Secondary structure model for the ITS-2 precursor rRNA of strongyloid nematodes of equids: implications for phylogenetic inference.
Abstract: In order to maximise the positional homology in the primary sequence alignment of the second internal transcribed spacer for 30 species of equine strongyloid nematodes, the secondary structures of the precursor ribosomal RNA were predicted using an approach combining an energy minimisation method and comparative sequence analysis. The results indicated that a common secondary structure model of the second internal transcribed spacer of these nematodes was maintained despite significant interspecific differences (2-56%) in primary sequences. The secondary structure model was then used to refine the primary second internal transcribed spacer sequence alignment. The 'manual' and 'structure' alignments were both subjected to phylogenetic analysis to compare the effect of using different sequence alignments on phylogenetic inference. The topologies of the phylogenetic trees inferred from the manual second internal transcribed spacer alignment were usually different to those derived from the structure second internal transcribed spacer alignment. The results suggested that the positional homology in the second internal transcribed spacer primary sequence alignment was maximised when the secondary structure model was taken into consideration.
Publication Date: 2000-08-29 PubMed ID: 10961851DOI: 10.1016/s0020-7519(99)00155-1Google Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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The research article focuses on improving the predictions of the evolutionary relationships among 30 species of equine strongyloid nematodes by considering the secondary structure model of their ribosomal RNA’s second internal transcribed spacer. The researchers used a combination of energy minimization method and comparative sequence analysis to predict this structure. They found that despite differences in primary sequences, a common secondary structure for this particular spacer remains, influencing the results of phylogenetic inference.
Methodology
- The researchers worked with the second internal transcribed spacer of the ribosomal RNA from 30 species of equine strongyloid nematodes.
- An energy minimisation method and comparative sequence analysis were utilised to predict the secondary structures of this RNA.
Findings
- Despite considerable interspecific variations (from 2% to 56%) in the primary sequences, a common secondary structure model was found to prevail.
- This secondary structure model was then used to refine the primary sequence alignment of the second internal transcribed spacer.
Phylogenetic Analysis
- The phylogenetic analysis was conducted twice — once with the ‘manual’ sequence alignment, and again with the ‘structure’ alignment, which was refined considering the secondary structure model.
- The topologies of the phylogenetic trees inferred from these two different types of alignments for the second internal transcribed spacer were compared.
Key Insights
- The results unveiled that the topology of phylogenetic trees produced from the ‘structure’ alignment was usually different from those derived from the ‘manual’ alignment.
- The findings suggest that taking the secondary structure model into account when creating the sequence alignment for the second internal transcribed spacer maximises positional homology, thus having a potential influence on the accuracy of phylogenetic predictions.
Cite This Article
APA
Hung GC, Chilton NB, Beveridge I, Gasser RB.
(2000).
Secondary structure model for the ITS-2 precursor rRNA of strongyloid nematodes of equids: implications for phylogenetic inference.
Int J Parasitol, 29(12), 1949-1964.
https://doi.org/10.1016/s0020-7519(99)00155-1 Publication
Researcher Affiliations
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia.
MeSH Terms
- Animals
- Base Sequence
- Horses / parasitology
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- RNA Precursors / chemistry
- RNA, Helminth / chemistry
- RNA, Ribosomal / chemistry
- Strongyloidea / classification
- Strongyloidea / genetics
Citations
This article has been cited 10 times.- Louro M, Kuzmina TA, Bredtmann CM, Diekmann I, de Carvalho LMM, von Samson-Himmelstjerna G, Krücken J. Genetic variability, cryptic species and phylogenetic relationship of six cyathostomin species based on mitochondrial and nuclear sequences. Sci Rep 2021 Apr 15;11(1):8245.
- Saeed MA, Beveridge I, Abbas G, Beasley A, Bauquier J, Wilkes E, Jacobson C, Hughes KJ, El-Hage C, O'Handley R, Hurley J, Cudmore L, Carrigan P, Walter L, Tennent-Brown B, Nielsen MK, Jabbar A. Systematic review of gastrointestinal nematodes of horses from Australia. Parasit Vectors 2019 Apr 29;12(1):188.
- C H B, Robbins RT, Szalanski AL. Secondary structure models of D2-D3 expansion segments of 28S rRNA for Hoplolaiminae species. J Nematol 2010 Sep;42(3):218-29.
- Coleman AW. Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Res 2007;35(10):3322-9.
- Wang S, Bao Z, Li N, Zhang L, Hu J. Analysis of the secondary structure of ITS1 in Pectinidae: implications for phylogenetic reconstruction and structural evolution. Mar Biotechnol (NY) 2007 Mar-Apr;9(2):231-42.
- Posedi J, Drögemüller M, Schnieder T, Höglund J, Lichtenfels JR, von Samson-Himmelstjerna G. Microchip capillary electrophoresis-based genetic comparison of closely related cyathostomin nematode parasites of horses using randomly amplified polymorphic DNA polymerase chain reaction. Parasitol Res 2004 Mar;92(5):421-9.
- Côté CA, Greer CL, Peculis BA. Dynamic conformational model for the role of ITS2 in pre-rRNA processing in yeast. RNA 2002 Jun;8(6):786-97.
- Huby-Chilton F, Beveridge I, Gasser RB, Chilton NB. Redescription of Zoniolaimus mawsonae Beveridge, 1983 (Nematoda: Strongyloidea) and the description of Z. latebrosus n. sp. from the red kangaroo Macropus rufus (Marsupialia: Macropodidae) based on morphological and molecular data. Syst Parasitol 2002 Feb;51(2):135-47.
- Chilton NB, Huby-Chilton F, Gasser RB, Beveridge I. Review of Papillostrongylus Johnston & Mawson, 1939 (Nematoda: Strongyloidea) from wallabies and kangaroos (Marsupialia: Macropodidae) using morphological and molecular techniques, with the description of P. barbatus n. sp. Syst Parasitol 2002 Feb;51(2):81-93.
- Jia H, Tang L, Fu Y, Xiong Y, Yan L, Shao C, Li K, Zhang D, Hu D. The first mitogenome of Petrovinema skrjabini from Equus ferus przewalskii: a phylogenetic analysis within the Strongylidae family. Parasit Vectors 2025 Jul 11;18(1):278.
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