KOPS - The Institutional Repository of the University of Konstanz

An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region

An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region

Cite This

Files in this item

Checksum: MD5:fd5e596040e87d9e4597b1e545132e9c

HUME, Benjamin C. C., Maren ZIEGLER, Julie POULAIN, Xavier POCHON, Sarah ROMAC, Emilie BOISSIN, Colomban DE VARGAS, Serge PLANES, Patrick WINCKER, Christian R. VOOLSTRA, 2018. An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region. In: PeerJ. PeerJ. 6, e4816. eISSN 2167-8359. Available under: doi: 10.7717/peerj.4816

@article{Hume2018impro-51035, title={An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region}, year={2018}, doi={10.7717/peerj.4816}, volume={6}, journal={PeerJ}, author={Hume, Benjamin C. C. and Ziegler, Maren and Poulain, Julie and Pochon, Xavier and Romac, Sarah and Boissin, Emilie and de Vargas, Colomban and Planes, Serge and Wincker, Patrick and Voolstra, Christian R.}, note={Article Number: e4816} }

<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:void="http://rdfs.org/ns/void#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/rdf/resource/123456789/51035"> <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/51035/3/Hume_2-1cub3ez3tah3s5.pdf"/> <dc:contributor>Wincker, Patrick</dc:contributor> <dc:creator>Planes, Serge</dc:creator> <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/28"/> <dc:creator>Boissin, Emilie</dc:creator> <dc:language>eng</dc:language> <dc:contributor>de Vargas, Colomban</dc:contributor> <dc:creator>Voolstra, Christian R.</dc:creator> <dcterms:title>An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region</dcterms:title> <dc:contributor>Planes, Serge</dc:contributor> <dc:contributor>Ziegler, Maren</dc:contributor> <dc:creator>Wincker, Patrick</dc:creator> <dc:creator>Romac, Sarah</dc:creator> <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/51035/3/Hume_2-1cub3ez3tah3s5.pdf"/> <dc:contributor>Pochon, Xavier</dc:contributor> <dc:creator>Ziegler, Maren</dc:creator> <dc:contributor>Poulain, Julie</dc:contributor> <dc:rights>Attribution 4.0 International</dc:rights> <dc:creator>Pochon, Xavier</dc:creator> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2020-09-25T09:05:38Z</dcterms:available> <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/28"/> <dc:contributor>Boissin, Emilie</dc:contributor> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2020-09-25T09:05:38Z</dc:date> <foaf:homepage rdf:resource="http://localhost:8080/jspui"/> <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/51035"/> <dc:creator>Poulain, Julie</dc:creator> <dc:creator>de Vargas, Colomban</dc:creator> <dc:contributor>Voolstra, Christian R.</dc:contributor> <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/> <dc:contributor>Romac, Sarah</dc:contributor> <dcterms:rights rdf:resource="http://creativecommons.org/licenses/by/4.0/"/> <dc:creator>Hume, Benjamin C. C.</dc:creator> <dc:contributor>Hume, Benjamin C. C.</dc:contributor> <dcterms:abstract xml:lang="eng">The Internal Transcribed Spacer 2 (ITS2) rRNA gene is a commonly targeted genetic marker to assess diversity of Symbiodinium, a dinoflagellate genus of algal endosymbionts that is pervasively associated with marine invertebrates, and notably reef-building corals. Here we tested three commonly used ITS2 primer pairs (SYM_VAR_5.8S2/SYM_VAR_REV, ITSintfor2/ITSReverse, and ITS-DINO/ITS2Rev2) with regard to amplification specificity and sensitivity towards Symbiodinium, as well as sub-genera taxonomic bias. We tested these primers over a range of sample types including three coral species, coral surrounding water, reef surface water, and open ocean water to assess their suitability for use in large-scale next generation sequencing projects and to develop a standardised PCR protocol. We found the SYM_VAR_5.8S2/SYM_VAR_REV primers to perform superior to the other tested ITS2 primers. We therefore used this primer pair to develop a standardised PCR protocol. To do this, we tested the effect of PCR-to-PCR variation, annealing temperature, cycle number, and different polymerase systems on the PCR efficacy. The Symbiodinium ITS2 PCR protocol developed here delivers improved specificity and sensitivity towards Symbiodinium with apparent minimal sub-genera taxonomic bias across all sample types. In particular, the protocol's ability to amplify Symbiodinium from a range of environmental sources will facilitate the study of Symbiodinium populations across biomes.</dcterms:abstract> <dcterms:issued>2018</dcterms:issued> </rdf:Description> </rdf:RDF>

Downloads since Sep 25, 2020 (Information about access statistics)

Hume_2-1cub3ez3tah3s5.pdf 72

This item appears in the following Collection(s)

Attribution 4.0 International Except where otherwise noted, this item's license is described as Attribution 4.0 International

Search KOPS


Browse

My Account