A framework for in situ molecular characterization of coral holobionts using nanopore sequencing
A framework for in situ molecular characterization of coral holobionts using nanopore sequencing
Abstract 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 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.
Voolstra Christian R、Ziegler Maren、Engelen Stefan、Cruaud Corinne、Planes Serge、Hume Benjamin CC、Wincker Patrick、Boissin Emilie、Poulain Julie、Carradec Quentin
Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST) Thuwal||Department of Biology, University of KonstanzDepartment of Animal Ecology & Systematics, Justus Liebig UniversityGenoscope, Institut de biologie Fran?ois-Jacob, Commissariat ¨¤ l?ˉEnergie Atomique (CEA), Universit¨| Paris-SaclayGenoscope, Institut de biologie Fran?ois-Jacob, Commissariat ¨¤ l?ˉEnergie Atomique (CEA), Universit¨| Paris-SaclayResearch Federation for the study of Global Ocean Systems Ecology and Evolution||PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Universit¨| de Perpignan||Laboratoire d?ˉExcellence ?°CORAIL?±Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST) ThuwalG¨|nomique M¨|tabolique, Genoscope, Institut Fran?ois Jacob, CEA, CNRS, Univ Evry, Universit¨| Paris-Saclay||Research Federation for the study of Global Ocean Systems Ecology and EvolutionPSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Universit¨| de Perpignan||Laboratoire d?ˉExcellence ?°CORAIL?±G¨|nomique M¨|tabolique, Genoscope, Institut Fran?ois Jacob, CEA, CNRS, Univ Evry, Universit¨| Paris-Saclay||Research Federation for the study of Global Ocean Systems Ecology and EvolutionG¨|nomique M¨|tabolique, Genoscope, Institut Fran?ois Jacob, CEA, CNRS, Univ Evry, Universit¨| Paris-Saclay||Research Federation for the study of Global Ocean Systems Ecology and Evolution
生物科学现状、生物科学发展环境生物学分子生物学
Voolstra Christian R,Ziegler Maren,Engelen Stefan,Cruaud Corinne,Planes Serge,Hume Benjamin CC,Wincker Patrick,Boissin Emilie,Poulain Julie,Carradec Quentin.A framework for in situ molecular characterization of coral holobionts using nanopore sequencing[EB/OL].(2025-03-28)[2025-06-16].https://www.biorxiv.org/content/10.1101/2020.05.25.071951.点此复制
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