A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications

Handle URI:
http://hdl.handle.net/10754/623428
Title:
A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications
Authors:
Arrigoni, Roberto; Vacherie, Benoît; Benzoni, Francesca; Stefani, Fabrizio; Karsenti, Eric; Jaillon, Olivier; Not, Fabrice; Nunes, Flavia; Payri, Claude; Wincker, Patrick; Barbe, Valérie
Abstract:
Scleractinian corals (i.e. hard corals) play a fundamental role in building and maintaining coral reefs, one of the most diverse ecosystems on Earth. Nevertheless, their phylogenies remain largely unresolved and little is known about dispersal and survival of their planktonic larval phase. The small subunit ribosomal RNA (SSU rRNA) is a commonly used gene for DNA barcoding in several metazoans, and small variable regions of SSU rRNA are widely adopted as barcode marker to investigate marine plankton community structure worldwide. Here, we provide a large sequence data set of the complete SSU rRNA gene from 298 specimens, representing all known extant reef coral families and a total of 106 genera. The secondary structure was extremely conserved within the order with few exceptions due to insertions or deletions occurring in the variable regions. Remarkable differences in SSU rRNA length and base composition were detected between and within acroporids (Acropora, Montipora, Isopora and Alveopora) compared to other corals. The V4 and V9 regions seem to be promising barcode loci because variation at commonly used barcode primer binding sites was extremely low, while their levels of divergence allowed families and genera to be distinguished. A time-calibrated phylogeny of Scleractinia is provided, and mutation rate heterogeneity is demonstrated across main lineages. The use of this data set as a valuable reference for investigating aspects of ecology, biology, molecular taxonomy and evolution of scleractinian corals is discussed.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Red Sea Research Center (RSRC)
Citation:
Arrigoni R, Vacherie B, Benzoni F, Stefani F, Karsenti E, et al. (2017) A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications. Molecular Ecology Resources. Available: http://dx.doi.org/10.1111/1755-0998.12640.
Publisher:
Wiley-Blackwell
Journal:
Molecular Ecology Resources
Issue Date:
27-Nov-2016
DOI:
10.1111/1755-0998.12640
Type:
Article
ISSN:
1755-098X
Sponsors:
We are grateful to E. Bourgois (Tara Expeditions), the Tara Oceans Consortium for allowing sampling during the Tara Oceans expedition in Djibouti, Gambier Islands and Mayotte. We thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS, EMBL, Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects POSEIDON/ANR-09-BLAN-0348, BIOMARKS/ANR-08-BDVA-003, PROMETHEUS/ANR-09-GENM-031 and TARA-GIRUS/ANR-09-PCS-GENM-218), EU FP7 (MicroB3/No.287589), FWO, BIO5, Biosphere 2, agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner and its captain and crew. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org). This article is contribution number 49 of the Tara Oceans Expedition 2009–2012. Collection in New Caledonia was possible thanks to JL Menou, G Lasne (Biotope), the IRD Service plongée and the R/V Alis Captain R Proner and crew (http://dx.doi.org/10.17600/12100060). The Niugini Biodiversity Expedition, P Bouchet (MNHN) and B Dreyfus (IRD) are acknowledged for collections in Papua New Guinea (http://dx.doi.org/10.17600/12100070). The Madang expedition specimens were obtained during the 'Our Planet Reviewed' Papua Niugini expedition organized by Muséum National d'Histoire Naturelle (MNHN), Pro Natura International (PNI), Institut de Recherche pour le Développement (IRD) and University of Papua New Guinea (UPNG), Principal Investigators Philippe Bouchet, Claude Payri and Sarah Samadi. The organizers acknowledge funding from the Total Foundation, Prince Albert II of Monaco Foundation, Fondation EDF, Stavros Niarchos Foundation and Entrepose Contracting, and in-kind support from the Divine Word University (DWU). The expedition operated under a permit delivered by the Papua New Guinea Department of Environment and Conservation. Collection in the Marquesas occurred during the 2011 Agences des Aires Marines Protégées (AAMP) ‘Pakaihi o te Moana’ expedition. Sampling in the Maldives was possible thanks to E Dutrieux (CREOCEAN). We are also grateful to E Dutrieux, CH Chaineau (Total SA), R Hirst and M Abdul Aziz (YLNG) for allowing and supporting research in Yemen. The first author is grateful to S Montano (UNIMIB-MaRHE Center) for his help in statistical analyses and to R Hardenstine (KAUST) for her fruitful comments on the text. We thank CA Chen, P Wirtz, A Gori, M Jansen, A Travaglini, C Riva, BW Hoeksema, AH Baird, M Hoogenboom and ZT Richards for kindly providing some coral samples. We thank the two anonymous reviewers for their constructive remarks that improved the manuscript and analyses.
