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dc.contributor.authorRoux, Simon
dc.contributor.authorSolonenko, Natalie E.
dc.contributor.authorDang, Vinh T.
dc.contributor.authorPoulos, Bonnie T.
dc.contributor.authorSchwenck, Sarah M.
dc.contributor.authorGoldsmith, Dawn B.
dc.contributor.authorColeman, Maureen L.
dc.contributor.authorBreitbart, Mya
dc.contributor.authorSullivan, Matthew B.
dc.date.accessioned2017-02-08T22:48:31Z
dc.date.available2017-02-08T22:48:31Z
dc.date.issued2016-12-08
dc.identifier.citationTowards quantitative viromics for both double-stranded and single-stranded DNA viruses 2016, 4:e2777 PeerJen
dc.identifier.issn2167-8359
dc.identifier.doi10.7717/peerj.2777
dc.identifier.urihttp://hdl.handle.net/10150/622482
dc.description.abstractBackground. Viruses strongly influence microbial population dynamics and ecosystem functions However, our ability to quantitatively evaluate those viral impads is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenornes (vromes). This leaves the ecology of nondsDNA viruses nearly unlmovvn, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation). Methods. Here we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses. Results. Mock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against) and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were 1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5%) of DNA virus communities, though individual ssDNA genomes, both eukaryoteinfecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) viruses and bacteriophages from the Microviridae family, can be among the most abundant viral genomes in a sample. Discussion. Together these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems.
dc.description.sponsorshipNational Science Foundation [1536989]; Gordon and Betty Moore Foundation [3790, GBMF2631]; Flinn Foundation; University of Arizona Technology and Research Initiative Fund through the Water, Environmental and Energy Solutions Initiative; Ecosystem Genomics Institute; NSF [MCB-0701984, DEB-1555854]en
dc.language.isoenen
dc.publisherPEERJ INCen
dc.relation.urlhttps://peerj.com/articles/2777en
dc.rights© 2016 Roux et al. Distributed under Creative Commons CC-BY 4.0.en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectssDNA virusesen
dc.subjectViral metagenomicsen
dc.subjectEnvironmental virologyen
dc.titleTowards quantitative viromics for both double-stranded and single-stranded DNA virusesen
dc.typeArticleen
dc.contributor.departmentUniv Arizona, Dept Ecol & Evolutionary Biolen
dc.identifier.journalPeerJen
dc.description.collectioninformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
dc.contributor.institutionDepartment of Microbiology, The Ohio State University, Columbus, OH, United States
dc.contributor.institutionDepartment of Microbiology, The Ohio State University, Columbus, OH, United States
dc.contributor.institutionDepartment of Microbiology, Ha Long University, Uong Bi, Quang Ninh, Vietnam
dc.contributor.institutionDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
dc.contributor.institutionDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
dc.contributor.institutionCollege of Marine Science, University of South Florida, St. Petersburg, FL, United States
dc.contributor.institutionDepartment of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
dc.contributor.institutionCollege of Marine Science, University of South Florida, St. Petersburg, FL, United States
dc.contributor.institutionDepartment of Microbiology, The Ohio State University, Columbus, OH, United States
refterms.dateFOA2018-09-11T17:33:11Z
html.description.abstractBackground. Viruses strongly influence microbial population dynamics and ecosystem functions However, our ability to quantitatively evaluate those viral impads is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenornes (vromes). This leaves the ecology of nondsDNA viruses nearly unlmovvn, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation). Methods. Here we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses. Results. Mock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against) and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were 1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5%) of DNA virus communities, though individual ssDNA genomes, both eukaryoteinfecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) viruses and bacteriophages from the Microviridae family, can be among the most abundant viral genomes in a sample. Discussion. Together these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems.


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© 2016 Roux et al. Distributed under Creative Commons CC-BY 4.0.
Except where otherwise noted, this item's license is described as © 2016 Roux et al. Distributed under Creative Commons CC-BY 4.0.