Sequencing platform and library preparation choices impact viral metagenomes

Persistent Link:
http://hdl.handle.net/10150/610023
Title:
Sequencing platform and library preparation choices impact viral metagenomes
Author:
Solonenko, Sergei; Ignacio-Espinoza, J.; Alberti, Adriana; Cruaud, Corinne; Hallam, Steven; Konstantinidis, Kostas; Tyson, Gene; Wincker, Patrick; Sullivan, Matthew
Affiliation:
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA; Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA; CEA, DSV, IG, Genoscope, 2 rue Gaston Crémieux CP5706, Evry, Cedex, 91057, France; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA; Austalian Center for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
Issue Date:
2013
Publisher:
BioMed Central
Citation:
Solonenko et al. BMC Genomics 2013, 14:320 http://www.biomedcentral.com/1471-2164/14/320
Journal:
BMC Genomics
Rights:
© 2013 Solonenko et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:Microbes drive the biogeochemistry that fuels the planet. Microbial viruses modulate their hosts directly through mortality and horizontal gene transfer, and indirectly by re-programming host metabolisms during infection. However, our ability to study these virus-host interactions is limited by methods that are low-throughput and heavily reliant upon the subset of organisms that are in culture. One way forward are culture-independent metagenomic approaches, but these novel methods are rarely rigorously tested, especially for studies of environmental viruses, air microbiomes, extreme environment microbiology and other areas with constrained sample amounts. Here we perform replicated experiments to evaluate Roche 454, Illumina HiSeq, and Ion Torrent PGM sequencing and library preparation protocols on virus metagenomes generated from as little as 10pg of DNA.RESULTS:Using %G+C content to compare metagenomes, we find that (i) metagenomes are highly replicable, (ii) some treatment effects are minimal, e.g., sequencing technology choice has 6-fold less impact than varying input DNA amount, and (iii) when restricted to a limited DNA concentration (<1mug), changing the amount of amplification produces little variation. These trends were also observed when examining the metagenomes for gene function and assembly performance, although the latter more closely aligned to sequencing effort and read length than preparation steps tested. Among Illumina library preparation options, transposon-based libraries diverged from all others and adaptor ligation was a critical step for optimizing sequencing yields.CONCLUSIONS:These data guide researchers in generating systematic, comparative datasets to understand complex ecosystems, and suggest that neither varied amplification nor sequencing platforms will deter such efforts.
EISSN:
1471-2164
DOI:
10.1186/1471-2164-14-320
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2164/14/320

Full metadata record

DC FieldValue Language
dc.contributor.authorSolonenko, Sergeien
dc.contributor.authorIgnacio-Espinoza, J.en
dc.contributor.authorAlberti, Adrianaen
dc.contributor.authorCruaud, Corinneen
dc.contributor.authorHallam, Stevenen
dc.contributor.authorKonstantinidis, Kostasen
dc.contributor.authorTyson, Geneen
dc.contributor.authorWincker, Patricken
dc.contributor.authorSullivan, Matthewen
dc.date.accessioned2016-05-20T08:56:43Z-
dc.date.available2016-05-20T08:56:43Z-
dc.date.issued2013en
dc.identifier.citationSolonenko et al. BMC Genomics 2013, 14:320 http://www.biomedcentral.com/1471-2164/14/320en
dc.identifier.doi10.1186/1471-2164-14-320en
dc.identifier.urihttp://hdl.handle.net/10150/610023-
dc.description.abstractBACKGROUND:Microbes drive the biogeochemistry that fuels the planet. Microbial viruses modulate their hosts directly through mortality and horizontal gene transfer, and indirectly by re-programming host metabolisms during infection. However, our ability to study these virus-host interactions is limited by methods that are low-throughput and heavily reliant upon the subset of organisms that are in culture. One way forward are culture-independent metagenomic approaches, but these novel methods are rarely rigorously tested, especially for studies of environmental viruses, air microbiomes, extreme environment microbiology and other areas with constrained sample amounts. Here we perform replicated experiments to evaluate Roche 454, Illumina HiSeq, and Ion Torrent PGM sequencing and library preparation protocols on virus metagenomes generated from as little as 10pg of DNA.RESULTS:Using %G+C content to compare metagenomes, we find that (i) metagenomes are highly replicable, (ii) some treatment effects are minimal, e.g., sequencing technology choice has 6-fold less impact than varying input DNA amount, and (iii) when restricted to a limited DNA concentration (<1mug), changing the amount of amplification produces little variation. These trends were also observed when examining the metagenomes for gene function and assembly performance, although the latter more closely aligned to sequencing effort and read length than preparation steps tested. Among Illumina library preparation options, transposon-based libraries diverged from all others and adaptor ligation was a critical step for optimizing sequencing yields.CONCLUSIONS:These data guide researchers in generating systematic, comparative datasets to understand complex ecosystems, and suggest that neither varied amplification nor sequencing platforms will deter such efforts.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/14/320en
dc.rights© 2013 Solonenko et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleSequencing platform and library preparation choices impact viral metagenomesen
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USAen
dc.contributor.departmentDepartment of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USAen
dc.contributor.departmentCEA, DSV, IG, Genoscope, 2 rue Gaston Crémieux CP5706, Evry, Cedex, 91057, Franceen
dc.contributor.departmentDepartment of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canadaen
dc.contributor.departmentDepartment of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USAen
dc.contributor.departmentAustalian Center for Ecogenomics, University of Queensland, Brisbane, QLD, Australiaen
dc.identifier.journalBMC Genomicsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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