Cloning and sequence analysis of the 18 S ribosomal RNA gene of tomato and a secondary structure model for the 18 S rRNA of angiosperms

1989 ◽  
Vol 219 (1-2) ◽  
pp. 17-25 ◽  
Author(s):  
Waltraud Schmidt-Puchta ◽  
Gertrud Kütemeier ◽  
Isolde Günther ◽  
Bernd Haas ◽  
Heinz L. Sänger
Keyword(s):  
Sequence Analysis ◽  
Secondary Structure ◽  
Ribosomal Rna ◽  
Structure Model ◽  
Secondary Structure Model ◽  
Ribosomal Rna Gene ◽  
18 S Ribosomal Rna

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 Secondary structure model for 23S ribosomal RNA

1981 ◽  
Vol 9 (22) ◽  
pp. 6167-6189 ◽  
Author(s):  
Harry F. Noller ◽  
JoAnn Kop ◽  
Virginia Wheaton ◽  
Jürgen Brosius ◽  
Robin R. Gutell ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Ribosomal Rna ◽  
Structure Model ◽  
Secondary Structure Model ◽  
23S Ribosomal Rna

scholarly journals Xenopus laevis28S ribosomal RNA: a secondary structure model and its evolutionary and functional implications

1984 ◽  
Vol 12 (15) ◽  
pp. 6197-6220 ◽  
Author(s):  
C.Graham Clark ◽  
Brian W. Tague ◽  
Vassie C. Ware ◽  
Susan A. Gerbi
Keyword(s):  
Secondary Structure ◽  
Ribosomal Rna ◽  
Structure Model ◽  
Secondary Structure Model ◽  
Functional Implications

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.

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