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bioRxiv · 10.1101/2024.09.27.615458

Chromosome-level genome assembly of a doubled haploid brook trout (Salvelinus fontinalis)

Lecomte, L.·Ferchaud, A.-L.·Normandeau, E.·Merot, C.·Langlois-Parise, I.·Therrien, J.-C.·Berube, P.·Djambazian, H.·Nawarathna, P. M.·Fraser, D.·Ragoussis, J.·Bernatchez, L.
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Abstract

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 a 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 the NCBI annotation pipeline, with 99% 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.

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Lecomte, L., Ferchaud, A.-L., Normandeau, E., Merot, C., Langlois-Parise, I., Therrien, J.-C., Berube, P., Djambazian, H., Nawarathna, P. M., Fraser, D., Ragoussis, J., Bernatchez, L.. 2024-10-01. Chromosome-level genome assembly of a doubled haploid brook trout (Salvelinus fontinalis). https://doi.org/10.1101/2024.09.27.615458

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