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Constraint of Base Pairing on HDV Genome Evolution

The hepatitis delta virus is a single-stranded circular RNA virus, which is characterized by high self-complementarity. About 70% of the genome sequences can form base-pairs with internal nucleotides. There are many studies on the evolution of the hepatitis delta virus. However, the secondary struct...

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Autores principales: Nagata, Saki, Kiyohara, Ryoji, Toh, Hiroyuki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8708965/
https://www.ncbi.nlm.nih.gov/pubmed/34960619
http://dx.doi.org/10.3390/v13122350
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author Nagata, Saki
Kiyohara, Ryoji
Toh, Hiroyuki
author_facet Nagata, Saki
Kiyohara, Ryoji
Toh, Hiroyuki
author_sort Nagata, Saki
collection PubMed
description The hepatitis delta virus is a single-stranded circular RNA virus, which is characterized by high self-complementarity. About 70% of the genome sequences can form base-pairs with internal nucleotides. There are many studies on the evolution of the hepatitis delta virus. However, the secondary structure has not been taken into account in these studies. In this study, we developed a method to examine the effect of base pairing as a constraint on the nucleotide substitutions during the evolution of the hepatitis delta virus. The method revealed that the base pairing can reduce the evolutionary rate in the non-coding region of the virus. In addition, it is suggested that the non-coding nucleotides without base pairing may be under some constraint, and that the intensity of the constraint is weaker than that by the base pairing but stronger than that on the synonymous site.
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spelling pubmed-87089652021-12-25 Constraint of Base Pairing on HDV Genome Evolution Nagata, Saki Kiyohara, Ryoji Toh, Hiroyuki Viruses Article The hepatitis delta virus is a single-stranded circular RNA virus, which is characterized by high self-complementarity. About 70% of the genome sequences can form base-pairs with internal nucleotides. There are many studies on the evolution of the hepatitis delta virus. However, the secondary structure has not been taken into account in these studies. In this study, we developed a method to examine the effect of base pairing as a constraint on the nucleotide substitutions during the evolution of the hepatitis delta virus. The method revealed that the base pairing can reduce the evolutionary rate in the non-coding region of the virus. In addition, it is suggested that the non-coding nucleotides without base pairing may be under some constraint, and that the intensity of the constraint is weaker than that by the base pairing but stronger than that on the synonymous site. MDPI 2021-11-23 /pmc/articles/PMC8708965/ /pubmed/34960619 http://dx.doi.org/10.3390/v13122350 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Nagata, Saki
Kiyohara, Ryoji
Toh, Hiroyuki
Constraint of Base Pairing on HDV Genome Evolution
title Constraint of Base Pairing on HDV Genome Evolution
title_full Constraint of Base Pairing on HDV Genome Evolution
title_fullStr Constraint of Base Pairing on HDV Genome Evolution
title_full_unstemmed Constraint of Base Pairing on HDV Genome Evolution
title_short Constraint of Base Pairing on HDV Genome Evolution
title_sort constraint of base pairing on hdv genome evolution
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8708965/
https://www.ncbi.nlm.nih.gov/pubmed/34960619
http://dx.doi.org/10.3390/v13122350
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