title: A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications.
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.
authors.affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.|Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milan, 20126, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Arrigoni
authors.affiliation: CEA/DSV/IG/Genoscope, Evry Cedex, France.
authors.forename: Benoît
authors.initials: B
authors.lastname: Vacherie
authors.affiliation: Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milan, 20126, Italy.|Institut de Recherche pour le Développement, UMR227 Coreus2, 101 Promenade Roger Laroque, BP A5, Noumea Cedex, 98848, New Caledonia.
authors.forename: Francesca
authors.initials: F
authors.lastname: Benzoni
authors.affiliation: Water Research Institute-National Research Council (IRSA-CNR), Via del Mulino 19, Brugherio, I-20861, Italy.
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Stefani
authors.affiliation: Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, Paris, F-75005, France.|Directors' Research, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg, 69117, Germany.
authors.forename: Eric
authors.initials: E
authors.lastname: Karsenti
authors.affiliation: CEA/DSV/IG/Genoscope, Evry Cedex, France.|Université d'Evry, UMR 8030, Evry, CP5706, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Jaillon
authors.affiliation: UPMC-CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France.
authors.forename: Fabrice
authors.initials: F
authors.lastname: Not
authors.affiliation: Ifremer Centre Bretagne, DYNECO, Laboratoire d'Écologie Benthique Côtière (LEBCO), 29280 Plouzané, France.
authors.forename: Flavia
authors.initials: F
authors.lastname: Nunes
authors.affiliation: Institut de Recherche pour le Développement, UMR227 Coreus2, 101 Promenade Roger Laroque, BP A5, Noumea Cedex, 98848, New Caledonia.
authors.forename: Claude
authors.initials: C
authors.lastname: Payri
authors.affiliation: CEA/DSV/IG/Genoscope, Evry Cedex, France.|Université d'Evry, UMR 8030, Evry, CP5706, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.affiliation: CEA/DSV/IG/Genoscope, Evry Cedex, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Barbe
mesh_terms: D000818:Animals; D037421:Anthozoa / Q000145:classification* / Q000235:genetics*; D016000:Cluster Analysis; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D020459:Genes, rRNA; D014644:Genetic Variation; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004275:DNA, Ribosomal; D012337:RNA, Ribosomal, 18S
keywords: cnidarians; gene structure and function; hard corals; hypervariable region; molecular evolution; systematics