Publikation:

A framework for in situ molecular characterization of coral holobionts using nanopore sequencing

Lade...
Vorschaubild

Dateien

Carradec_2-178coq9068ax35.pdf
Carradec_2-178coq9068ax35.pdfGröße: 2.46 MBDownloads: 257

Datum

2020

Autor:innen

Carradec, Quentin
Poulain, Julie
Boissin, Emilie
Ziegler, Maren
Engelen, Stefan
Cruaud, Corinne
Planes, Serge
Wincker, Patrick

Herausgeber:innen

Kontakt

ISSN der Zeitschrift

Electronic ISSN

ISBN

Bibliografische Daten

Verlag

Schriftenreihe

Auflagebezeichnung

ArXiv-ID

Internationale Patentnummer

Link zur Lizenz

Angaben zur Forschungsförderung

Projekt

Open Access-Veröffentlichung
Open Access Gold
Core Facility der Universität Konstanz

Gesperrt bis

Titel in einer weiteren Sprache

Publikationstyp
Zeitschriftenartikel
Publikationsstatus
Published

Erschienen in

Scientific Reports. Springer Nature. 2020, 10(1), 15893. eISSN 2045-2322. Available under: doi: 10.1038/s41598-020-72589-0

Zusammenfassung

Molecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. This requires bulky instruments and controlled laboratory conditions which are impractical for environmental experiments in remote areas. Recent advances in sequencing technologies now permit rapid sequencing in the field; however, development of specific protocols and pipelines for the effective processing of complex microbial systems are currently lacking. Here, we used a combination of 3 marker genes targeting the coral animal host, its symbiotic alga, and the associated bacterial microbiome to characterize 60 coral colonies collected and processed in situ, during the Tara Pacific expedition. We used Oxford Nanopore Technologies to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 h. Reef scale network analysis of coral-associated bacteria reveals broadly distributed taxa, as well as host-specific associations. Protocols and tools used in this work may be applicable for rapid coral holobiont surveys, immediate adaptation of sampling strategy in the field, and to make informed and timely decisions in the context of the current challenges affecting coral reefs worldwide.

Zusammenfassung in einer weiteren Sprache

Fachgebiet (DDC)
570 Biowissenschaften, Biologie

Schlagwörter

Konferenz

Rezension
undefined / . - undefined, undefined

Forschungsvorhaben

Organisationseinheiten

Zeitschriftenheft

Zugehörige Datensätze in KOPS

Zitieren

ISO 690CARRADEC, Quentin, Julie POULAIN, Emilie BOISSIN, Benjamin C. C. HUME, Christian R. VOOLSTRA, Maren ZIEGLER, Stefan ENGELEN, Corinne CRUAUD, Serge PLANES, Patrick WINCKER, 2020. A framework for in situ molecular characterization of coral holobionts using nanopore sequencing. In: Scientific Reports. Springer Nature. 2020, 10(1), 15893. eISSN 2045-2322. Available under: doi: 10.1038/s41598-020-72589-0
BibTex
@article{Carradec2020-09-28frame-51143,
  year={2020},
  doi={10.1038/s41598-020-72589-0},
  title={A framework for in situ molecular characterization of coral holobionts using nanopore sequencing},
  number={1},
  volume={10},
  journal={Scientific Reports},
  author={Carradec, Quentin and Poulain, Julie and Boissin, Emilie and Hume, Benjamin C. C. and Voolstra, Christian R. and Ziegler, Maren and Engelen, Stefan and Cruaud, Corinne and Planes, Serge and Wincker, Patrick},
  note={Article Number: 15893}
}
RDF
<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/server/rdf/resource/123456789/51143">
    <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/51143"/>
    <dc:creator>Wincker, Patrick</dc:creator>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2020-09-30T13:36:42Z</dc:date>
    <dc:contributor>Engelen, Stefan</dc:contributor>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dc:rights>Attribution 4.0 International</dc:rights>
    <dc:creator>Voolstra, Christian R.</dc:creator>
    <dcterms:title>A framework for in situ molecular characterization of coral holobionts using nanopore sequencing</dcterms:title>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dc:creator>Hume, Benjamin C. C.</dc:creator>
    <dc:contributor>Ziegler, Maren</dc:contributor>
    <dcterms:abstract xml:lang="eng">Molecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. This requires bulky instruments and controlled laboratory conditions which are impractical for environmental experiments in remote areas. Recent advances in sequencing technologies now permit rapid sequencing in the field; however, development of specific protocols and pipelines for the effective processing of complex microbial systems are currently lacking. Here, we used a combination of 3 marker genes targeting the coral animal host, its symbiotic alga, and the associated bacterial microbiome to characterize 60 coral colonies collected and processed in situ, during the Tara Pacific expedition. We used Oxford Nanopore Technologies to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 h. Reef scale network analysis of coral-associated bacteria reveals broadly distributed taxa, as well as host-specific associations. Protocols and tools used in this work may be applicable for rapid coral holobiont surveys, immediate adaptation of sampling strategy in the field, and to make informed and timely decisions in the context of the current challenges affecting coral reefs worldwide.</dcterms:abstract>
    <dc:contributor>Carradec, Quentin</dc:contributor>
    <dc:contributor>Poulain, Julie</dc:contributor>
    <dcterms:rights rdf:resource="http://creativecommons.org/licenses/by/4.0/"/>
    <dc:creator>Boissin, Emilie</dc:creator>
    <dc:creator>Cruaud, Corinne</dc:creator>
    <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/51143/1/Carradec_2-178coq9068ax35.pdf"/>
    <dc:contributor>Hume, Benjamin C. C.</dc:contributor>
    <dc:contributor>Cruaud, Corinne</dc:contributor>
    <dc:creator>Carradec, Quentin</dc:creator>
    <dc:contributor>Boissin, Emilie</dc:contributor>
    <dc:contributor>Planes, Serge</dc:contributor>
    <dc:creator>Engelen, Stefan</dc:creator>
    <dc:creator>Planes, Serge</dc:creator>
    <dc:contributor>Wincker, Patrick</dc:contributor>
    <dc:language>eng</dc:language>
    <dcterms:issued>2020-09-28</dcterms:issued>
    <dc:contributor>Voolstra, Christian R.</dc:contributor>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2020-09-30T13:36:42Z</dcterms:available>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/51143/1/Carradec_2-178coq9068ax35.pdf"/>
    <dc:creator>Poulain, Julie</dc:creator>
    <dc:creator>Ziegler, Maren</dc:creator>
  </rdf:Description>
</rdf:RDF>

Interner Vermerk

xmlui.Submission.submit.DescribeStep.inputForms.label.kops_note_fromSubmitter

Kontakt
URL der Originalveröffentl.

Prüfdatum der URL

Prüfungsdatum der Dissertation

Finanzierungsart

Kommentar zur Publikation

Allianzlizenz
Corresponding Authors der Uni Konstanz vorhanden
Internationale Co-Autor:innen
Universitätsbibliographie
Ja
Begutachtet
Ja
Diese Publikation teilen