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
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):
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):
The Ocean Floor - Earth's Uncharted Interface (ClusterOceanFloor)
Funding:
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)
Med_Cap_2 * Latitude: 36.686500 * Longitude: 15.138139 * Date/Time: 2019-09-21T00:00:00 * Elevation: -4.0 m * Location: Capo Passero * Method/Device: Sampling by snorkeling (SNORKELING)
Med_Ple_1 * Latitude: 37.039667 * Longitude: 15.306472 * Date/Time: 2019-09-20T00:00:00 * Elevation: -2.0 m * Location: Plemmirio * Method/Device: Sampling by snorkeling (SNORKELING)
Med_Shi_1 * Latitude: 32.825778 * Longitude: 34.955028 * Date/Time: 2019-10-23T00:00:00 * Elevation: -0.5 m * Location: Shikmona * Method/Device: Sampling by snorkeling (SNORKELING)
Med_Shi_2 * Latitude: 32.825833 * Longitude: 34.954833 * Date/Time: 2019-10-23T00:00:00 * Elevation: -1.5 m * Location: Shikmona * Method/Device: Sampling by snorkeling (SNORKELING)
Pac_Jap_1 * Latitude: 26.651819 * Longitude: 127.856243 * Location: Okinawa * Method/Device: Sampling by snorkeling (SNORKELING)
Red_Eil_1 * Latitude: 29.502000 * Longitude: 34.917833 * Date/Time: 2019-10-27T00:00:00 * Elevation: -2.0 m * Location: Eilat * Method/Device: Sampling by snorkeling (SNORKELING)
Parameter(s):
| # | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
|---|---|---|---|---|---|---|
| 1 | Event label | Event | Raposo, Débora | |||
| 2 | DATE/TIME | Date/Time | Raposo, Débora | Geocode – Collection date | ||
| 3 | LATITUDE | Latitude | Raposo, Débora | Geocode | ||
| 4 | LONGITUDE | Longitude | Raposo, Débora | Geocode | ||
| 5 | DEPTH, water | Depth water | m | Raposo, Débora | Geocode – Total depth of water column | |
| 6 | Year of observation | Year obs | a AD | Raposo, Débora | ||
| 7 | Country | Country | Raposo, Débora | |||
| 8 | Ocean | Ocean | Raposo, Débora | |||
| 9 | Location | Location | Raposo, Débora | |||
| 10 | Kingdom | Kingdom | Raposo, Débora | |||
| 11 | Species | Species | Raposo, Débora | |||
| 12 | Species, unique identification (URI) | Species UID (URI) | Raposo, Débora | |||
| 13 | Habitat specialization | Habitat spec | Raposo, Débora | |||
| 14 | Sample code/label | Sample label | Raposo, Débora | |||
| 15 | Voucher Specimen Code | Voucher Spec Code | Raposo, Débora | |||
| 16 | Identification number | ID no | Raposo, Débora | Clone ID | ||
| 17 | Instrument | Instrument | Raposo, Débora | DNA Analyzer, Applied Biosystems, 3730xl | Sequencing platform | |
| 18 | Source material | Source mat | Raposo, Débora | Source material for sequencing, PCR = selected from designed primers | ||
| 19 | Sequencing mode | Seq mode | Raposo, Débora | paired-end or single | ||
| 20 | Sequence length | Seq l | bp | Raposo, Débora | Nominal Length = the expected size of the insert. | |
| 21 | Sequence type | Seq type | Raposo, Débora | |||
| 22 | Method comment | Method comm | Raposo, Débora | DNA extraction method | ||
| 23 | Genotype | Genotype | Raposo, Débora | Genotypes after Prazeres et al. 2020 | ||
| 24 | Accession number, genetics | Access no gen | Raposo, Débora | |||
| 25 | Genetic sequence | Gensequence | Raposo, Débora |
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
7460 data points
Download Data
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