A Hexapod nuclear SSU rRNA secondary-structure model and catalog of taxon-specific structural variation

2006 ◽  
Vol 306B (1) ◽  
pp. 70-88 ◽  
Author(s):  
Bernhard Misof ◽  
Oliver Niehuis ◽  
Inge Bischoff ◽  
Andreas Rickert ◽  
Dirk Erpenbeck ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Structural Variation ◽  
Ssu Rrna ◽  
Structure Model ◽  
Secondary Structure Model ◽  
Rrna Secondary Structure

Phylogeny of Criconematina Siddiqi, 1980 (Nematoda: Tylenchida) based on morphology and D2-D3 expansion segments of the 28S-rRNA gene sequences with application of a secondary structure model

Nematology ◽  
2005 ◽  
Vol 7 (6) ◽  
pp. 927-944 ◽  
Author(s):  
Renato Crozzoli ◽  
Franco Lamberti ◽  
Nicola Vovlas ◽  
James Baldwin ◽  
Sergei Subbotin ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Secondary Structure ◽  
Sequence Divergence ◽  
Complex Model ◽  
Rrna Gene ◽  
28S Rrna ◽  
Structure Model ◽  
Secondary Structure Model ◽  
Loop Region ◽  
Unidentified Species

AbstractThe suborder Criconematina is a large group of ecto- and endoparasitic nematodes, including several species of major agricultural importance. The D2-D3 expansion segments of the 28S nuclear ribosomal RNA gene were amplified and sequenced from 23 nominal and six unidentified species from the genera Mesocriconema, Criconemoides, Ogma, Criconema, Xenocriconemella, Hemicriconemoides, Hemicycliophora, Paratylenchus, Tylenchulus, Trophonema and Sphaeronema, together with outgroup taxa from Tylenchidae (Aglenchus) and Atylenchidae (Eutylenchus). A sequence alignment optimised using the secondary structure model was analysed using maximum parsimony, maximum likelihood and Bayesian inference approaches under two models. All analyses yielded a similar topology with differences primarily in the position of poorly supported clades. Although some molecular trees differ from the previous morphologically based hypotheses of criconematid phylogeny, maximum likelihood tests did not yield statistically significant differences between some of the tested classical morphological and molecular topologies. DNA data support monophyly for the genera Mesocriconema, Hemicriconemoides and Criconema and reject the hypothesis of a single origin of criconematids with a cuticular sheath or 'double cuticle'. Application of the complex model of rRNA evolution, considering paired nucleotides for the stem and unpaired nucleotides for the loop region, resulted in a majority rule consensus Bayesian tree with unresolved relationships between main clades. This lack of resolution is expected by the low number of independently evolving nucleotides. Sequence divergence in this DNA segment between populations of Mesocriconema xenoplax, M. sphaerocephalum and Hemicriconemoides cocophillus suggest the presence of several sibling species under these taxa names.

Temperature-based variation of rRNA secondary structure models: a case study in the insect Drosophila simulans, the land snail Isabellaria adriani, and the crustacean Daphnia pulex

2001 ◽  
Vol 79 (2) ◽  
pp. 334-345 ◽  
Author(s):  
Georg FJ Armbruster
Keyword(s):  
Secondary Structure ◽  
Daphnia Pulex ◽  
Land Snail ◽  
Small Subunit ◽  
Drosophila Simulans ◽  
Ssu Rrna ◽  
Rrna Molecule ◽  
Different Temperatures ◽  
Secondary Structure Models ◽  
Rrna Secondary Structure

The influence of a temperature default on ribosomal RNA (rRNA) secondary structure models was studied with the "Mfold" energy-optimization program. Folding models of the internal transcribed spacer (ITS) 1 rRNA for both Drosophila simulans (Insecta) and Isabellaria adriani (Gastropoda) were generated at two different temperatures. The folding models are compared with the models previously shown for the ITS-1 of D. melanogaster Oregon R strain and I. adriani. A search for phylogenetically informative ITS-1 folding motifs was conducted for D. simulans. In I. adriani, a new approach for ITS-1 secondary structure analyses is suggested. The paper also elucidates results inferred from three energy-optimizing programs (Mfold, GeneBee, and STAR). These three folding programs give different information on the structure and free energy of a ITS-1 rRNA molecule. Furthermore, secondary-structure models of the small subunit (ssu) rRNA of Daphnia pulex (Crustacea: Cladocera) were investigated. The ssu rRNA molecule is usually folded according to alignment information. Here, ssu folding patterns are computed with Mfold using two temperature conditions. The two Mfold models are compared with the alignment model previously suggested for D. pulex. Three cladoceran-specific motifs and a short stem motif within the ssu rRNA of eukaryotes are discussed with respect to structure and phylogenetic information.

scholarly journals Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence

1980 ◽  
Vol 8 (10) ◽  
pp. 2275-2294 ◽  
Author(s):  
C.R. Woese ◽  
L.J. Magrum ◽  
R. Gupta ◽  
R.B. Siegel ◽  
D.A. Stahl ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Ribosomal Rna ◽  
16S Ribosomal Rna ◽  
Structure Model ◽  
Secondary Structure Model ◽  
Chemical Evidence

scholarly journals Sequences of three molluscan 5 S ribosomal RNAs confirm the validity of a dynamic secondary structure model

1982 ◽  
Vol 10 (15) ◽  
pp. 4679-4685 ◽  
Author(s):  
Bao-Ling Fang ◽  
Raymond De Baere ◽  
Antoon Vandenberghe ◽  
Rupert De Wachter
Keyword(s):  
Secondary Structure ◽  
Structure Model ◽  
Ribosomal Rnas ◽  
Secondary Structure Model
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