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dc.contributor.authorArif, Chatchanit
dc.contributor.authorDaniels, Camille Arian
dc.contributor.authorBayer, Till
dc.contributor.authorBanguera Hinestroza, Eulalia
dc.contributor.authorBarbrook, Adrian
dc.contributor.authorHowe, Christopher J.
dc.contributor.authorLaJeunesse, Todd C.
dc.contributor.authorVoolstra, Christian R.
dc.date.accessioned2015-04-15T14:05:35Z
dc.date.available2015-04-15T14:05:35Z
dc.date.issued2014-09
dc.identifier.citationAssessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region 2014, 23 (17):4418 Molecular Ecology
dc.identifier.issn09621083
dc.identifier.pmid25052021
dc.identifier.doi10.1111/mec.12869
dc.identifier.urihttp://hdl.handle.net/10754/550142
dc.description.abstractThe persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.
dc.publisherWiley-Blackwell
dc.relation.urlhttp://doi.wiley.com/10.1111/mec.12869
dc.rightsThis is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
dc.subjectcoral reefs
dc.subjectdinoflagellates
dc.subjectinternal transcribed spacer 2
dc.subjectnext-generation sequencing
dc.subjectoperational taxonomic unit
dc.subjectSymbiodinium
dc.titleAssessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region
dc.typeArticle
dc.contributor.departmentRed Sea Research Center (RSRC)
dc.identifier.journalMolecular Ecology
dc.identifier.pmcidPMC4285332
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionGEOMAR Helmholtz Centre for Ocean Research Kiel; 24105 Kiel Germany
dc.contributor.institutionDepartment of Biochemistry; University of Cambridge; Building O Downing Site Tennis Court Road Cambridge CB2 1QW UK
dc.contributor.institutionDepartment of Biochemistry; University of Cambridge; Building O Downing Site Tennis Court Road Cambridge CB2 1QW UK
dc.contributor.institutionDepartment of Biology; Penn State University; University Park PA 16802 USA
kaust.personArif, Chatchanit
kaust.personDaniels, Camille Arian
kaust.personVoolstra, Christian R.
kaust.personBanguera Hinestroza, Eulalia
refterms.dateFOA2018-06-14T04:53:02Z


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