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A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications
- Source :
- Molecular ecology resources, 17 (2017): 1054–1071. doi:10.1111/1755-0998.12640, info:cnr-pdr/source/autori:Arrigoni, Roberto; Vacherie, Benoit; Benzoni, Francesca; Stefani, Fabrizio; Karsenti, Eric; Jaillon, Olivier; Not, Fabrice; Nunes, Flavia; Payri, Claude; Wincker, Patrick; Barbe, Valerrie/titolo:A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications/doi:10.1111%2F1755-0998.12640/rivista:Molecular ecology resources (Print)/anno:2017/pagina_da:1054/pagina_a:1071/intervallo_pagine:1054–1071/volume:17
- Publication Year :
- 2017
-
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.
- Subjects :
- 0301 basic medicine
Scleractinia
DNA, Ribosomal
DNA barcoding
Montipora
cnidarians
03 medical and health sciences
Phylogenetics
systematic
RNA, Ribosomal, 18S
Genetics
Animals
Cluster Analysis
DNA Barcoding, Taxonomic
Acropora
cnidarian
systematics
Phylogeny
Ecology, Evolution, Behavior and Systematics
geography
geography.geographical_feature_category
biology
Phylogenetic tree
Ecology
hard corals
molecular evolution
fungi
Genetic Variation
Genes, rRNA
Sequence Analysis, DNA
Coral reef
Ribosomal RNA
Anthozoa
biology.organism_classification
hypervariable region
hard coral
030104 developmental biology
gene structure and function
Nucleic Acid Conformation
Biotechnology
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Molecular ecology resources, 17 (2017): 1054–1071. doi:10.1111/1755-0998.12640, info:cnr-pdr/source/autori:Arrigoni, Roberto; Vacherie, Benoit; Benzoni, Francesca; Stefani, Fabrizio; Karsenti, Eric; Jaillon, Olivier; Not, Fabrice; Nunes, Flavia; Payri, Claude; Wincker, Patrick; Barbe, Valerrie/titolo:A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications/doi:10.1111%2F1755-0998.12640/rivista:Molecular ecology resources (Print)/anno:2017/pagina_da:1054/pagina_a:1071/intervallo_pagine:1054–1071/volume:17
- Accession number :
- edsair.doi.dedup.....6501240ede7512af8e9b30ce5e9e9bdb