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Raposo, Débora; Zufall, Rebecca A; Caruso, Antonio; Titelboim, Danna; Abramovich, Sigal; Hassenrück, Christiane; Kucera, Michal; Morard, Raphael (2022): SSU+ITS rRNA gene sequences, and associated metadata, of the larger benthic foraminifera Amphistegina lobifera across its invasive range [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.950041

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Published: 2022-11-01 • DOI registered: 2022-12-01

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Abstract:
The larger benthic foraminifera species Amphistegina lobifera has been successfully invading the Mediterranean Sea, despite different temperature regimes from their original source location in the Red Sea. To investigate possible genetic (pre)adaptations in the invasive populations, we analyzed the population structure of Amphistegina lobifera across the invasive range (source, pioneer invaders, and invasion front).
We snorkelled at four sites across the invasive range to collect living foraminifera individuals attached to macroalgae and pebbles. Each individual was isolated and stored at -80°C until DNA extraction. We amplified the SSU and the hypervariable ITS rRNA 18S gene regions and purified the PCR products. The purified PCR products were cloned, a final PCR was performed and the samples were sent for Sanger sequencing. We compared our results to other populations across the globe (for which only the SSU region is available).
Our dataset includes the sequences of the SSU+ITS rRNA regions, which are available on NCBI under the accession numbers OP610171-OP610543, and the associated metadata.
Keyword(s):
Benthic foraminifera; invasion; Lessepsian migration; Mediterranean Sea; population structure
Related to:
S. Raposo, Débora; A. Zufall, Rebecca; Caruso, Antonio; Titelboim, Danna; Abramovich, Sigal; Hassenrück, Christiane; Kucera, Michal; Morard, Raphaël (2023): Invasion success of a Lessepsian symbiont-bearing foraminifera linked to high dispersal ability, preadaptation and suppression of sexual reproduction. Scientific Reports, 13(1), 12578, https://doi.org/10.1038/s41598-023-39652-y
Further details:
Prazeres, Martina; Morard, Raphael; Roberts, Thomas Edward; Doo, Steve S; Jompa, Jamaluddin; Schmidt, Christiane; Stuhr, Marleen; Renema, Willem; Kucera, Michal (2020): High dispersal capacity and biogeographic breaks shape the genetic diversity of a globally distributed reef‐dwelling calcifier. Ecology and Evolution, 10(12), 5976-5989, https://doi.org/10.1002/ece3.6335
Weiner, Agnes K M; Morard, Raphael; Weinkauf, Manuel F G; Darling, Kate F; André, Aurore; Quillévéré, Frédéric; Ujiie, Yurika; Douady, Christophe J; De Vargas, Colomban; Kucera, Michal (accepted): Methodology for Single-Cell Genetic Analysis of Planktonic Foraminifera for Studies of Protist Diversity and Evolution. Frontiers in Marine Science, 3, https://doi.org/10.3389/fmars.2016.00255
Project(s):
Center for Marine Environmental Sciences (MARUM)
The Ocean Floor – Earth's Uncharted Interface (OceanFloor_EUI)
Funding:
Bundesministerium für Bildung und Forschung, Bonn (BMBF), grant/award no. 03F0820A: ForaInva
German Research Foundation (DFG), grant/award no. 390741603: EXC 2077: The Ocean Floor – Earth's Uncharted Interface
Coverage:
Median Latitude: 34.137553 * Median Longitude: 26.969877 * South-bound Latitude: 26.651819 * West-bound Longitude: 15.137911 * North-bound Latitude: 37.039667 * East-bound Longitude: 127.856243
Date/Time Start: 2019-09-20T00:00:00 * Date/Time End: 2019-10-27T00:00:00
Minimum DEPTH, water: 0.5 m * Maximum DEPTH, water: 5.0 m
Event(s):
Med_Avo_1 * Latitude: 36.883639 * Longitude: 15.139583 * Date/Time: 2019-09-23T00:00:00 * Elevation: -0.5 m * Location: Avola * Method/Device: Sampling by snorkeling (SNORKELING)
Med_Avo_2 * Latitude: 36.883972 * Longitude: 15.140278 * Date/Time: 2019-09-23T00:00:00 * Elevation: -1.5 m * Location: Avola * Method/Device: Sampling by snorkeling (SNORKELING)
Med_Cap_1 * Latitude: 36.686483 * Longitude: 15.137911 * Date/Time: 2019-09-21T00:00:00 * Elevation: -2.0 m * Location: Capo Passero * Method/Device: Sampling by snorkeling (SNORKELING)
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Event labelEventRaposo, Débora
2DATE/TIMEDate/TimeRaposo, DéboraGeocode – Collection date
3LATITUDELatitudeRaposo, DéboraGeocode
4LONGITUDELongitudeRaposo, DéboraGeocode
5DEPTH, waterDepth watermRaposo, DéboraGeocode – Total depth of water column
6Year of observationYear obsa ADRaposo, Débora
7CountryCountryRaposo, Débora
8OceanOceanRaposo, Débora
9LocationLocationRaposo, Débora
10KingdomKingdomRaposo, Débora
11SpeciesSpeciesRaposo, Débora
12Species, unique identification (URI)Species UID (URI)Raposo, Débora
13Habitat specializationHabitat specRaposo, Débora
14Sample code/labelSample labelRaposo, Débora
15Voucher Specimen CodeVoucher Spec CodeRaposo, Débora
16Identification numberID noRaposo, DéboraClone ID
17InstrumentInstrumentRaposo, DéboraDNA Analyzer, Applied Biosystems, 3730xlSequencing platform
18Source materialSource matRaposo, DéboraSource material for sequencing, PCR = selected from designed primers
19Sequencing modeSeq modeRaposo, Déborapaired-end or single
20Sequence lengthSeq lbpRaposo, DéboraNominal Length = the expected size of the insert.
21Sequence typeSeq typeRaposo, Débora
22Method commentMethod commRaposo, DéboraDNA extraction method
23GenotypeGenotypeRaposo, DéboraGenotypes after Prazeres et al. 2020
24Accession number, geneticsAccess no genRaposo, Débora
25Genetic sequenceGensequenceRaposo, Débora
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
7460 data points

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