Next Article in Journal
Early Events in Chikungunya Virus Infection—From Virus CellBinding to Membrane Fusion
Next Article in Special Issue
Mate-Pair Sequencing as a Powerful Clinical Tool for the Characterization of Cancers with a DNA Viral Etiology
Previous Article in Journal
Modes of Human T Cell Leukemia Virus Type 1 Transmission, Replication and Persistence
Article Menu

Export Article

Open AccessArticle
Viruses 2015, 7(7), 3625-3646; doi:10.3390/v7072788

Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations

1
Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université François Rabelais de Tours, Faculté des Sciences et Techniques, Avenue Monge-Parc Grandmont, 37200 Tours, France
2
Institut de Génomique, CEA, Génoscope, 2 rue Gaston Crémieux, 91057 Evry, France
Current address: D
*
Author to whom correspondence should be addressed.
Academic Editor: Johnson Mak
Received: 21 May 2015 / Revised: 30 June 2015 / Accepted: 1 July 2015 / Published: 7 July 2015
View Full-Text   |   Download PDF [789 KB, uploaded 7 July 2015]   |  

Abstract

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. View Full-Text
Keywords: genome population variation; quasispecies theory; AcMNPV; high-throughput sequencing genome population variation; quasispecies theory; AcMNPV; high-throughput sequencing
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Chateigner, A.; Bézier, A.; Labrousse, C.; Jiolle, D.; Barbe, V.; Herniou, E.A. Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations. Viruses 2015, 7, 3625-3646.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Viruses EISSN 1999-4915 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top