Clams are coastal resources widely exploited by both fishing and aquaculture. Most inhabit shallow waters, especially lagoons, that are transitional zones between the sea and land. In the Mediterranean French lagoons, two clam species are usually exploited, the native European clam, Ruditapes decussatus, and the introduced Manila clam, Ruditapes philippinarum. However, several other clam species can be found such as the pink clam or the golden carpet shell. Those animals are relatively small, spend most of their lives buried and are difficult to identify based on shell morphology. Consequently, they are very difficult to detect in the field. Therefore, we tested a metabarcoding approach to detect clam species from environmental DNA (eDNA) samples. After an in silico comparison between an universal and a group-specific metabarcode, we conducted an in vivo experiment to characterise this metabarcode on the targeted group of species and tested it in situ in two French lagoons.

The dataset is encompassing two files describing:

1. the 130 Amplicon Sequence Variants (ASVs) obtained after the bioinformatic analysis of the raw sequence data (see related dataset). They correspond to a small fragment of the 16S ribosomal gene, mainly from three clam species. They were obtained from water samples in an experimental design, and in situ locations in the Thau and Berre lagoons. The file (SEANOE_130ASVs. xls) is giving the sequence, the taxonomy associated, as well as the number of sequences by ASV in each of the aquariums containing or not clams, in the different sites in the Thau and Berre lagoons, and in the tissue positive controls. A link is made by column “Haplotype_ID (clams)” with the 9 clam haplotypes of the second file.
2. the 9 clam haplotypes present in the tissue samples from the experimental design (tab “Haplotypes in tissue samples”) and the comparison of the percentage of each haplotype in each aquarium between eDNA and tissue samples (tab"EDNA tissue comparison"). This file is named SEANOE_haplotypes.xls.