KOPS - The Institutional Repository of the University of Konstanz

SymPortal : a novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling

SymPortal : a novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling

Cite This

Files in this item

Checksum: MD5:2441762e8dd7ca9a6005afefc7ba01e1

HUME, Benjamin C. C., Edward G. SMITH, Maren ZIEGLER, Hugh J. M. WARRINGTON, John A. BURT, Todd C. LAJEUNESSE, Joerg WIEDENMANN, Christian R. VOOLSTRA, 2019. SymPortal : a novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling. In: Molecular ecology resources. 19(4), pp. 1063-1080. ISSN 1471-8278. eISSN 1471-8286. Available under: doi: 10.1111/1755-0998.13004

@article{Hume2019-07SymPo-46239, title={SymPortal : a novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling}, year={2019}, doi={10.1111/1755-0998.13004}, number={4}, volume={19}, issn={1471-8278}, journal={Molecular ecology resources}, pages={1063--1080}, author={Hume, Benjamin C. C. and Smith, Edward G. and Ziegler, Maren and Warrington, Hugh J. M. and Burt, John A. and LaJeunesse, Todd C. and Wiedenmann, Joerg and Voolstra, Christian R.} }

<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/123456789/46239"> <dc:creator>Voolstra, Christian R.</dc:creator> <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/46239/1/Hume_2-1jbpv2tc483oc9.pdf"/> <dc:creator>Wiedenmann, Joerg</dc:creator> <dc:language>eng</dc:language> <dc:contributor>Burt, John A.</dc:contributor> <dc:contributor>Voolstra, Christian R.</dc:contributor> <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/28"/> <foaf:homepage rdf:resource="http://localhost:8080/jspui"/> <dc:contributor>Wiedenmann, Joerg</dc:contributor> <dcterms:rights rdf:resource="http://creativecommons.org/licenses/by/4.0/"/> <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/46239/1/Hume_2-1jbpv2tc483oc9.pdf"/> <dcterms:abstract xml:lang="eng">We present SymPortal (SymPortal.org), a novel analytical framework and platform for genetically resolving the algal symbionts of reef corals using next-generation sequencing (NGS) data of the ITS2 rDNA. Although the ITS2 marker is widely used to genetically characterize taxa within the family Symbiodiniaceae (formerly the genus Symbiodinium), the multicopy nature of the marker complicates its use. Commonly, the intragenomic diversity resultant from this multicopy nature is collapsed by analytical approaches, thereby focusing on only the most abundant sequences. In contrast, SymPortal employs logic to identify within-sample informative intragenomic sequences, which we have termed 'defining intragenomic variants' (DIVs), to identify ITS2-type profiles representative of putative Symbiodiniaceae taxa. By making use of this intragenomic ITS2 diversity, SymPortal is able to resolve genetic delineations using the ITS2 marker at a level that was previously only possible by using additional genetic markers. We demonstrate this by comparing this novel approach to the most commonly used alternative approach for NGS ITS2 data, the 97% similarity clustering to operational taxonomic units (OTUs). The SymPortal platform accepts NGS raw sequencing data as input to provide an easy-to-use, standardization-enforced, and community-driven framework that integrates with a database to gain resolving power with increased use. We consider that SymPortal, in conjunction with ongoing large-scale sampling and sequencing efforts, should play an instrumental role in making future sampling efforts more comparable and in maximizing their efficacy in working towards the classification of the global Symbiodiniaceae diversity.</dcterms:abstract> <dc:contributor>Smith, Edward G.</dc:contributor> <dc:creator>Warrington, Hugh J. M.</dc:creator> <dc:rights>Attribution 4.0 International</dc:rights> <dc:contributor>LaJeunesse, Todd C.</dc:contributor> <dcterms:title>SymPortal : a novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling</dcterms:title> <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/28"/> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2019-07-05T13:04:02Z</dc:date> <dc:creator>LaJeunesse, Todd C.</dc:creator> <dc:contributor>Warrington, Hugh J. M.</dc:contributor> <dc:creator>Hume, Benjamin C. C.</dc:creator> <dcterms:issued>2019-07</dcterms:issued> <dc:contributor>Ziegler, Maren</dc:contributor> <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/> <dc:creator>Smith, Edward G.</dc:creator> <dc:creator>Ziegler, Maren</dc:creator> <dc:contributor>Hume, Benjamin C. C.</dc:contributor> <dc:creator>Burt, John A.</dc:creator> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2019-07-05T13:04:02Z</dcterms:available> <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/46239"/> </rdf:Description> </rdf:RDF>

Downloads since Jul 5, 2019 (Information about access statistics)

Hume_2-1jbpv2tc483oc9.pdf 139

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