Genetic diversity of Paramecium species on the basis of multiple loci analysis and ITS secondary structure models

2019 ◽  
Vol 121 (8-9) ◽  
pp. 3837-3853 ◽  
Author(s):  
Fareeda Tasneem ◽  
Farah R. Shakoori ◽  
Muhammad Ilyas ◽  
Naveed Shahzad ◽  
Alexey Potekhin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Secondary Structure ◽  
Multiple Loci ◽  
Secondary Structure Models

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 RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses

2020 ◽  
Author(s):  
Ramya Rangan ◽  
Ivan N. Zheludev ◽  
Rhiju Das
Keyword(s):  
Secondary Structure ◽  
Viral Genome ◽  
Rna Secondary Structure ◽  
Therapeutic Strategies ◽  
Genome Sequences ◽  
Sequence Alignments ◽  
Secondary Structure Models ◽  
Prior Literature ◽  
Rna Genome ◽  
Genomic Regions

AbstractAs the COVID-19 outbreak spreads, there is a growing need for a compilation of conserved RNA genome regions in the SARS-CoV-2 virus along with their structural propensities to guide development of antivirals and diagnostics. Using sequence alignments spanning a range of betacoronaviruses, we rank genomic regions by RNA sequence conservation, identifying 79 regions of length at least 15 nucleotides as exactly conserved over SARS-related complete genome sequences available near the beginning of the COVID-19 outbreak. We then confirm the conservation of the majority of these genome regions across 739 SARS-CoV-2 sequences reported to date from the current COVID-19 outbreak, and we present a curated list of 30 ‘SARS-related-conserved’ regions. We find that known RNA structured elements curated as Rfam families and in prior literature are enriched in these conserved genome regions, and we predict additional conserved, stable secondary structures across the viral genome. We provide 106 ‘SARS-CoV-2-conserved-structured’ regions as potential targets for antivirals that bind to structured RNA. We further provide detailed secondary structure models for the 5’ UTR, frame-shifting element, and 3’ UTR. Last, we predict regions of the SARS-CoV-2 viral genome have low propensity for RNA secondary structure and are conserved within SARS-CoV-2 strains. These 59 ‘SARS-CoV-2-conserved-unstructured’ genomic regions may be most easily targeted in primer-based diagnostic and oligonucleotide-based therapeutic strategies.

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