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dc.contributor.authorCarradec, Quentin
dc.contributor.authorPoulain, Julie
dc.contributor.authorBoissin, Emilie
dc.contributor.authorHume, Benjamin C C
dc.contributor.authorVoolstra, Christian R.
dc.contributor.authorZiegler, Maren
dc.contributor.authorEngelen, Stefan
dc.contributor.authorCruaud, Corinne
dc.contributor.authorPlanes, Serge
dc.contributor.authorWincker, Patrick
dc.date.accessioned2020-09-30T07:46:53Z
dc.date.available2020-06-17T11:45:44Z
dc.date.available2020-09-30T07:46:53Z
dc.date.issued2020-09-28
dc.date.submitted2020-05-01
dc.identifier.citationCarradec, Q., Poulain, J., Boissin, E., Hume, B. C. C., Voolstra, C. R., Ziegler, M., … Wincker, P. (2020). A framework for in situ molecular characterization of coral holobionts using nanopore sequencing. Scientific Reports, 10(1). doi:10.1038/s41598-020-72589-0
dc.identifier.issn2045-2322
dc.identifier.pmid32985530
dc.identifier.doi10.1038/s41598-020-72589-0
dc.identifier.doi10.1038/s41598-021-81544-6
dc.identifier.urihttp://hdl.handle.net/10754/663643
dc.description.abstractMolecular 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.
dc.description.sponsorshipThis project has been funded through the Tara Pacific consortium, France Genomique grant number ANR-10-INBS-09, and the Genoscope/CEA. We are keen to thank the commitment of the people and the following institutions and sponsors who made this singular expedition possible: CNRS, CSM, PSL, KAUST, Genoscope/CEA, ANR-CORALGENE, agnès b., the Veolia Environment Foundation, Region Bretagne, Serge Ferrari, Billerudkorsnas, AmerisourceBergen Company, Lorient Agglomération, Oceans by Disney, the Prince Albert II de Monaco Foundation, L′Oreal, Biotherm, France Collectivites, Kankyo Station, Fonds Francais pour l′Environnement Mondial (FFEM), Etienne Bourgois, UNESCO-IOC, the Tara Foundation teams and crew. Tara Pacific would not exist without the continuous support of the participating institutes. This publication is number 5 of the Tara Pacific Consortium.
dc.publisherSpringer Nature
dc.relation.urlhttp://www.nature.com/articles/s41598-020-72589-0
dc.rightsThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.titleA framework for in situ molecular characterization of coral holobionts using nanopore sequencing.
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentEnvironmental Science and Engineering Program
dc.contributor.departmentMarine Science Program
dc.contributor.departmentRed Sea Research Center (RSRC)
dc.contributor.departmentRed Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
dc.contributor.departmentReef Genomics Lab
dc.identifier.journalScientific reports
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionGénomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France.
dc.contributor.institutionResearch Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 rue Michel‑Ange, 75016 Paris, France.
dc.contributor.institutionPSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France.
dc.contributor.institutionLaboratoire d’Excellence “CORAIL”, 52 Avenue Paul Alduy, 66860 Perpignan Cedex, France.
dc.contributor.institutionDepartment of Biology, University of Konstanz, 78457 Konstanz, Germany.
dc.contributor.institutionDepartment of Animal Ecology & Systematics, Justus Liebig University, Giessen, Germany.
dc.contributor.institutionGenoscope, Institut de Biologie François-Jacob, Commissariat l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France.
dc.identifier.volume10
dc.identifier.issue1
kaust.personHume, Benjamin C C
kaust.personVoolstra, Christian R.
dc.date.accepted2020-09-03
refterms.dateFOA2020-06-17T11:46:20Z
dc.date.published-online2020-09-28
dc.date.published-print2020-12


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This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
Except where otherwise noted, this item's license is described as This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
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