The 18S rRNA from Odontophrynus americanus 2n and 4n (Amphibia, Anura) reveals unusual extra sequences in the variable region V2

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 421-428 ◽  
Author(s):  
Lúcia E Alvares ◽  
Jan Wuyts ◽  
Yves Van de Peer ◽  
Eduardo P Silva ◽  
Luiz L Coutinho ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Xenopus Laevis ◽  
Ribosomal Dna ◽  
18S Rrna ◽  
Variable Region ◽  
Tetraploid Species ◽  
Nucleotide Substitutions ◽  
Variable Regions

The nucleotide sequence of the rDNA 18S region isolated from diploid and tetraploid species of the amphibian Odontophrynus americanus was determined and used to predict the secondary structure of the corresponding 18S rRNA molecules. Comparison of the primary and secondary structures for the 2n and 4n species confirmed that these species are very closely related. Only three nucleotide substitutions were observed, accounting for 99% identity between the 18S sequences, whereas several changes were detected by comparison with the Xenopus laevis 18S sequence (96% identity). Most changes were located in highly variable regions of the molecule. A noticeable feature of the Odontophrynus 18S rRNA was the presence of unusual extra sequences in the V2 region, between helices 9 and 11. These extra sequences do not fit the model for secondary structure predicted for vertebrate 18S rRNA.Key words: Odontophrynus americanus, Amphibia, polyploidy, 18S ribosomal DNA, molecular evolution.

scholarly journals Molecular evolution of the plant R regulatory gene family.

Genetics ◽  
1994 ◽  
Vol 138 (3) ◽  
pp. 849-854
Author(s):  
M D Purugganan ◽  
S R Wessler
Keyword(s):  
Molecular Evolution ◽  
Gene Family ◽  
Plant Species ◽  
Regulatory Gene ◽  
Nonsynonymous Substitution ◽  
R Genes ◽  
Nucleotide Substitutions ◽  
Variable Regions ◽  
Helix Loop Helix ◽  
Regulatory Loci

Abstract Anthocyanin pigmentation patterns in different plant species are controlled in part by members of the myc-like R regulatory gene family. We have examined the molecular evolution of this gene family in seven plant species. Three regions of the R protein show sequence conservation between monocot and dicot R genes. These regions encode the basic helix-loop-helix domain, as well as conserved N-terminal and C-terminal domains; mean replacement rates for these conserved regions are 1.02 x 10(-9) nonsynonymous nucleotide substitutions per site per year. More than one-half of the protein, however, is diverging rapidly, with nonsynonymous substitution rates of 4.08 x 10(-9) substitutions per site per year. Detailed analysis of R homologs within the grasses (Poaceae) confirm that these variable regions are indeed evolving faster than the flanking conserved domains. Both nucleotide substitutions and small insertion/deletions contribute to the diversification of the variable regions within these regulatory genes. These results demonstrate that large tracts of sequence in these regulatory loci are evolving at a fairly rapid rate.

scholarly journals Nucleotide sequence of the region between the 18S rRNA sequence and the 28S rRNA sequence of rat ribosomal DNA

1982 ◽  
Vol 10 (12) ◽  
pp. 3667-3680 ◽  
Author(s):  
Chirala S. Subrahmanyam ◽  
Brandt Cassidy ◽  
Harris Busch ◽  
Lawrence I. Rothblum
Keyword(s):  
Nucleotide Sequence ◽  
Ribosomal Dna ◽  
18S Rrna ◽  
28S Rrna ◽  
Rrna Sequence

scholarly journals Organization of 5S rDNA repeated unit of Quercus imbricaria Michx.

2020 ◽  
Vol 17 (2) ◽  
pp. 179-186 ◽  
Author(s):  
A. S. Stratiichuk ◽  
T. O. Derevenko ◽  
Y. O. Tynkevych
Keyword(s):  
Molecular Evolution ◽  
Secondary Structure ◽  
Pcr Amplification ◽  
5S Rdna ◽  
5S Rrna ◽  
Molecular Organization ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Sequence Elements ◽  
Related Plant

Aim. The 5S rDNA repeats represent a universal model for the investigation of molecular evolution of repeated sequences. Also, comparison of 5S rDNA was successfully applied for the elucidation of phylogenetic relationships between the closely related plant species. However, there is practically no data regarding the molecular organization of 5S rDNA repeats in members of the section Lobatae, one of the largest groups of the genus Quercus. Accordingly, our aim was to investigate the 5S rDNA organization for Q. imbricaria, a species that belongs to this section. Methods. DNA extraction, PCR amplification, cloning and sequencing. Results. A complete 5S rDNA repeat of Q. imbricaria was cloned and sequenced. It has been found that in the oak genome, the 5S rDNA coding region contains five nucleotide substitutions as compared to that in Arabidopsis. Nevertheless, the predicted secondary structure of the transcript retains all typical features of 5S rRNA. Presumptive sequence elements of the external promoter were identified in the IGS. Conclusions. The nucleotide substitutions that occur in the 5S rRNA during evolution appear to be compensatory, resulting in conservation of its secondary structure. Due to considerable differences among the species of different sections, the 5S rDNA IGS can be applied for the taxonomic studies in the genus Quercus. Keywords: 5S rDNA, molecular evolution, Quercus, Lobatae.

Genetic Identification of Algas on The Basis of The Analysis of 18s rRNA and rbcl of Genes Nucleotide Sequence and Development of Technology of Aquaculture Cultivation

2014 ◽  
Vol 2 (42) ◽  
pp. 291-291
Author(s):  
Z.B. Tekebayeva ◽  
A.B. Shevtsov ◽  
X.K. Rakhymzhan ◽  
K.A. Aituganov ◽  
G.A. Babayeva ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
18S Rrna ◽  
Genetic Identification

scholarly journals Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Michela Quadrini
Keyword(s):  
Hydrogen Bonding ◽  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Thermus Thermophilus ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Structural Effect ◽  
Biological Processes ◽  
Structural Pattern ◽  
Rna Molecules

Abstract RNA molecules play crucial roles in various biological processes. Their three-dimensional configurations determine the functions and, in turn, influences the interaction with other molecules. RNAs and their interaction structures, the so-called RNA–RNA interactions, can be abstracted in terms of secondary structures, i.e., a list of the nucleotide bases paired by hydrogen bonding within its nucleotide sequence. Each secondary structure, in turn, can be abstracted into cores and shadows. Both are determined by collapsing nucleotides and arcs properly. We formalize all of these abstractions as arc diagrams, whose arcs determine loops. A secondary structure, represented by an arc diagram, is pseudoknot-free if its arc diagram does not present any crossing among arcs otherwise, it is said pseudoknotted. In this study, we face the problem of identifying a given structural pattern into secondary structures or the associated cores or shadow of both RNAs and RNA–RNA interactions, characterized by arbitrary pseudoknots. These abstractions are mapped into a matrix, whose elements represent the relations among loops. Therefore, we face the problem of taking advantage of matrices and submatrices. The algorithms, implemented in Python, work in polynomial time. We test our approach on a set of 16S ribosomal RNAs with inhibitors of Thermus thermophilus, and we quantify the structural effect of the inhibitors.

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