Genomic resources for the monitoring and management of Tometes trilobatus, Hoplias aimara and Myloplus rhomboidalis, three exploited freshwater fish species in French Guiana

Abstract

The Neotropical region, hosts a quarter of all freshwater fish species, while providing important food resources for local human populations. The management of neotropical freshwater ecosystems is thus of primary importance for both biodiversity conservation and local human sustainability. Recent technological advances in the field of genomics offer new tools for managers and practitioners to monitor entire fish assemblages using environmental DNA (eDNA) metabarcoding, or to detect specific species or populations using targeted eDNA. The availability of species genomics information is thus crucial to implement eDNA monitoring methods. Nevertheless, specific primers allowing species-centred approaches are lacking for most species. In French Guiana, only 18 mitochondrial genomes of freshwater fishes have been published out of more than 400 species known from French Guiana. In this study, we provide genomic resources for Myloplus rhomboidalis (locally called Koumarou), Hoplias aimara (Aimara) and Tometes trilobatus (Pakou), three exploited fish species in French Guiana. We provide complete mitochondrial genomes and tools for the detection of the three fish species by developing a targeted species approach using digital PCR (dPCR) for each species.