A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Red Sea Research Center (RSRC)
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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.
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.
SponsorsWe 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.
JournalMolecular Ecology Resources