Nucleotide sequence of Citrus limon 26S rRNA gene and secondary structure model of its RNA

1990 ◽  
Vol 14 (2) ◽  
pp. 147-161 ◽  
Author(s):  
Vladimir O. Kolosha ◽  
Istvan Fodor
Keyword(s):  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Citrus Limon ◽  
Rrna Gene ◽  
Structure Model ◽  
Secondary Structure Model ◽  
26S Rrna

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.

scholarly journals Evidence on the conformation of HeLa-cell 5.8S ribosomal ribonucleic acid from the reaction of specific cytidine residues with sodium bisulphite

1978 ◽  
Vol 173 (2) ◽  
pp. 521-532 ◽  
Author(s):  
J M Kelly ◽  
J P Goddard ◽  
B E H Maden
Keyword(s):  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Hela Cell ◽  
Primary Structure ◽  
The Other ◽  
Structure Model ◽  
Secondary Structure Model ◽  
Sodium Bisulphite ◽  
5.8S Rrna ◽  
Ribosomal Ribonucleic Acid

The reaction of HeLa-cell 5.8S rRNA with NaHSO3 under conditions in which exposed cytidine residues are deaminated to uridine was studied. It was possible to estimate the reactivities of most of the 46 cytidine residues in the nucleotide sequence by comparing ‘fingerprints’ of the bisulphite-treated RNA with those of untreated RNA. The findings were consistent with the main features of the secondary-structure model for mammalian 5.85S rRNA proposed by Nazar, Sitz, & Busch [J. Biol. Chem (1975) 250, 8591–8597]. Five out of six regions that are depicted in the model as single-stranded loops contain cytidine residues that are reactive towards bisulphite at 25 degrees C (the other loop contains no cytidine). The cytidine residue nearest to the 3′-terminus is also reactive. Several cytidines residues that are internally located within proposed double-helical regions show little or no reactivity towards bisulphite, but the cytidine residues of several C.G pairs at the ends of helical regions show some reactivity, and one of the proposed loops appears to contain six nucleotides, rather than the minimum of four suggested by the primary structure. Two cytidine residues that are thought to be ‘looped out’ by small helix imperfections also show some reactivity.

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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