Abstract
The limited availability of DNA reference libraries is a key limitation to developing biodiversity inventories using environmental DNA techniques. This dataset provides a 12S mitochondrial DNA reference library covering 88.92% of the species of freshwater fish inhabiting French Guiana. It contains 1,557 references, covering 369 species distributed across 51 families. It also covers the intraspecific diversity of most of these species. DNA was extracted from 1,439 specimens collected during over 25 field expeditions. DNA collections from museum records were used to complement the data for a further 118 specimens. The sequences cover two widely used eDNA primers for fishes (Teleo1 and 12S-V5) enabling identification of most Guianese freshwater fish species using eDNA metabarcoding. Beyond French Guiana, the dataset covers 6.31% of Neotropical fish species, 23.05% of genera, and 56.04% of families, making it valuable for broader regional studies. This dataset provides a comprehensive and reliable DNA reference library for the Neotropical fish, filling an important biodiversity gap in a remote, biodiversity-rich region that is difficult to sample.
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Data availability
The dataset is available on Figshare37 at https://doi.org/10.6084/m9.figshare.29168144. The sequences were deposited in NCBI GenBank and EMBL-EBI data resources (accession numbers PX415477-PX417033), and are available under ENA Study PRJNA1399107 (2026)36.
Code availability
Sequences were aligned using MAFFT38 version 7 and the distance tree was built using the BIONJ algorithm39 as implemented in PhyML40 version 3.3. Taxonomic assignment was achieved using the Last Common Ancestor algorithm implemented in the ECOTAG program of the Obitools suite33. Statistical analyses were implemented using R version 4.3.2 and the R package ‘rfishbase’ to access the Fishbase database. No custom code was used.
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Acknowledgements
This work was supported by the DEBIT project (ANR-17-CE02-0007), CNRS Nouragues, DEAL/DGTM Guyane, OEG, PAG, Our Planet Reviewed, VIGILIFE Sentinel Rivers and the Office Francais pour la Biodiversité (Project IPBG). It also benefited from Investissement d’Avenir grants managed by the Agence Nationale de la Recherche (CEBA: ANR-10-LABX-25-01, DRIIHM: ANR-11-LABX-0010).
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S.B. and J.M. designed the study; S.B., O.C., R.C., G.Q., S.L., R.V. and J.M. collected samples; R.C. provided DNA from museum specimens; S.B, R.C., G.Q., S.L and R.V. identified all specimens on the field or in the laboratory; Y.C. and R.C. extracted DNA; Y.C. performed the sequencing; J.M. performed the phylogenetic analyses; S.B. Y.C., C.C. and J.M. curated the sequences; All authors organized data and cleaned the database; C.C., O.C. and J.M. analysed data; S.B. drafted the manuscript with contributions from all other authors.
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Brosse, S., Cuenot, Y., Condachou, C. et al. Near complete 12S DNA reference library for the freshwater fish of French Guiana, northern Amazonian region.
Sci Data (2026). https://doi.org/10.1038/s41597-026-06811-5
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DOI: https://doi.org/10.1038/s41597-026-06811-5
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