isolates belonging to 10 species, Agrocybe aegerita, Agrocybe dura, Agrocybe chaxingu, Agrocybe erebia, Agrocybe firma, Agrocybe praecox, Agrocybe paludosa, Agrocybe pediades, Agrocybe alnetorum, and Agrocybe vervacti. Sequencing of the PCR products showed that the three domains in the isolates belonging to the same species were the same length and had the same sequence, while variations were found among the 10 species. Alignment of the sequences showed that nucleotide motifs encountered in the smallest sequence of each variable domain were also found in the largest sequence, indicating that the sequences evolved by insertion-deletion events. Determination of the secondary structure of each domain revealed that the insertion-deletion events commonly occurred in regions not directly involved in the secondary structure (i.e., the loops). Moreover, conserved sequences ranging from 4 to 25 nucleotides long were found at the beginning and end of each domain and could constitute genus-specific sequences. Comparisons of the V4, V6, and V9 secondary structures resulted in identification of the following four groups: (i) group I, which was characterized by the presence of additional P23-1 and P23-3 helices in the V4 domain and the lack of the P49-1 helix in V9 and included A. aegerita, A. chaxingu, and A. erebia; (ii) group II, which had the P23-3 helix in V4 and the P49-1 helix in V9 and included A. pediades; (iii) group III, which did not have additional helices in V4, had the P49-1 helix in V9 and included A. paludosa, A. firma, A. alnetorum, and A. praecox; and (iv) group IV, which lacked both the V4 additional helices and the P49-1 helix in V9 and included A. vervacti and A. dura. This grouping of species was supported by the structure of a consensus tree based on the variable domain sequences. The conservation of the sequences of the V4, V6, and V9 domains of the mitochondrial SSU rRNA within species and the high degree of interspecific variation found in the Agrocybe species studied open the way for these sequences to be used as specific molecular markers of the Basidiomycota.

Dataset Information

5.8S rRNA Sequence and Secondary Structure in Parabronema skrjabini and Related Habronematidae Species.

Publications

5.8S rRNA Sequence and Secondary Structure in <i>Parabronema skrjabini</i> and Related Habronematidae Species.

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