18S Metabarcoding Genetic Observations of Marine Species in the Port of Wallhamn, Sweden (2022)

Dataset type

This dataset that contains primary occurrence data for species.

Description

This dataset contains genetic observations of marine species in the port of Wallhamn between June and September 2022.

The observations were made using water and plankton samples, as well as samples from Autonomous Reef Monitoring Structures (ARMS) units.

Species were identified using 18S metabarcoding.

The dataset includes ASVs (amplicon sequence variants) and their associated metadata.

This dataset was published via the SBDI ASV portal https://asv-portal.biodiversitydata.se/).

Geographic Description

This dataset covers the port of Wallhamn (Sweden) which has both a commercial/industrial part in the North and a marina in the South.

Data quality

Negative controls (blank samples) were created by the same extraction procedure but without the sampled material. No DNA could be detected in these samples, with neither Nanodrop nor Qubit. The blank samples were included in the preparation of

libraries (below) as a further control for contamination during the extraction of DNA. Another negative control was performed during PCR.

Methods

DNA was extracted from the filters with the Nucleospin eDNA water kit (Macherey-Nagel) using the Nagel) using the technique and standard developed in the laboratory. Concentration of DNA in the extracts was measured with the Qubit® fluorometer. Note that this measures concentration of all DNA in the sample and not specific DNA from the target species. This is done to ensure that the extractions have worked.The genetic analysis and comparison was based on two molecular markers (COI and 18S). These markers were amplified for each sample. Same PCR protocols were used for metabarcoding of the ARMS, eDNA and plankton samples

The DNA libraries were sequenced with Illumina MiSeq, 2 x 300 bp.The analysis was performed in the R-environment with a DADA2 package.

After initial quality control, the sequences were filtered for low quality, as well as adapters and primers were removed. Sequencing errors were corrected by calculating an error model; and after that singletons and chimeras were removed using the “pseudo-pooling” function in DADA2.The filtered and quality-controlled COI sequences were matched against the BOLD database with the python package BOLDigger. The 18S sequences were matched against the PR2 database. All subsequent analysis was performed with customized R scripts where identified species were matched against different NIS and IAS species reference lists.

Type of content

Includes: Point occurrence data.

Citation

Obst M (2024). 18S Metabarcoding Genetic Observations of Marine Species in the Port of Wallhamn, Sweden (2022). Version 1.3. University of Gothenburg. Occurrence dataset. https://www.gbif.se/ipt/resource?r=gu-2022-wallhamn-18s&v=1.3

Rights

This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

Digitised records

Metadata last updated on 2024-11-04 07:34:53.0