Vertical and horizontal environmental DNA (eDNA) patterns of fish in a shallow and well-mixed North Sea area

Dataset type

Deze dataset bevat primaire waarnemingsgegevens voor soorten.

Beschrijving

This dataset contains eDNA metabarcoding data of fish species detected in 17 locations in the Belgian Part of the North Sea (BPNS). The seawater samples were collected during a field campaigns in 2022. The fish species were identified using 12S eDNA metabarcoding. The dataset includes amplicon sequence variants and their associated metadata. [This dataset was processed using the GBIF eDNA converter tool.]

Geografische beschrijving

Belgian part of the North Sea

Methoden

1. eDNA extraction and Library preparation. After overnight incubation with the lysisbuffer at 56°C, the eDNA was extracted using the DNeasy Blood and Tissue kit (Qiagen).

Library preparation The genetic analysis was based on 12S. A one-step amplification protocol was used in triplicate using fusion primers (Sigma Aldrich), which contained the template specific primer sequence and a unique barcode tag of 6 to 10 nucleotides. After amplification, the PCR replicates were pooled and purified using magnetic CleanNGS beads (CleanNA). After purification, the three 12S libraries were quality checked on the BioAnalyzer. The eDNA libraries were sequenced with Illumina MiSeq, 2 x 300 bp.

2. Bioinformatic processing The quality of the raw Illumina MiSeq sequencing reads was verified with FASTQC v0.11.9. The paired-end reads were then reorientated, demultiplexed and trimmed by using cutadapt. After demultiplexing, DADA2 was used for denoising, dereplication, merging, and removing of chimeric reads from the demultiplexed sequences. The taxonomic assignment of the resulting ASV sequences was performed against a custom made reference database using RDP classifier in DADA2 with a minimum bootstrapping support of 80. ASVs that remained unassigned at species level with RDP were successively run with BLASTn v2.12.0 against the custom made reference databases and the GenBank nucleotide database (from march 2023). After taxonomic assignment, the count table was cleaned by using MicroDecon using the field, filter, DNA extraction and PCR negative control samples.

Type inhoud

Omvat: Puntvoorkomstengegevens.

Bronvermelding

Dukan N, Cornelis I, Brosens D, Derycke S (2024). Vertical and horizontal environmental DNA (eDNA) patterns of fish in a shallow and well-mixed North Sea area. Version 1.7. Flanders Research Institute for Agriculture, Fisheries and Food (ILVO). Occurrence dataset. https://ipt.inbo.be/resource?r=ilvo-metabarcoding-1&v=1.7

Rechten

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

Gedigitaliseerde records

Metadata voor het laatst bijgewerkt op 2025-06-23 11:56:19.0