101. Evaluating the Ribosomal Internal Transcribed Spacer (ITS) as a Candidate Dinoflagellate Barcode Marker
- Author
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Benoît Véron, Frithjof C. Küpper, Florence Le Gall, Mary Alice Coffroth, Robert A. Andersen, Hayley Skelton, Jerry J. Brand, Ian Jameson, Emily L. Lilly, Rowena Stern, Daniel Vaulot, Patrick J. Keeling, Fumai Kasai, Sir AlisterHardyFoundationforOceanScience, TheLaboratory,CitadelHill,PlymouthPL12PB,UK, Bigelow Laboratory for Ocean Sciences, Australian National Algae Culture Collection, Industrial Research Organisation Marine and Atmospheric Research, Scottish Association for Marine Science (SAMS), University at Buffalo [SUNY] (SUNY Buffalo), State University of New York (SUNY), Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University of Texas at Austin [Austin], Department of Marine Sciences, University of Connecticut (UCONN), National Institute for Environmental Studies (NIES), Biology Department - Virginia Military Institute, Department of Botany, University of Britsh Columbia [Vancouver], Genome Canada, United Kingdom Natural Environment Research Council [Oceans 2025 NF3, MGF 154], National Science Foundation [OCE 04-24994, OCE-09-26822], University of British Columbia [Vancouver], and Kolokotronis, Sergios-Orestis
- Subjects
0106 biological sciences ,[SDV]Life Sciences [q-bio] ,lcsh:Medicine ,01 natural sciences ,DNA barcoding ,Biochemistry ,Symbiodinium ,DNA amplification ,lcsh:Science ,Phylogeny ,0303 health sciences ,Multidisciplinary ,Ecology ,Cytochrome b ,Microbial Mutation ,Biodiversity ,DNA Barcoding ,Nucleic acids ,[SDE]Environmental Sciences ,Dinoflagellida ,Phycology ,Research Article ,Genetic Markers ,Species complex ,Ecological Metrics ,Life on Land ,General Science & Technology ,Biophysics ,Marine Biology ,Biology ,Alveolate ,Microbiology ,Electron Transport Complex IV ,03 medical and health sciences ,Marine Monitoring ,Botany ,Genetics ,Animals ,DNA Barcoding, Taxonomic ,Internal transcribed spacer ,030304 developmental biology ,010604 marine biology & hydrobiology ,lcsh:R ,Species diversity ,Taxonomic ,Species Diversity ,DNA ,biology.organism_classification ,Genetic marker ,Evolutionary biology ,Microbial Evolution ,Genetic Polymorphism ,lcsh:Q ,Ribosomes ,Population Genetics - Abstract
International audience; Background: DNA barcoding offers an efficient way to determine species identification and to measure biodiversity. For dinoflagellates, an ancient alveolate group of about 2000 described extant species, DNA barcoding studies have revealed large amounts of unrecognized species diversity, most of which is not represented in culture collections. To date, two mitochondrial gene markers, Cytochrome Oxidase I (COI) and Cytochrome b oxidase (COB), have been used to assess DNA barcoding in dinoflagellates, and both failed to amplify all taxa and suffered from low resolution. Nevertheless, both genes yielded many examples of morphospecies showing cryptic speciation and morphologically distinct named species being genetically similar, highlighting the need for a common marker. For example, a large number of cultured Symbiodinium strains have neither taxonomic identification, nor a common measure of diversity that can be used to compare this genus to other dinoflagellates. Methodology/Principal Findings: The purpose of this study was to evaluate the Internal Transcribed Spacer units 1 and 2 (ITS) of the rDNA operon, as a high resolution marker for distinguishing species dinoflagellates in culture. In our study, from 78 different species, the ITS barcode clearly differentiated species from genera and could identify 96% of strains to a known species or sub-genus grouping. 8.3% showed evidence of being cryptic species. A quarter of strains identified had no previous species identification. The greatest levels of hidden biodiversity came from Scrippsiella and the Pfiesteriaceae family, whilst Heterocapsa strains showed a high level of mismatch to their given species name. Conclusions/Significance: The ITS marker was successful in confirming species, revealing hidden diversity in culture collections. This marker, however, may have limited use for environmental barcoding due to paralogues, the potential for unidentifiable chimaeras and priming across taxa. In these cases ITS would serve well in combination with other markers or for specific taxon studies.
- Published
- 2012
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