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Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations
Viruses rely on widespread genetic variation and large population size for adaptation. Large DNA virus populations are thought to harbor little variation though natural populations may be polymorphic. To measure the genetic variation present in a dsDNA virus population, we deep sequenced a natural s...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517117/ https://www.ncbi.nlm.nih.gov/pubmed/26198241 http://dx.doi.org/10.3390/v7072788 |
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author | Chateigner, Aurélien Bézier, Annie Labrousse, Carole Jiolle, Davy Barbe, Valérie Herniou, Elisabeth A. |
author_facet | Chateigner, Aurélien Bézier, Annie Labrousse, Carole Jiolle, Davy Barbe, Valérie Herniou, Elisabeth A. |
author_sort | Chateigner, Aurélien |
collection | PubMed |
description | Viruses rely on widespread genetic variation and large population size for adaptation. Large DNA virus populations are thought to harbor little variation though natural populations may be polymorphic. To measure the genetic variation present in a dsDNA virus population, we deep sequenced a natural strain of the baculovirus Autographa californica multiple nucleopolyhedrovirus. With 124,221X average genome coverage of our 133,926 bp long consensus, we could detect low frequency mutations (0.025%). K-means clustering was used to classify the mutations in four categories according to their frequency in the population. We found 60 high frequency non-synonymous mutations under balancing selection distributed in all functional classes. These mutants could alter viral adaptation dynamics, either through competitive or synergistic processes. Lastly, we developed a technique for the delimitation of large deletions in next generation sequencing data. We found that large deletions occur along the entire viral genome, with hotspots located in homologous repeat regions (hrs). Present in 25.4% of the genomes, these deletion mutants presumably require functional complementation to complete their infection cycle. They might thus have a large impact on the fitness of the baculovirus population. Altogether, we found a wide breadth of genomic variation in the baculovirus population, suggesting it has high adaptive potential. |
format | Online Article Text |
id | pubmed-4517117 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-45171172015-07-28 Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations Chateigner, Aurélien Bézier, Annie Labrousse, Carole Jiolle, Davy Barbe, Valérie Herniou, Elisabeth A. Viruses Article Viruses rely on widespread genetic variation and large population size for adaptation. Large DNA virus populations are thought to harbor little variation though natural populations may be polymorphic. To measure the genetic variation present in a dsDNA virus population, we deep sequenced a natural strain of the baculovirus Autographa californica multiple nucleopolyhedrovirus. With 124,221X average genome coverage of our 133,926 bp long consensus, we could detect low frequency mutations (0.025%). K-means clustering was used to classify the mutations in four categories according to their frequency in the population. We found 60 high frequency non-synonymous mutations under balancing selection distributed in all functional classes. These mutants could alter viral adaptation dynamics, either through competitive or synergistic processes. Lastly, we developed a technique for the delimitation of large deletions in next generation sequencing data. We found that large deletions occur along the entire viral genome, with hotspots located in homologous repeat regions (hrs). Present in 25.4% of the genomes, these deletion mutants presumably require functional complementation to complete their infection cycle. They might thus have a large impact on the fitness of the baculovirus population. Altogether, we found a wide breadth of genomic variation in the baculovirus population, suggesting it has high adaptive potential. MDPI 2015-07-07 /pmc/articles/PMC4517117/ /pubmed/26198241 http://dx.doi.org/10.3390/v7072788 Text en © 2015 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Chateigner, Aurélien Bézier, Annie Labrousse, Carole Jiolle, Davy Barbe, Valérie Herniou, Elisabeth A. Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations |
title | Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations |
title_full | Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations |
title_fullStr | Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations |
title_full_unstemmed | Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations |
title_short | Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations |
title_sort | ultra deep sequencing of a baculovirus population reveals widespread genomic variations |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517117/ https://www.ncbi.nlm.nih.gov/pubmed/26198241 http://dx.doi.org/10.3390/v7072788 |
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