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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2021
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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. |
format | Online Article Text |
id | pubmed-8708965 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT nagatasaki constraintofbasepairingonhdvgenomeevolution AT kiyohararyoji constraintofbasepairingonhdvgenomeevolution AT tohhiroyuki constraintofbasepairingonhdvgenomeevolution |