DOI: 10.5061/dryad.hj53jd8
title: Data from: Metabarcoding on planktonic larval stages: an efficient approach for detecting and investigating life cycle dynamics of benthic aliens

description: High-throughput sequencing (HTS) technologies offer new promise to support
 surveillance programs targeting marine non-indigenous species (NIS).
 Metabarcoding might surpass traditional monitoring methods, for example
 through its ability to detect rare species, a key feature in early
 detection of NIS. Another interest of this approach is the identification
 of organisms difficult to identify based on morphology only (e.g., early
 developmental stages), making it relevant in the context of management
 programs. Because many marine benthic NIS have a bi-phasic bentho-pelagic
 life cycle, targeting their pelagic larval stages in zooplankton may allow
 early detection and assessment of their establishment and potential
 spread. We illustrate this approach with an analysis of bulk-DNA retrieved
 from a time-series of zooplankton samples collected over 22 months in one
 bay in Brittany (France). Using HTS of amplicons obtained with two markers
 (COI and 18S) and a metabarcoding approach, 12 NIS were identified and
 their temporal larval dynamics were monitored. Importantly, we chose to
 focus on a closed list of species, from four metazoan classes encompassing
 52 NIS reported within the study area or nearby seas, with molecular
 references available or obtained locally for 42 of them. The use of a
 custom-designed database allowed the detection of three NIS otherwise not
 detected when using public databases. Interestingly, NIS known to have a
 short-lived larval stage were detected (e.g., the bryozoan Bugula neritina
 or the tunicate Corella eumyota). For two molluscs Ruditapes philippinarum
 and Crepidula fornicata, metabarcoding results were compared to those
 obtained using traditional methods (i.e., barcoding of individual larvae
 and morphology, respectively) to show the reliability of the approach in
 detecting and assessing the extent of their reproductive periods. Our
 results also revealed that the Pacific oyster Crassostrea gigas, a
 notorious invasive species, failed to reproduce in the study bay, showing
 that metabarcoding on larval stages also provides information regarding
 the establishment success (or failure) of NIS. While metabarcoding has its
 limitations and biases, this study demonstrates its effectiveness for
 surveillance of targeted NIS, notably to support management strategies
 like the European Marine Strategy Framework Directive (MSFD).
description: Table with species and
 corresponding Genbank accession numberTable describing all
 locally produced reference sequences for either 18S or COI. For each
 sequence, the voucher code, as listed in the corresponding reference
 database (see 'CustomReference_database' fasta files), is
 provided with the organism name and class, the marker, and the GenBank
 accession number.Species_AccessionNumber.xlsxCustom-designed Reference database for COIThis fasta file is the custom-designed reference database, for COI, used for taxonomical assignment. It is composed of 3131 sequences covering 410 species. All sequences extracted from public databases have their public code (e.g., GenBank accession number) registered as the “AccNum” argument in the sequence header. If the reference has been produced locally, its voucher code is indicated in the header of the sequence. These sequences were deposited in GenBank and their accession number are listed in the Species_AccessionNumber excel file.CustomReference_database_COI.fastaCustom-designed Reference database for 18SThis fasta file is the custom-designed reference databases for 18S used for taxonomical assignment. It is composed of 408 sequences covering 314 species. All sequences extracted from public databases have their public code (e.g., GenBank accession number) registered as the “AccNum” argument in the sequence header. If the reference has been produced locally, its voucher code is indicated in the header of the sequence. These sequences were deposited in GenBank and their accession number are listed in the Species_AccessionNumber.xlsx excel file.CustomReference_database_18S.fastaMetabarcoding pipeline for detection of non-indigenous speciesThis zip file contains the metabarcoding pipeline for non-indigenous species detection in Snakefile format with required scripts and configuration files. A README is available for more information about how the pipeline works and the scripts included. All parameters used for our study are detailed in the config_metabarcoding file and can be changed there.Pipeline_Metabarcoding.zip