Additional Links:
http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12640/full
Appears in Collections:
Articles; Red Sea Research Center (RSRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorArrigoni, Robertoen
dc.contributor.authorVacherie, Benoîten
dc.contributor.authorBenzoni, Francescaen
dc.contributor.authorStefani, Fabrizioen
dc.contributor.authorKarsenti, Ericen
dc.contributor.authorJaillon, Olivieren
dc.contributor.authorNot, Fabriceen
dc.contributor.authorNunes, Flaviaen
dc.contributor.authorPayri, Claudeen
dc.contributor.authorWincker, Patricken
dc.contributor.authorBarbe, Valérieen
dc.date.accessioned2017-05-09T12:54:45Z-
dc.date.available2017-05-09T12:54:45Z-
dc.date.issued2016-11-27en
dc.identifier.citationArrigoni R, Vacherie B, Benzoni F, Stefani F, Karsenti E, et al. (2017) A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications. Molecular Ecology Resources. Available: http://dx.doi.org/10.1111/1755-0998.12640.en
dc.identifier.issn1755-098Xen
dc.identifier.doi10.1111/1755-0998.12640en
dc.identifier.urihttp://hdl.handle.net/10754/623428-
dc.description.abstractScleractinian corals (i.e. hard corals) play a fundamental role in building and maintaining coral reefs, one of the most diverse ecosystems on Earth. Nevertheless, their phylogenies remain largely unresolved and little is known about dispersal and survival of their planktonic larval phase. The small subunit ribosomal RNA (SSU rRNA) is a commonly used gene for DNA barcoding in several metazoans, and small variable regions of SSU rRNA are widely adopted as barcode marker to investigate marine plankton community structure worldwide. Here, we provide a large sequence data set of the complete SSU rRNA gene from 298 specimens, representing all known extant reef coral families and a total of 106 genera. The secondary structure was extremely conserved within the order with few exceptions due to insertions or deletions occurring in the variable regions. Remarkable differences in SSU rRNA length and base composition were detected between and within acroporids (Acropora, Montipora, Isopora and Alveopora) compared to other corals. The V4 and V9 regions seem to be promising barcode loci because variation at commonly used barcode primer binding sites was extremely low, while their levels of divergence allowed families and genera to be distinguished. A time-calibrated phylogeny of Scleractinia is provided, and mutation rate heterogeneity is demonstrated across main lineages. The use of this data set as a valuable reference for investigating aspects of ecology, biology, molecular taxonomy and evolution of scleractinian corals is discussed.en
dc.description.sponsorshipWe are grateful to E. Bourgois (Tara Expeditions), the Tara Oceans Consortium for allowing sampling during the Tara Oceans expedition in Djibouti, Gambier Islands and Mayotte. We thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS, EMBL, Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects POSEIDON/ANR-09-BLAN-0348, BIOMARKS/ANR-08-BDVA-003, PROMETHEUS/ANR-09-GENM-031 and TARA-GIRUS/ANR-09-PCS-GENM-218), EU FP7 (MicroB3/No.287589), FWO, BIO5, Biosphere 2, agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner and its captain and crew. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org). This article is contribution number 49 of the Tara Oceans Expedition 2009–2012. Collection in New Caledonia was possible thanks to JL Menou, G Lasne (Biotope), the IRD Service plongée and the R/V Alis Captain R Proner and crew (http://dx.doi.org/10.17600/12100060). The Niugini Biodiversity Expedition, P Bouchet (MNHN) and B Dreyfus (IRD) are acknowledged for collections in Papua New Guinea (http://dx.doi.org/10.17600/12100070). The Madang expedition specimens were obtained during the 'Our Planet Reviewed' Papua Niugini expedition organized by Muséum National d'Histoire Naturelle (MNHN), Pro Natura International (PNI), Institut de Recherche pour le Développement (IRD) and University of Papua New Guinea (UPNG), Principal Investigators Philippe Bouchet, Claude Payri and Sarah Samadi. The organizers acknowledge funding from the Total Foundation, Prince Albert II of Monaco Foundation, Fondation EDF, Stavros Niarchos Foundation and Entrepose Contracting, and in-kind support from the Divine Word University (DWU). The expedition operated under a permit delivered by the Papua New Guinea Department of Environment and Conservation. Collection in the Marquesas occurred during the 2011 Agences des Aires Marines Protégées (AAMP) ‘Pakaihi o te Moana’ expedition. Sampling in the Maldives was possible thanks to E Dutrieux (CREOCEAN). We are also grateful to E Dutrieux, CH Chaineau (Total SA), R Hirst and M Abdul Aziz (YLNG) for allowing and supporting research in Yemen. The first author is grateful to S Montano (UNIMIB-MaRHE Center) for his help in statistical analyses and to R Hardenstine (KAUST) for her fruitful comments on the text. We thank CA Chen, P Wirtz, A Gori, M Jansen, A Travaglini, C Riva, BW Hoeksema, AH Baird, M Hoogenboom and ZT Richards for kindly providing some coral samples. We thank the two anonymous reviewers for their constructive remarks that improved the manuscript and analyses.en
dc.publisherWiley-Blackwellen
dc.relation.urlhttp://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12640/fullen
dc.titleA new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applicationsen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.identifier.journalMolecular Ecology Resourcesen
dc.contributor.institutionDepartment of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milan 20126 Italyen
dc.contributor.institutionCEA/DSV/IG/Genoscope; Evry Cedex Franceen
dc.contributor.institutionInstitut de Recherche pour le Développement; UMR227 Coreus2; 101 Promenade Roger Laroque BP A5 Noumea Cedex 98848 New Caledoniaen
dc.contributor.institutionWater Research Institute-National Research Council (IRSA-CNR); Via del Mulino 19 Brugherio I-20861 Italyen
dc.contributor.institutionEcole Normale Supérieure; Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197; Paris F-75005 Franceen
dc.contributor.institutionDirectors’ Research; European Molecular Biology Laboratory; Meyerhofstr. 1 Heidelberg 69117 Germanyen
dc.contributor.institutionUniversité d'Evry; UMR 8030; Evry CP5706 Franceen
dc.contributor.institutionUPMC-CNRS; UMR 7144; Station Biologique de Roscoff; Place Georges Teissier Roscoff 29680 Franceen
dc.contributor.institutionIfremer Centre Bretagne; DYNECO; Laboratoire d’Écologie Benthique Côtière (LEBCO); 29280 Plouzané Franceen
kaust.authorArrigoni, Robertoen
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