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

Viruses
Yanze LiHiroyuki Ogata

Abstract

"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 phylogenetically 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 re...Continue Reading

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Citations

Oct 8, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·David M NeedhamAlexandra Z Worden
Apr 7, 2020·Nature Communications·Mohammad MoniruzzamanFrank O Aylward
May 14, 2020·Nature Reviews. Microbiology·Shinichi SunagawaColomban de Vargas
Dec 11, 2021·The Science of the Total Environment·Li BiHang-Wei Hu

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Datasets Mentioned

BETA
PRJEB7988
DRA006230

Methods Mentioned

BETA
PCR
electrophoresis
Assay

Software Mentioned

EMBOSS primersearch
qiime
USEARCH
Python ETE3 package
Biopython
FLASh
Multiple Alignment using Fast Fourier Transform ( MAFFT )
BLASTP
EST
Pplacer

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