Chromosome-level genome assembly of a doubled haploid brook trout ( <i>Salvelinus fontinalis</i> )

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 the 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.