Next Article in Journal
Zoonotic Potential of Influenza A Viruses: A Comprehensive Overview
Next Article in Special Issue
High Throughput Manufacturing of Bacteriophages Using Continuous Stirred Tank Bioreactors Connected in Series to Ensure Optimum Host Bacteria Physiology for Phage Production
Previous Article in Journal
Strategies to Encapsulate the Staphylococcus aureus Bacteriophage phiIPLA-RODI
Previous Article in Special Issue
RNA Phage Biology in a Metagenomic Era
Open AccessArticle

Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters

1
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
2
Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
3
Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan
*
Author to whom correspondence should be addressed.
These authors equally contributed to this study.
Viruses 2018, 10(9), 496; https://doi.org/10.3390/v10090496
Received: 11 August 2018 / Revised: 12 September 2018 / Accepted: 12 September 2018 / Published: 13 September 2018
(This article belongs to the Special Issue Viruses of Microbes V: Biodiversity and Future Applications)
“Megaviridae” is a proposed family of giant viruses infecting unicellular eukaryotes. These viruses are ubiquitous in the sea and have impact on marine microbial community structure and dynamics through their lytic infection cycle. However, their diversity and biogeography have been poorly characterized due to the scarce detection of Megaviridae sequences in metagenomes, as well as the limitation of reference sequences used to design specific primers for this viral group. Here, we propose a set of 82 degenerated primers (referred to as MEGAPRIMER), targeting DNA polymerase genes (polBs) of Megaviridae. MEGAPRIMER was designed based on 921 Megaviridae polBs from sequenced genomes and metagenomes. By applying this primer set to environmental DNA meta-barcoding of a coastal seawater sample, we report 5595 non-singleton operational taxonomic units (OTUs) of Megaviridae at 97% nucleotide sequence identity. The majority of the OTUs were found to form diverse clades, which were phylogenetically distantly related to known viruses such as Mimivirus. The Megaviridae OTUs detected in this study outnumber the giant virus OTUs identified in previous individual studies by more than an order of magnitude. Hence, MEGAPRIMER represents a useful tool to study the diversity of Megaviridae at the population level in natural environments. View Full-Text
Keywords: Megaviridae; meta-barcode; B family DNA polymerase (PolB); metagenome; Mimiviridae Megaviridae; meta-barcode; B family DNA polymerase (PolB); metagenome; Mimiviridae
Show Figures

Figure 1

MDPI and ACS Style

Li, Y.; Hingamp, P.; Watai, H.; Endo, H.; Yoshida, T.; Ogata, H. Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters. Viruses 2018, 10, 496.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Search more from Scilit
 
Search
Back to TopTop