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dc.contributor.authorCarradec, Quentin
dc.contributor.authorPoulain, Julie
dc.contributor.authorBoissin, Emilie
dc.contributor.authorHume, Benjamin CC
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.identifier.citationCarradec, Q., Poulain, J., Boissin, E., Hume, B. C., Voolstra, C. R., Ziegler, M., … Wincker, P. (2020). A framework for in situ molecular characterization of coral holobionts using nanopore sequencing. doi:10.1101/2020.05.25.071951
dc.description.abstractAbstractMolecular 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 hours. 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.sponsorshipJP, QC and PW designed the study. QC wrote the paper with substantial input from JP, BH, EB, CV, MZ, SP and PW. EB collected coral samples. JP coordinated in situ experiments and nanopore sequencing assisted by QC. QC, BH, MZ and EB performed barcoding data analyses. JP, QC, CC and SE contributed to the development of protocols and tools for nanopore sequencing and analysis. All authors discussed the results and commented on the manuscript.
dc.publisherCold Spring Harbor Laboratory
dc.rightsArchived with thanks to Cold Spring Harbor Laboratory
dc.titleA framework for in situ molecular characterization of coral holobionts using nanopore sequencing
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.departmentMarine Science Program
dc.contributor.departmentRed Sea Research Center (RSRC)
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
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, FR2022/Tara Oceans GO-SEE, 3 rue Michel-Ange, 75016 Paris, France.
dc.contributor.institutionResearch 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, Universitätsstraße 10, 78457 Konstanz, Germany.
dc.contributor.institutionDepartment of Animal Ecology & Systematics, Justus Liebig University, Giessen, Germany.
dc.contributor.institutionGenoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France.
kaust.personHume, Benjamin CC
kaust.personVoolstra, Christian R.

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