Barcoding COI B.azoricus MoMARSAT
6 DNA sequences of Bathymodiolus azoricus from COI barcode analysis, Capelinhos Lucky Strike area, Mid-Atlantic Ridge.
Simple
- Title
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Barcoding COI B.azoricus MoMARSAT
- Date (Creation)
- 2017-04-25
- Date (Publication)
- 2023-04-13
- Citation identifier
- FR-330-715-368-00032-IFR_BIOINFO_BARCODING_AZORICUS_MOMARSAT
- Abstract
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6 DNA sequences of Bathymodiolus azoricus from COI barcode analysis, Capelinhos Lucky Strike area, Mid-Atlantic Ridge.
- Credit
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Ifremer - Laboratoire Environnement Profond
- Point of contact
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Organisation name Individual name Electronic mail address Role IFREMER
Publisher Department of Biology, University of Victoria, Victoria, British Columbia, Canada
Alfaro Lucas Joan Manel
Author Centre d’Estudis Avançats de Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
Martin Daniel
Author Université de Liège, Liège, Belgium
Michel Loïc
Author Université de Brest, Ifremer, CNRS, Unité BEEP, Plouzané, Bretagne, France
Cathalot Cecile
Author Université de Brest, Ifremer, CNRS, Unité BEEP, Plouzané, Bretagne, France
Laes Agathe
Author IFREMER
Fuchs Sandra
Author IFREMER
Sarrazin Jozee
Author
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Thèmes Sextant
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/Biological Environment/Bioinformatics
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GEMET - INSPIRE themes, version 1.0
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Habitats and biotopes
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Type de jeux de donnée ODATIS
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/Sequences
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ODATIS aggregation parameters and Essential Variable names
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Bioinformatics
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- Use limitation
- CC-BY (Creative Commons - Attribution)
- Access constraints
- License
- Use constraints
- License
- Spatial representation type
- Vector
- Language
- English
- Character set
- UTF8
- Topic category
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- Oceans
- Begin date
- 2017-04-25
- End date
- 2020-03-01
- Distribution format
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Name Version
- OnLine resource
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Protocol Linkage Name WWW:LINK-1.0-http--publication-URL
https://doi.org/10.17882/90421 Main publication
NETWORK:LINK
/home/ref-bioinfo-public/ifremer/lep/bazoricus-momarsat WWW:DOWNLOAD-1.0-link--download
https://data-dataref.ifremer.fr/bioinfo/ifremer/lep/bazoricus-momarsat/data/raw-sequence/ Download link
- OnLine resource
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Protocol Linkage Name WWW:LINK-1.0-http--metadata-URL
https://doi.org/10.12770/72f13a1b-3770-4108-828c-b12aa4249987 Digital Object Identifier (DOI)
- Hierarchy level
- Dataset
Conformance result
- Title
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RÈGLEMENT (UE) N o 1089/2010 DE LA COMMISSION du 23 novembre 2010 portant modalités d'application de la directive 2007/2/CE du Parlement européen et du Conseil en ce qui concerne l'interopérabilité des séries et des services de données géographiques
- Date (Publication)
- 2010-12-08
- Explanation
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See the referenced specification
- Pass
- Statement
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Study area, sampling and sample processing.
Capelinhos was revisited during the Momarsat 2014 ( https://doi.org/10.17600/14000300) and 2015 ( https://doi.org/10.17600/15000200) cruises on board of the R/V Pourquoi Pas? which visually inspected chimneys, diffuse flow areas and the periphery using the ROV Victor6000. In 2014, three temperature probes were deployed on a large-size mussel bed on a diffuse flow area at the base of one edifice. The probes registered temperatures every 15 minutes for 10 9 months, form the 24th July 2014 to the 20th/23rd April 2015. In 2015, prior to faunal sampling associated to mussels, sulfide (ƩS) and iron (Fe(II)) concentrations were measured in situ using the chemical analyzer CHEMINI (Vuillemin et al. 2009) over the targeted mussel bed. Samples were collected using Victor6000's manipulator arm (three to four grabs per sample) and placed in isotherm boxes. After grabs, a suction sampler was used on each sampling area to collect all remaining fauna. Sampled area was estimated analyzing Victor6000's videos with the software ImageJ. Once on board, samples were sieved through 250 µm (directly fixed in 96° ethanol) and 20 µm (fixed with 4% buffered formalin, then in 96°ethanol, not considered in this study) mesh-sizes. Individuals were sorted, identified to the lowest taxonomic level possible using stereo- and binocular microscopes (except for mussel specimens, which were barcoded to identify the species), and counted (only individuals with complete anterior regions). Meiofaunal organisms (e.g., copepods and nematodes) found in the macrofaunal samples were included in the analyses.
Genetic analyses.
We used the mitochondrial cytochrome oxidase I (mtCOI) to identify mussel specimens. In short, we extracted 10–50 mg of mussel tissue to be digested until total digestion with proteinase K at 60ºC in 0.5 ml pK-CTAB lysis buffer (containing 2% CTAB (Cetiltrimetilamina), 1 M NaCl, 1% PVP (Polyvinylpirrolidina), 20 mM EDTA pH8, 100 mM Tris-HCl pH 8, 0.1 mg mL-1 proteinase K).
Then, we: (1) extracted genomic DNA using the phenol/chloroform protocol, (2) precipitated it with Isopropanol and washes with ethanol 70%, (3) resuspended and stored the pellet at -20°CºC in molecular quality steril water until amplifications, (4) obtained partial sequences of the mtCOI gene using the specific primers
BathCOI-F 5’-GTGGTCTGGAATAATTGGAAC-3’ and
BathCOI-R 5’- ATAAAAAGATGTATTRAARTGACG-3’
(following Olu-Le Roy et al. (2007)), and (5) amplified the DNA as follows: an initial step of denaturation at 94ºC for two minutes, five cycles of 35s/94ºC, 35s/48ºC and 70s/72ºC, thirty-five cycles of 35s/94ºC, 35s/52ºC, 70s/72ºC, and an final elongation at 72ºC for 10 min. We perform PCR reactions into a 25-ml reaction volume (1X PCR buffer, 2,2 mM MgCl2, 0.5 mM of each dNTPs, 0.55 µM of each primer, 0.02 U of Taq polymerase (GoTaq Promega), and 20 ng genomic DNA). The PCR products were purified and sequenced the 3730XL Sequencer by thermofisher (Macrogen Europe, The Netherlands) following the manufacturer’s protocol.
Metadata
- File identifier
- 72f13a1b-3770-4108-828c-b12aa4249987
- Metadata language
- English
- Character set
- UTF8
- Hierarchy level
- Dataset
- Date stamp
- 2023-10-13T09:52:54.329Z
- Metadata standard name
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ISO 19115:2003/19139 - SEXTANT
- Metadata standard version
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1.0
- Metadata author
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Organisation name Individual name Electronic mail address Role IFREMER
Fuchs Sandra
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