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dc.contributor.authorWang, Yong
dc.contributor.authorQian, Pei-Yuan
dc.date.accessioned2014-08-27T09:44:43Z
dc.date.available2014-08-27T09:44:43Z
dc.date.issued2009-10-09
dc.identifier.citationWang Y, Qian P-Y (2009) Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies. PLoS ONE 4: e7401. doi:10.1371/journal.pone.0007401.
dc.identifier.issn19326203
dc.identifier.pmid19816594
dc.identifier.doi10.1371/journal.pone.0007401
dc.identifier.urihttp://hdl.handle.net/10754/325281
dc.description.abstractBacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions that are informative in taxonomic assignment. One problem is that the percentage coverage and application scope of the primers used in previous studies are largely unknown. In this study, conservative fragments of available rDNA sequences were first mined and then used to search for candidate primers within the fragments by measuring the coverage rate defined as the percentage of bacterial sequences containing the target. Thirty predicted primers with a high coverage rate (>90%) were identified, which were basically located in the same conservative regions as known primers in previous reports, whereas 30% of the known primers were associated with a coverage rate of <90%. The application scope of the primers was also examined by calculating the percentages of failed detections in bacterial phyla. Primers A519-539, E969- 983, E1063-1081, U515 and E517, are highly recommended because of their high coverage in almost all phyla. As expected, the three predominant phyla, Firmicutes, Gemmatimonadetes and Proteobacteria, are best covered by the predicted primers. The primers recommended in this report shall facilitate a comprehensive and reliable survey of bacterial diversity in metagenomic studies. © 2009 Wang, Qian.
dc.description.sponsorshipKAUST Global Partnership. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
dc.language.isoen
dc.publisherPublic Library of Science (PLoS)
dc.rightsWang, Qian. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.rightsArchived with thanks to PLoS ONE
dc.subjectbacterial DNA
dc.subjectbacterial RNA
dc.subjectDNA 16S
dc.subjectRNA 16S
dc.subjectprimer DNA
dc.subjectribosome DNA
dc.subjectbacterial gene
dc.subjectcontrolled study
dc.subjectgene amplification
dc.subjectgenetic conservation
dc.subjectgenomic fragment
dc.subjectmetagenomics
dc.subjectphylum
dc.subjectRNA sequence
dc.subjectarchaebacterium
dc.subjectbacterium
dc.subjectcyanobacterium
dc.subjectEscherichia coli
dc.subjectgenetic database
dc.subjectgenetic polymorphism
dc.subjectgenetics
dc.subjectgenomics
dc.subjectmethodology
dc.subjectBacteria (microorganisms)
dc.subjectFirmicutes
dc.subjectGemmatimonadetes
dc.subjectProteobacteria
dc.subjectuncultured bacterium
dc.subjectArchaea
dc.subjectBacteria
dc.subjectCyanobacteria
dc.subjectDatabases, Genetic
dc.subjectDNA Primers
dc.subjectDNA, Ribosomal
dc.subjectEscherichia coli
dc.subjectGenes, Bacterial
dc.subjectGenomics
dc.subjectMetagenomics
dc.subjectPolymorphism, Genetic
dc.subjectRNA, Bacterial
dc.subjectRNA, Ribosomal, 16S
dc.titleConservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies
dc.typeArticle
dc.contributor.departmentCompetitive Research Funds
dc.identifier.journalPLoS ONE
dc.identifier.pmcidPMC2754607
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionUnidad Académica de Sistemas Arrecifales (Puerto Morelos), Instituto de Ciencias Del Mar y Limnología, Universidad Nacional Autõnoma de México, Puerto Morelos, QR 77580, Mexico
dc.contributor.institutionSchool of Natural Sciences, University of California Merced, 5200 North Lake Road, Merced, CA 95343, United States
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personWang, Yong
kaust.personQian, Pei-Yuan
kaust.grant.programKAUST Global Partnership Program
refterms.dateFOA2018-06-14T05:00:18Z


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