Previous research suggests that the mesopelagic realm contains 90% of the planet ́s total fish biomass, which has raised interest in exploitation of this new potential resource. Yet, knowledge of how this exploitation can affect ocean ecosystems is lacking mostly due to the difficult access to remote mesopelagic layers. Recently, environmental DNA (eDNA) extracted from water samples has been shown to contain information on species living around. Yet, inferring taxonomic composition from eDNA requires reference databases containing the correspondence between DNA sequences (barcodes) and species names. Here, by performing a gap analysis of DNA reference databases for European marine fishes, we show that mesopelagic fish represent a small fraction of bony fishes for which sequences of the most commonly used genes as barcodes (COI and 12S) are available, and that coverage gaps are non-homogeneously distributed among families. Although COI is available for about 75% of mesopelagic species, the fact that the barcodes developed for this gene are universal, makes it not suitable for studying fish diversity. Thus, future efforts should be addressed to improve reference libraries for 12S, and studies focusing on single species should rely on qPCR assays such as the one developed here for Maurolicus.
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