Generating viral metagenomes from the coral holobiont

Weynberg, Karen D., Wood-Charlson, Elisha M., Suttle, Curtis A. and van Oppen, Madeleine J. H. (2014) Generating viral metagenomes from the coral holobiont. Frontiers in Microbiology, 5 . doi:10.3389/fmicb.2014.00206

Author Weynberg, Karen D.
Wood-Charlson, Elisha M.
Suttle, Curtis A.
van Oppen, Madeleine J. H.
Title Generating viral metagenomes from the coral holobiont
Journal name Frontiers in Microbiology   Check publisher's open access policy
ISSN 1664-302X
Publication date 2014-05-07
Sub-type Article (original research)
DOI 10.3389/fmicb.2014.00206
Open Access Status DOI
Volume 5
Total pages 11
Place of publication Lausanne, Switzerland
Publisher Frontiers Research Foundation
Language eng
Formatted abstract
Reef-building corals comprise multipartite symbioses where the cnidarian animal is host to an array of eukaryotic and prokaryotic organisms, and the viruses that infect them. These viruses are critical elements of the coral holobiont, serving not only as agents of mortality, but also as potential vectors for lateral gene flow, and as elements encoding a variety of auxiliary metabolic functions. Consequently, understanding the functioning and health of the coral holobiont requires detailed knowledge of the associated viral assemblage and its function. Currently, the most tractable way of uncovering viral diversity and function is through metagenomic approaches, which is inherently difficult in corals because of the complex holobiont community, an extracellular mucus layer that all corals secrete, and the variety of sizes and structures of nucleic acids found in viruses. Here we present the first protocol for isolating, purifying and amplifying viral nucleic acids from corals based on mechanical disruption of cells. This method produces at least 50% higher yields of viral nucleic acids, has very low levels of cellular sequence contamination and captures wider viral diversity than previously used chemical-based extraction methods. We demonstrate that our mechanical-based method profiles a greater diversity of DNA and RNA genomes, including virus groups such as Retro-transcribing and ssRNA viruses, which are absent from metagenomes generated via chemical-based methods. In addition, we briefly present (and make publically available) the first paired DNA and RNA viral metagenomes from the coral Acropora tenuis.
Keyword Chloroform
Viral metagenomics
Virus diversity
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
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Citation counts: TR Web of Science Citation Count  Cited 21 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 25 times in Scopus Article | Citations
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Created: Thu, 14 Sep 2017, 16:12:04 EST by Karen Weynberg on behalf of School of Chemistry & Molecular Biosciences