1 Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, G1V 0A6, Canada.
2 Parks Canada, Office of the Chief Ecosystem Scientist, Protected Areas Establishment, 30 Rue Victoria, Gatineau, QC, J8X 0B3, Canada.
3 Plateforme de bio-informatique de l'IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, 1030, Avenue de la Médecine, Québec, QC, G1V 0A6, Canada.
4 UMR 6553 Ecobio, OSUR, CNRS, Université de Rennes, 263 Avenue du Général Leclerc, Rennes, 35004, France.
5 Laboratoire de Recherche en Sciences Environnementales et Médicales (LARSEM), Université Laval, 1030, Avenue de la Médecine, Québec, QC, G1V 0A6, Canada.
6 McGill Genome Centre, Department of Human Genetics, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, 740 Dr Penfield Ave, Montréal, QC, H3A 0G1, Canada.
7 CellCarta, 201 President Kennedy Ave, Suite 3900, Montréal, QC, H2X 3Y7, Canada.
8 Departm

Brook trout (Salvelinus fontinalis) is a socioeconomically important fish species for fisheries, aquaculture and aquatic conservation. We produced a 2.5 Gb reference assembly by combining Hi-C chromosome conformation capture with high-coverage short- and long-read sequencing of a fully homozygous mitotic gynogenic doubled haploid fish, which facilitates assembly of highly complex salmonid genomes. The assembly has an N50 of 50.98 Mb and 88.9% of the total assembled sequence length is anchored into 42 main chromosomes, of which 63.44% represents repeated contents, including 1,461,010 DNA transposons. 56,058 genes were found, with 98.6% of the 3,640 expected conserved orthologs BUSCO genes (actinopterygii_odb10 lineage database). Additionally, we found significant homology within the 42 chromosomes, as expected for this pseudo-tetraploid species, as well as with the sister species lake trout (Salvelinus namaycush) and Atlantic salmon (Salmo salar). This assembly will serve as a reliable genomic resource for brook trout, thus enabling a wider range of reference-based applications to support ongoing research and management decision-making for the species.