DOI: 10.5061/dryad.s7h44j1g3
title: Data from: Fishing in the gene-pool: Implementing trawl-associated eDNA metaprobe for large scale monitoring of fish assemblages

description: Marine biodiversity monitoring in the Mediterranean’s increasingly
 threatened ecosystems is crucial for effective ecosystem conservation and
 management. Here, we leveraged the Mediterranean International Trawl
 Survey program (MEDITS) to implement eDNA sampling through the recently
 tested ‘metaprobe’ procedure and characterize fish assemblages in three
 separate areas off the Italian coasts: Northern Adriatic Sea (NoAS),
 Ligurian and Northern Tyrrhenian Sea (LNTS), and Sardinian Sea (SaS). By
 combining the information from two homologous mitochondrial 12S
 metabarcodes––i.e., Elas02 and Tele02 targeting elasmobranchs and
 teleosts, respectively––we identified 108 species, over 60% of which
 overlapped with those caught by the trawl net. We produced an accurate
 reconstruction of fish community composition of the examined sites,
 reflecting differences in species assemblages linked with both geographic
 area and depth range. Metaprobe eDNA data consistently returned a
 biodiversity ‘bonus’ mostly consisting of pelagic taxa not captured
 through bottom trawl surveys, including rare and endangered taxa (e.g.,
 elasmobranchs). Overall, the spatial characterisation of the assemblages
 across the surveyed areas was better delineated and more robust using eDNA
 metabarcoding than trawl data. Our results support the operationalisation
 of the metaprobe as a simple, inexpensive, versatile sampling tool, in
 association with pre-existing ship surveys, to overcome many of the
 limitations of marine data collection and strengthen marine management.
description: # Data from: Fishing in the gene-pool: implementing trawl-associated eDNA
 meta probe for large scale monitoring of fish assemblages
 [https://doi.org/10.5061/dryad.s7h44j1g3](https://doi.org/10.5061/dryad.s7h44j1g3) Authors: Giulia Maiello, Andrea Bellodi, Alessia Cariani, Paolo Carpentieri, Laura Carugati, Davide Cicala, Alice Ferrari, Cristina Follesa, Alessandro Ligas, Paolo Sartor, Alice Sbrana, Peter Shum, Matteo Stefani, Lorenzo Talarico, Stefano Mariani, Tommaso Russo #### Description of the data This project contains raw reads data from rolls of gauze metaprobe samples collected in 21 sampling sites in the central Tyrrhenian Sea, Sardinian Sea, and Adriatic Sea. Raw reads files and ngsfilter files with sample barcodes are from two different libraries including the same samples amplified with 12S Tele02 and 12S Elas02 primers respectively. **File 1: Elas02_S1_L001_R1_001.fastq.gz** Elas02 forward FastQ file from the Illumina iSeq 2x150 bp run **File 2: Elas02_S1_L001_R2_001.fastq.gz** Elas02 reverse FastQ file from the Illumina iSeq 2x150 bp run **File 3: Tele02_S1_L001_R1_001.fastq.gz** Tele02 forward FastQ file from the Illumina iSeq 2x150 bp run **File 4: Tele02_S1_L001_R2_001.fastq.gz** Tele02 reverse FastQ file from the Illumina iSeq 2x150 bp run **File 5: ngsfilterElas02.txt** Elas02 12S primers and unique dual-tag combinations (forward and reverse) associated with each of the 49 amplicons (42 samples, 4 extraction negatives, 2 PCR negatives and 1 PCR positive control) of the Elas02 12S library **File 6: ngsfilterTele02.txt** Tele02 12S primers and unique dual-tag combinations (forward and reverse) associated with each of the 49 amplicons (42 samples, 4 extraction negatives, 2 PCR negatives and 1 PCR positive control) of the Tele02 12S library